Annual/Termination Reports:

[10/26/2001] [08/25/2005] [10/28/2005]

Report Information

Participants

David Becker Aventis CropScience David.becker@aventis.com;
N.R. Benson University of Arkansas rbenson@uaex.edu;
Sterling B. Blanche Louisiana State University sblanche@agcenter.lsu.edu;
Freddie M. Bourland University of Arkansas bourland@uark.edu;
Daryl T. Bowman North Carolina State Univesity Daryl_bowman@ncsu.edu;
Paulo C. Canci Delta & Pine Land Company paulocanci@mdm-aldodao.com.br;
Roy. G. Cantrell New Mexico State University rcantrel@mnsu.edu;
Peng W. Chee University of Georgia pwchee@arches.uga.edu;
Clay B. Cole USDA-ARS claybrodycole@hotmail.com;
Greg Constable CSIRO gregc@mv.pi.csiro.au;
Charles G. Cook Syngenta Seeds, Inc. Charlie.cook@syngenta.com;
Shannon Crawley USDA-ARS Src1@ra.msstate.edu;
John B. Creech Mississippi State University jcreech@drec.msstate.edu;
Jay H. Daniell Delta & Pine Land Company;
Leigh M. Dawdy Texas A&M University L-dawdy@tamu.edu;
Ivan Dickson Louisiana State University idickson@agctr.lsu.edu;
Charles P. Downer Associated Farmers Delinting bdowner@afdseed.com;
Timothy P. Drew Cotton Seed International Tim.drew@csi.net.au;
Cynthia C. Green Delta & Pine Land Company Cynthia.green@deltaandpine.com;
Osman A. Gutierrez USDA-ARS osman@ra.msstate.edu;
Joseph J. Gwyn Aventis Cottonseed International Jefferson.gwyn@aventis.com;
Russell W. Hays USDA-ARS rwhool@ra.msstate.edu;
Johnie N. Jenkins USDA-ARS jjenkins@ra.msstate.edu;
Gay M. Jividen Cotton Incorporated gjividen@cottoninc.com;
Joseph T. Johnson Monsanto Joseph.t.Johnson@monsanto.com;
Jack E. Jones Jajo Genetics janhejo@home.com;
Don L. Keim Delta & Pine Land Company Don.l.keim@deltaandpine.com;
Russell J. Kohel USDA-ARS kohel@qutun.tamu.edu;
William R. Lambert Delta & Pine Land Company willlambert@planttel.net;
Brenda F. Lauterbach Texas A&M University b-lauterbach@tamu.edu;
Garland E. Lytie CPCSD lytle@cpcsd.com;
Joel F. Mahill Phytogen Seed Company LLC jfmahill@dowagro.com;
Lloyd May University of Georgia lmay@tifotn.cpes.peachnet.edu;
Jack C. McCarty USDA-ARS jcm@ra.msstate.edu;
Amanda B. McFall University of Arkansas mmcfall@uaex.edu;
George R. McPherson Phytogen Seed Company LLC grmcpherson@dowagro.com;
William R. Meredith, Jr. USDA-ARS wmeredith@ars.usda.gov;
James F. Mitchell Monsanto James.f.Mitchell@monsanto.com;
Gerald O. Myers Louisiana State University gmyers@agctr.lsu.edu;
David V. Negrotto Syngenta Biotechnology, Inc.
David.negrotto@syngenta.com;
James M. Olvey Olvey & Associates, Inc.;
A.E. Percival USDA-ARS percival@tamu.edu;
Richard G. Percy USDA-ARS rpercy@ag.arizona.edu;
Sukumar Saha USDA-ARS saha@ra.msstate.edu;
Albert Santos Delta & Pine Land Company Albert.santos@deltaandpine.com;
Preston E. Sasser Cotton Incorporated psasser@cottoninc.com;
Jodi A. Scheffler USDA-ARS jscheffler@ars.usda.gov;
Khairy M. Soliman Alabama A&M University ksoliman@aamu.edu;
Michael G. Swindle Aventis CropScience Michael.swindle@aventis.com;
Anna J. Talbot Texas Ag Expt. Station a-talbot@tamu.edu;
Earl W. Taliercio USDA-ARS etaliercio@ars.usda.gov;
Peggy M. Thaxton Texas A&M University p-thaxton@tamu.edu;
Linda K. Trolinder Aventis CropScience Linda.trolinder@aventis.com;
Rickie B. Turley USDA-ARS rturley@ars.usda.gov;
Mauricio Ulloa USDA-ARS mulloa@ars.usda.gov;
Cynthia A. Waddell New Mexico State University cwaddell@nmsu.edu;
Ted P. Wallace Mississippi State University twallace@pss.msstate.edu;
Curtis Williams Delta & Pine Land Company;
Johnny Wynne North Carolina State University Johnny_Wynne@ncsu.edu;
John Yu USDA-ARS zyu@qutun.tamu.edu;
Hongbin Zhang Texas A&M University Hbz7049@pop.tamu.edu;
Jinfa Zhang Monsanto Jinfa.zhang@monsanto.com;
Lowell Zelinski CPCSD zelinski@cpcsd.com;
Andy White Stoneville Pedigreed Seed awhite@stoneville.com;



Project Leadership
Chair: Gerald O. Myers (mailto:gmyers@agctr.lsu.edu);
Chair elect: John Creech (jcreech@drec.msstate.edu);
Vice-chair: Jeff Gwyn (Jefferson.gwyn@aventis.com);
Secretary: Ted Wallace (twallace@pss.msstate.edu);
Advisor: Johnny Wynne (Johnny_Wynne@ncsu.edu);

Brief Summary of Minutes

This was the first meeting of Mulistate Research Project S-304. Self introductions of attendees was made. Dr. Johnny Wynne, SAAESD Advisor, then gave the group some background on the approval of S-304. Dr. Gerald Myers, chair of the project writing committee, then introduced the details of the project to all members in attendance. Reports on progress toward project objectives were solicited and asked to be sent in by the end of September.

Accomplishments

A proposal for new Multistate Research Project entitled Development of Genetic Resources for Cotton was developed during the latter half of 2000 through the activities of SRDC-9801 Developing Genetic Resources for Cotton Improvement. The proposal seeked to expand and contemporize the cotton research activities of a previous Regional Project, S-258, which terminated in 1999. In addition, the new project sought to include the major functions of the Southern Regional Information Exchange Group (SRIEG-61) Cotton Germplasm: Acquisition, Evaluation, and Utilization which was scheduled to terminate in 2001. The proposal was approved by USDA-CSREES for a five year period from October 1, 2000 through September 30, 2005.<br /> <br /> There are six objectives detailed in the new Multistate Research Project:<br /> To acquire, curate, characterize, and evaluate the species, races, and genetic types of Gossypium (cotton).<br /> To develop, maintain, and distribute molecular genetic, genetic, and cytogenetic tools for the evaluation and enhancement of cotton germplasm.<br /> To adapt and develop methodologies to evaluate, modify, and utilize cotton germplasm.<br /> Germplasm enhancement for biotic and abiotic stress resistance and agronomic traits. <br /> To refine and develop cotton breeding and variety testing methodologies and techniques.<br /> To develop cotton bioinformatic systems. <br /> <br /> Activities undertaken during the last year (2000-2001) related to the achievement of these objectives are detailed in this report.<br /> <br /> Objective 1: To acquire, curate, characterize, and evaluate the species, races, and genetic types of cotton.<br /> <br /> Curator Cotton Collection Report, 2001. Period Covered from: 01/00 to: 06/01(ARS-TX)<br /> <br /> Accessions Presently Maintained at College Station<br /> Varieties (mostly G. hirsutum) 2531<br /> Race Stocks (mostly G. hirsutum) 2102<br /> Pima Types (G. barbadense) 1399<br /> Asiatic (G. arboreum) 1698<br /> Asiatic (G. herbaceum) 168<br /> Wild Species (Diploid & Tetraploid) 544<br /> Total 8442<br /> <br /> <br /> <br /> A total of 1408 accessions were increased in 2000. Twelve hundred and ten at the Tecoman, Mexico, Winter Nursery.-- 725 G. arboreum, 57 race stocks, and 28 G. barbadense stocks, plus 400 accessions obtained from Uzbekistan in 1999. One hundred and ninety eight lines from several former Soviet Republics were increased at Rio Farms, Monte Alto, Texas. Sent for increase in 2000-01 were 1400 accessions. Two hundred accessions obtained from Uzbekistan in 1999; 570 accessions obtained from Russia in November of 2000; and 630 accessions of 374 race stocks and 256 G. barbadense lines. Eighty-six photoperiodic lines, with low seed quantities are presently being grown in a screen cage at Weslaco, Texas. Included are wild, semi-wild, and domesticated species. Eighty seven accessions with extremely low seed quantities and/or poor seed germination, and 12 wild diploid and tetraploid species are being grown for additional seed in two greenhouses here at College Station. The accessions grown each year at the various locations are evaluated for their various agronomic characteristics to ensure the purity of each line. (ARX-TX)<br /> <br /> Seven hundred and forty four lines were given PI numbers and added to the collection. (ARS-TX)<br /> <br /> Seeds of 2798 accessions in 81 seed requests were provided from the Collection to geneticists, plant breeders, and other individuals, and includes both domestic (2448 accessions - 64 orders) and international (350 accessions - 17 orders) requests in CY00. (ARS-TX)<br /> <br /> New genes from wild tetraploid: G. mustelinum accession AD4-8 was sourced from the USDA-ARS working cotton collection in College Station, Texas, to begin efforts to convert this tetraploid species into more breeder accessible forms. To date, we have found it to be hard seeded, photoperiodic, and recalcitrant to flowering. We plan to mine G. mustelinum for valuable QTLs, through an advanced backcross breeding approach with the recurrent parent, germplasm line PD 94042. (AES-GA)<br /> <br /> Germplasm seed increase: We have increased seed of over 1,200 accessions of the US Cotton Germplasm Collection. About 600 new accessions from Uzbekistan, that are part of the Former Soviet Union cotton germplasm collection, were increased and added to the US collection. (ARS-TX A&M)<br /> <br /> Identification of chloroplast specific functional genes: Cytoplasm of any organism plays major role in its biological processes. Unfortunately very little is known about the functional genes located in the cytoplasmic genome. We identified cytoplasmic specific functional genes at the molecular level using a cytoplasmic specific mutant (Cyto-V ) in collaboration with Dr. R. Percy, USDA/ARS. We have identified several cytoplasmic specific transcripts or functional genes in cotton using reciprocal crosses. We also detected differences in the protein-banding specific to thylakoid membrane of the plastids. This is the first report on molecular identification of chloroplast controlled genes in cotton. This research will not only help to study and understand the genetics, biochemistry and development of plastids genome in cotton, but also aids in identifying the promoters and markers specific to plastid genes. (ARS-MS, ARS-AZ)<br /> <br /> Identification of regenerable lines: There is a critical need in cotton transformation research for identification of suitable regenerable lines other than Cocker 312. In collaboration with scientists at Alabama A&M University and Dr. K Rahasekaran , USDA, ARS, New Orleans, we developed a suitable cotton regeneration system and identified for the first time regeneration of an improved Upland cotton cultivar (G. hirsutum), a Gossypium arboreum line and a G. barbadense line. This research will be very useful for cotton transformation research.(ARS-MS, ARS-LA, AES-AL A&M)<br /> <br /> Converted Race Stocks: Converted Race Stocks/*3/TAM 94L-25: 79 CRS have been crossed and backcrossed to an elite breeding line (TAM 94L-25) to produce the BC3F1 generation. These will be advanced to the BC3F2 generation in 2002 (seed lost in 2001), for release to the public. Currently available are the BC1F2 and the BC2F2 OP and selfed seed. (AES-TX A&M)<br /> <br /> Multi-adversity Resistance: The MAR program received 50 cotton acquisitions from Dr. Edward Percival, USDA-ARS, College Station. These cottons were from India, Pakistan and Uzebekistan and were evaluated for bacterial blight resistance and insect resistance. The cottons also were characterized as to species, leaf type, and level of pubescence. All the cotton acquisitions were susceptible to bacterial blight. Individual plants were selected based on boll load due to insect resistance and will be evaluated in 2002. Fiber quality also will be determined on the individual plant selections. (AES-TX A&M)<br /> <br /> Objective 2: To develop, maintain, and distribute molecular genetic, genetic and cytogenetic tools for the evaluation and enhancement of cotton germplasm.<br /> <br /> Integrated gemomic map: We have have constructed components of an integrated genetic and physical map of the cotton genome. We developed three complementary libraries of high-quality, large insert bacterial artificial chromosome (BAC) clones that are the largest cotton BAC clones reported, averaging 143 Kb. (ARS-TX A&M)<br /> <br /> Tools for seedling disease resistance: F2 seed from Pima S-7 x Acala 44 were grown and selfed in the field this 2001 summer. The genetic material from the F2 plants and F3 plants will be used to evaluate seed-seedling resistance and fiber quality. In cooperation with Dr. Jeff Chen at Texas A&M University, a total of 617 polymorphic fragments amplified from 53 primer pairs have been selected for mapping in the F2 population and will be readily used in construction of cotton linkage maps. The markers will be used for assisting selection of seedling diseases and fiber quantitative trait loci (QTLs) in cotton breeding programs. In addition, several F1 plant populations between Pima S-7 and Hartz 1220, Stoneville 132, Lankart 57, Stoneville 213 and nine MAR germplasm lines were grown in the field this summer to produce F2 seed for use in molecular mapping. (AES-TX A&M)<br /> <br /> New SSR markers: Currently only about 300 SSR markers are commercially available. At least ten times more markers are needed in order to apply the benefits of marker technology to a plant breeding program. We developed 320 new SSR markers in collaboration with Dr. Alan Pepper at Texas A&M University in cotton. Several thousands additional SSR markers are in the sequencing phase in our new genomic lab at Stoneville. (ARS-MS, AES-TX A&M)<br /> Molecular tool for functional genome analysis: Among many other molecular methods in cotton the analysis of differential gene expression is very difficult due to many challenges including simple and efficient methods that can detect large numbers of highly reproducible differentially expressed cDNAs or functional genes. An innovative molecular method was developed to screen differentially expressed cDNAs in cotton using AFLP and SSR-specific primers by automated capillary electrophoresis. There are only a few reports in crops other than cotton on AFLP marker-based differential gene expression studies and no reports on any crops on SSR-based screening methods of cDNAs. This PCR based method was very easy to use and efficient and detected large number of variation within the functional genes in cotton. We identified for the first time about 130 SSR-containing ESTs that will be very valuable markers for the analysis of both functional and structural genomes of upland cotton. (ARS-MS)<br /> <br /> A unique set of chromosomal substitution lines: In collaboration with Dr. D.M. Stelly at Texas A&M University we created a unique set of backcrossed chromosome substitution lines (BCnF1). These lines are genetically identical except that each differs by the replacement of a specific homologous pair of chromosomes from Pima 3-79 (Gossypium barbadense) into Upland cotton (G. hirsutum). The exceptional fiber length and fineness of Pima cotton give it a 30% to 50% price advantage over the more widely grown Upland cotton because of its superior spinning and manufacturing performance. The introgression of genes from G. barbadense into G. hirsutum, holds considerable promise but has historically been a difficult area due to genomic incompatibility between the two species. As a result the work is unlikely to be carried out at private seed companies. The interspecific backcrossed chromosome substitution lines will provide a novel resource to the breeders to overcome the problems of genomic incompatibility at the whole genome level between the two species and create a unique set of chromosome comprehensive germplasm introgression products in Upland cotton. This research will benefit the United States cotton producers in the global competition and also satisfy the evolving needs of our cotton industries. Observation of different chromosome substitution lines in such a uniform genetic background will also provide an unique opportunity to detect the effect of the group of genes that a specific chromosome carries and thus will also aid in cotton genome mapping program. Currently we are increasing seeds from all of these unique cytogenetic lines for evaluating the improved agronomic and fiber characteristics in field trials.(ARS-MS, AES- TX A&M)<br /> <br /> Objective 3: To adapt and develop methodologies to evaluate, modify, and utilize cotton germplasm.<br /> <br /> Recombinant Inbred Map: Cotton unfortunately lacks linkage maps that are significant from a plant breeding standpoint. The molecular marker linkage maps that have been assembled for the n=26 cottons, G. hirsutum and G.barbadense are incomplete, involving very few markers. No published map has attained 26 linkage groups. We have completed screening about 200 polymorphic DNA markers covering more than 50% of the chromosomes (primarily SSR markers and a few AFLP) against 200 RI lines. (ARS-MS)<br /> <br /> Converted Race Stocks Mapping Population Development: In conjunction with Dr. Roy Cantrell at New Mexico State University a mapping population of plants is being developed in order to associate useful traits within the Converted Race Stocks with SSR markers. Plants are being grown currently to produce the BC3 or final backcross. (AES-TX A&M, AES-NM)<br /> <br /> Objective 4: Germplasm enhancement for biotic and abiotic stress resistance and agronomic traits. <br /> <br /> Release of Upland cotton germplasm: PD 94045 (G. hirsutum L.) cotton was released in 2000 for its combination of desirable fiber properties, yield potential, and wide adaptation. (AES-GA)<br /> <br /> Release of Pima germplasm possessing improved fiber length and strength: Five germplasm lines of cotton (Gossypium barbadense L.), designated as 93252, 93260, 94217, 94218, and 94220 (Reg. No. to , PI to ), were developed by the USDA-ARS in cooperation with the University of Arizona, Maricopa Agricultural Center and were released in 2001. All five lines produce significantly longer and stronger fiber than is currently available in commercial American Pima cultivars. The lines possess agronomically acceptable yield potentials, maturity intervals, and plant heights, and exhibit good levels of heat tolerance. Lines 93252, 93260, 94217, 94218, and 94220 provide public and private breeders with agronomically improved resources for concurrent improvement of fiber length and strength in Pima cotton.<br /> Agronomic and fiber properties of the five lines were evaluated in replicated tests at Maricopa and Safford, AZ in 1999, and Shafter, CA in 2000. Averaged across tests, all lines (with the exception of 93260) produced lint yields exceeding 90% of the yield of the commercial cultivar Pima S-7' (Turcotte, et al., 1992). Plant heights of all lines were equivalent to the plant height of Pima S-7. Fiber bundle strengths of 93252, 93260, 94217, 94218, and 94220 exceeded that of Pima S-7 (305 kN m kg-1), and ranged from 340 to 384 kN m kg-1. Fiber length (2.5% span length) of the lines ranged from 37.8 mm to 38.3 mm, as compared to 35.0 mm for Pima S-7. Fiber length uniformities of lines 93252, 94217, and 94220 were equivalent to that of Pima S-7, whereas lines 93260 and 94218 exhibited lower fiber length uniformities. Fiber micronaire of the lines ranged from 4.3 to 3.7, as compared to 4.5 for Pima S-7. The lower micronaire values of 93260 (3.7) and 94220 (3.8) suggests that these lines might incur penalties in adverse environmental situations. Lint percentages of the five lines, determined from hand-picked samples, ranged from 34.0 to 36.3% and were lower than that of Pima S-7 (37.8%). (ARS-AZ)<br /> <br /> Nematode resistance: F3 plants from a cross of M315 (root-knot resistant) and TX 110 (putatively reniform resistant) are being screened for resistance to both nematodes. The goal is to obtain a single plant that has resistance to both. We are in the very early stages of establishing molecular analysis to determine if markers can be assigned to resistance to these pests. Work done in collaboration with Dr. Jim Starr, Texas A&M, Plant Pathology. (AES-TX A&M)<br /> <br /> New sources of root-knot nematode resistance: The southern root-knot nematode, Meloidogyne incognita race 3 (Kofoid & White) is a widespread pathogen of Upland cotton (Gossypium hirsutum L.) in the United States. Progress in the development of productive cultivars in root-knot infested soils is dependent upon the identification of germplasm sources containing genes conferring resistance and/or tolerance this pest. The objective of this research was to screen 150 accessions from the Texas Race Stock collection previously uncharacterized for their reaction to the root-knot nematode. This was done in a sick plot nursery by rating the degree of galling present. Of the 150 accessions evaluated, 146 were rated at maturity using an indexed scoring system ranging from 0 (no galling present) to 5 (severe galling). The range of galling scores was from 1.7  5.0 with a mean of 3.75. The average gall score of the resistant check, Stoneville LA887, was 2.04. Twenty-four accessions had galling index scores of less than 3 and ten TX accessions (TX-1028, TX-1483, TX-1437, TX-1355, TX-2311, TX-2324, TX-695, TX-2362, TX-1585, and TX-1240) had gall scores not significantly different than the resistant check. Two of these, TX-1028 and TX-1483 had average gall scores lower than the resistant check.. Several of the resistant accessions were from countries outside the center of diversity for Upland cotton, indicating that useful diversity can arise outside of germplasm centers. (AES-LA, ARS-TX)<br /> <br /> DNA markers for root-knot nematode resistance genes: We detected about 23 polymorphic SSR markers between RKN and susceptible lines. We are currently evaluating F2 population based on this polymorphic markers to construct a linkage map of DNA markers and RKN genes. Screened RKN-induced cotton root cDNA library for candidate mRNAs related to RKN resistance. Three cDNA clones were isolated, sequenced and named MIC-1, 2, and 3 (Meloidogyne Induced Cotton- genes). Southern and northern blot characterization with these clones as probe revealed evidence of a gene family whose expression is root specific and induced specifically in the resistant cotton line by RKN infection. The lack of any significant homology with sequences in the major gene databases suggested a novel gene family of unknown function. We are in process of over expressing the corresponding protein(s) in a bacterial system in order to produce antiserum as a tool for cellular localization studies in conjunction with in situ hybridization. We plan on using recently available BAC clones to isolate and sequence full length genes of this unique family with particular interest in analysis of putative nematode inducible promoter regions.<br /> <br /> Pest/disease resistance gene homologs in cotton are being identified and mapped to aid in location of these and other potential nematode resistance genes. Several sequences homologous to fungal wilt resistance genes have been cloned and are being further characterized due to possibility that they are tightly linked to RKN resistance genes (i.e. RKN resistant isolines are known to show resistance to fungal wilt). (ARS-MS) <br /> <br /> Investigation of tolerance to Early Foliar Decline (bronzing) in Pima cotton: In recent years a phenomenon variously referred to as bronzing, bronze wilt, or early foliar decline (EFD) has occurred in Pima cotton in the San Joaquin valley of California, where it has been implicated in yield and fiber quality losses. A project was begun in 1998 with the objectives of determining the heritability of tolerance to EFD, documenting the detrimental effects of EFD upon yield and fiber quality, demonstrating the relationship between EFD severity and plant maturity, and creating earlier, tolerant germplasm. In 1999, F3 progeny of individual plant selections were grown and evaluated for EFD in small plots at Buttonwillow and Tulare, CA. Replicated trials of F4 progeny (20 lines per population) were conducted at the above locations in 2000. At the Tulare location, EFD ratings among F 4 lines of the three populations were negatively correlated with nodes above bloom counts (-0.47 - -0.84), plant heights (-0.60 - -0.73), and yield (-0.60 - -0.82). At the Buttonwillow location where EFD expression occurred later in the season, EFD ratings correlated negatively with plant height (-0.60 and -0.71) and yield (-0.46 and -0.63) in two of the three populations. Fiber micronaire was negatively associated with EFD severity in all populations at Tulare (-0.59 - -0.80), as was fiber elongation in two populations (-0.44 and -0.55). The heritability of EFD expression between individual plants and individual progeny rows of the F2 and F3 generations was low (14-19%), and did not improve appreciably between the F3 and F4 generation progeny (18-24%). When F3 and F4 progeny were standardized to have a similar EFD ranges, heritability between the two generations improved (37-46%). Heritability of EFD expression within lines of the F4 generation, as measured by variance component estimates, was quite high (83-89%). Low heritability estimates between F2:F3 generations preclude efficient selection for EFD tolerance in individual F2 plants. Higher heritability estimates between F2:F3 generations suggest that selection may be feasible in unreplicated early generation progeny rows, planted at multiple locations. The greatest selection efficiencies, as indicated by the highest heritability estimates, will occur in replicated advanced generation tests. The negative relationship of EFD severity with nodes above bloom or plant height suggests difficulty in attempting simultaneous selection for EFD tolerance and early maturity. From the results of this investigation it appears that the impact of early foliar decline upon yield and fiber quality is dependent upon the time of initial onset and speed of progression of the disorder. (ARS-AZ)<br /> <br /> Seedling Drought Tolerance in the Converted Race Stocks: 79 converted race stocks have been screened for seedling drought tolerance and tolerance/susceptibility is being confirmed for the most tolerant and most susceptible. Once the re-screen confirms seedling drought tolerance/susceptibility, parents will be selected for a half-diallel to measure inheritance of the trait. A limited number of tests will be performed to determine specific mechanisms controlling seedling drought tolerance. (AES-TX A&M)<br /> <br /> Fiber length in upland cotton: Three upland genotypes (TAM 94L-25, Fibermax 832, and TTU 202) have been crossed in a half diallel with Tamcot Camd-e, and Acala 1517-99 to determine if the genes for near long staple in L-25, Fibermax 832, and TTU 202 are allelic and determine transgressive segregation in the F2 generation. (AES-TX A&M)<br /> <br /> Multi-Adversity Resistance Program: Yield potential in Texas is affected by a number of stresses, including drought, diseases, and insect pests such as the boll weevil, whitefly, bollworm complex, fleahopper, thrips, aphids, and nematodes. The main focus of the Multi-Adversity Resistance (MAR) Program is to breed, develop, and release cotton strains and varieties with high yield and fiber quality, earliness, higher levels of resistance to pests and abiotic stresses, and drought tolerance. The established MAR techniques and procedures involve a modified recurrent selection program in which each cycle includes extensive seed, seedling and plant screening and selection in the laboratory and greenhouse, followed by a four-stage field testing and evaluation system. To assure adaptation and stability of performance, the evaluation includes tests at ten locations in Texas. The 10 field testing locations include the major Texas cotton growing regions from the Rio Grande Valley in South Texas to as far north as Lubbock representing a wide range of diverse environments including moderate to severe water stress, and insect and disease pressures. New germplasm is developed at College Station. About 120 strains are evaluated each year with and without supplemental irrigation, and with and without insecticide treatment. The MAR program also conducts breeding research with morphological variants such as leaf shapes, pubescence levels, frego bracts, plant color, and nectarilessness. (AEX-TX A&M)<br /> <br /> Objective 5: To refine and develop cotton breeding and variety testing method-ologies and techniques.<br /> <br /> Comparision of breeding methods: To compare genetic gain from selection via pedigree with that of bulk selection, six hybrid populations were developed during the summer of 2001. Of these six populations, four will be used in the final study. F2 seed will be produced in the winter nursery near Tecoman, Mexico. (AES-NC)<br /> <br /> Recovery of recurrent parent: Several CRS/TAM 94L25 generations are being evaluated for recovery of the recurrent parent, i.e. TAM 94L-25. Agronomic, morphologic, and fiber quality data will be examined for parents, F1 and BCF1 generations. (Ross Rosenbaum, M.S. candidate) (AES-Texas A&M)<br /> <br /> Visual genotype evaluation: To determine guidelines for efficient and discriminating genotype evaluation the yield plots in the preliminary trials (NC) or Official State Strains Tests (LA) will be evaluated visually and assigned a numeric value for yield potential during the fall of 2001. This will be compared to actual harvested yields. (AES-NC, AES-LA)<br /> <br /> Comparative analysis of marker assisted selction in a backcross breeding program: We have utilized SSR markers to test the efficiency of backcross breeding program based on conventional methods. We demonstrated that an integrated approach of SSR markers and conventional breeding methods could be more useful to make rapid progress in breeding compared to only conventional selection method for phenotype in introgressing day-neutral genes in wild race stocks. (ARS-MS)<br /> <br /> Use of SSR marker to predict about hybrid performances in cotton breeding: We demonstrated that the genetic distance between the lines based on SSR markers has a significant correlation with lint percentage and other agronomic characters of their F2 hybrids. (ARS-MS)<br /> <br /> Objective 6: To develop cotton bioinformatic systems.<br /> <br /> CottonDB: We provided the maintenance and updating of the National Plant Genome Database, CottonDB, http://ars-genome@cornell.edu. (ARS-TX A&M)<br />

Publications

Green, J.K., S.G. Turnipseed, M.J. Sullivan, and O.L. May. 2001. Treatment thresholds for stink bugs (Hemiptera: Pentatomidae) in cotton J. Econ. Ent. 94(2): 403-409.<br /> <br /> Karaca, M. S. Saha, J. Jenkins, A. Zipf, R. Kohel, and D.M. Stelly. 2001. DNA markers linked to the Ligon Lintless (Li1) mutant in cotton. J. Heredity. (Submitted)<br /> <br /> Kohel, R.J., J.E. Quisenberry, G. Cartwright, and J. Yu. 2000. Linkage analysis of transgenes inserted into cotton, Gossypium hirsutum L., via Agrobacterium tumefaciens transformation. Journal of Cotton Science. 4:66-69.<br /> <br /> Liu, S., S. Saha, D. Stelly, B. Burr, and R.G. Cantrell. 2000. The use of cotton aneuploid for the chromosomal assignment of microsatellite loci. Journal of Heredity 91:326-332.<br /> <br /> May, O.L. 2001. Registration of PD 94045 cotton germplasm line. Crop Sci. 41: 279-280.<br /> <br /> May, O.L. 2001. New strategies to improve cotton yield and quality. ACTA Gossypii Sinica Cotton Science 13(1): 54-58.<br /> <br /> May, O.L., R.F. Davis, and S.H. Baker. 2001. Registration of GA 161 cotton. Crop Sci. 41: (In press).<br /> <br /> May, O. L. 2002. Quality Improvement of Upland Cotton (Gossypium hirsutum L.) Fiber. J. Crop Prod. 5(1): (In press).<br /> <br /> Reddy, O.U., A.E. Pepper, I. Abdurakmonov, S. Saha, J. Jenkins, T. Brook, and K.M. El-Zik. 2001. New dinucleotide and trinucleotide microsatellite resources for cotton genome research. J. Cotton Science. 5(2):103-113.<br /> <br /> Saha, S., J.N. Jenkins, and J.C. McCarty. 2000. A novel strategy for general sustainability and resistance management in pest and pathogen-resistant crops. J. of New Seeds 3:53-61.<br /> <br /> Saha, S., M. Karaca, J. Jenkins, O.U. Reddy, A.E. Pepper, and R. Kantety. 2001. SSR markers are useful resources for the analysis of functional genes. Gnome Research. (Submitted).<br /> <br /> Sakhanokho, H., A. Zipf, K. Rajasekaran, S. Saha., and G.C. Sharma. 2001. Induction of highly embryogenic calli and plant regeneration in Upland (Gossypium hirsutum) and Pima (Gossypium barbadense L.) cottons. Crop Science. 41:1235-1240.<br /> <br /> Yuan, Y.L., Y.H. Chen, C.M. Tang, S.R. Jing, S.L. Liu, J.J. Pan, R.J. Kohel, and T.Z. Zhang. 2000. Effects of the dominant glandless gene Gl2e on agronomic and fibre characters of Upland cotton. Plant Breeding. 118:59-64.<br /> <br /> Proceedings<br /> <br /> May, O.L. 2001. Performance of PD 97000 Series Germplasm Lines and Notice of Their Release. p. 434-435. In D.A. Richter (ed.) Proc. Beltwide Cotton Conf., 9-13 January, Anaheim, CA.<br /> <br /> May, O.L. 2001. Transgenically enhanced cotton fiber strength exhibits vanishing act. In R. Irwin (ed.) Virginia Polytechnic Institute Information Systems for Biotechnology News Report. ().<br /> <br /> May, O.L. 2001. Enhancement of cotton fiber length and strength properties for a 21st century textile industry. In C.R. Benedict and G.M. Jividen (ed.) Proc. Genetic Control of Cotton Fiber Quality Conf., Cotton Incorporated, 5-6 Dec. 2000. San Antonio, TX. (In press). <br /> <br /> May, O.L. 2001. Breeding improvements  what does the future hold ? In C. Chewning (ed.) Proc. 14th Engineered Fiber Selection System Conference 11-13 June 2001. Greenville, SC. Cotton Inc., Raleigh, NC. (In press).<br /> <br /> Myers, G.O, S. A. Fitch, A. E. Percival, P.D. Colyer, W. D. Caldwell, and P. R. Vernon. 2001. Root-knot nemaotode screen of 150 Texas Race Stock accessions. p. 121-124. In D.A. Richter (ed.) Proc. Beltwide Cotton Conf., 9-13 January, Anaheim, CA.<br /> <br /> Yu, J., R.J. Kohel, H.B. Zhang, J.M. Dong, and L.I. Decanini. 2000. Construction of a cotton BAC library and its applications to gene isolation. Proceedings of the 8th International Conference on the Status of Plant and Animal Genome Research. p. 87.<br /> <br /> Experiment Station Bulletins<br /> <br /> Caldwell, W.D., R.C. Griffin, D.J. Boquet, E.M. Holman, S. Moore, J.I. Dickson, P.D. Colyer, G.O. Myers, J. Thomas, A.B. Coco, M. Wolcott and M. Reeder. 2000 Cotton Variety Trials in Louisiana. La. Agric. Expt. Stn. Mimeo Series No. 129.<br /> <br /> Day, J.L., A.E. Coy, W.D. Branch, O.L. May, S.S. Lahue, and L.G. Thompson. 2001. 2000 Peanut, Cotton, and Tobacco Performance Tests. Coll. Agric. and Environ. Sci. Res. Rpt. 671.<br /> <br /> Abstacts<br /> <br /> Bourland, F.M., O.L. May, and R.L. Nichols. 2001. Challenges in Cotton Cultivar Testing. Agron. Abstr. (In press).<br /> <br /> May, O.L. and A.S. Culpepper. 2001. Cotton Germplasm With Enhanced Glyphosate Resistance. Agron. Abstr. (In press).<br /> <br /> McGriff, D.E., and O.L. May. 2001. Evaluation of Transgenic vs. Conventional Cotton Cultivars. Agron. Abstr. (In press).<br /> <br /> Books; Book Chapters<br /> <br /> Genetic Improvement of Cotton: Emerging Technologies. 2001. Edited by J.N. Jenkins and S. Saha, Science Publishers Inc., Enfield, New Hampshire, USA<br /> <br /> Khan, M.A., G.O. Myers and J. McD. Stewart. 2001. Molecular markers, genomics, and cotton improvement. In: M.S. Kang (ed). Crop Improvement: Challenges in the 21st Centry. Food Products Press, Binghamton, NY. (in press).<br /> <br /> Saha, S., M. Karaca, J.N. Jenkins, and D. Lang. 2000. Improved methods for screening cotton cDNAs using fluorochrome-labeled AFLP- and SSR-specific primers. In: Emerging Technologies in Cotton Breeding, edited by J.N. Jenkins and S. Saha, Science Publishers Inc., Enfield, New Hampshire, USA, pp 239-255.<br /> <br />

Impact Statements

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Report Information

Participants

Brief Summary of Minutes

1. Comments by SAES representative
Dr. Bob Westerman (Oklahoma State University) began my commenting that he has been pleased with the projects accomplishments and progress to date. He reminded us that the current project expires on Sept. 30, 2005. In preparation for this expiration we need to determine the future path we wish to take. There are two main options: 1) continue as a Multi-State Project (MSP) or 2) become a State Coordinating Committee (SCC) (equivalent to the old SRIEGs). Either way we need to identify a writing committee to develop a proposal for establishing a Development Committee (DC). A DC is normally authorized for 2 years so that a more detailed MSP or SCC proposal can be written. During the time that a DC is in effect the group would continue much as it is. A proposal for forming a DC is relatively short (< 5 pages) but needs to be completed by the end of February so that the SAES Directors can consider at their spring meeting in late March/early April.

There are disadvantages and advantages whichever way the group decides to go, with either a MSP or a SCC. The advantage of a MSP is that there is the option for money allocation by Experiment Stations and gives SAES Directors more flexibility in charging off salaries against CSREES allocations. MSP projects tend to be much more researcher driven. Both researchers and extension can be represented within a SCC. Participation (at least informally) by private industry in a MSP is allowed. Both MSPs and SCCs require annual reports and minutes but these are slightly more detailed in a MSP. While you dont have to have a Hatch project to be a member of a MSP, this is typically encouraged by administration for the reason noted above. Either way we choose to go, MSP or SCC, we need to form a DC and write a brief proposal so that it can be authorized. In writing the DC proposal (and ultimately an MSP or SCC proposal) the current projects objectives will need to be rewritten (or at least tweaked) and probably put in a broader societal context.

It was decided by those present that an email vote on going forward as a MSP or as a SCC would be taken during early February so that the DC writing committee knows how to target the DC proposal.

2. Identify Development Committee to write project/timeline
Given officer rotations, Peng Chee (2005 vice-chair) will chair the writing committee for the development of the DC proposal. Volunteers are sought to aid Peng. As mentioned earlier, this DC proposal needs to be completed by the end of February. Public researchers are encouraged to check with their administration on the benefits/disadvantages of being a MSP or a SCC.

3. Identify committee for S-304 final report
John Yu (2005 chair) will take the lead in writing the S-304 Final Report.

4. Discuss a Vote of Support for the Cotton Incorporated Genetics Initiative
While nobody claimed this agenda item, it was thought that this would be of benefit to Roy Cantrell (Cotton Incorporated), the cotton industry, and ultimately to many of us as he seeks continued support of the CI Genetics Initiative. This received a unanimous vote of support and Ted Wallace (outgoing chair) was charged with writing. It is important to show how monies from the initiative are being leveraged by what MSP funds do.

5. Overview of USDA Coordinated Agriculture Project
Barbara Triplett informed the group about efforts underway to develop a proposal for the NRI funded CAP project specific for cotton. These are large projects covering 4-5 years, $4-5 million, and are multi-institutional. For the cotton CAP proposal to have any chance of success the cooperation/ contributions of traditional geneticists and breeders is essential. The overall goal of the CAP project is to translate genomics technology to plant breeders. A preliminary meeting in December 2004 was held and a follow up meeting is scheduled for later this spring (April/May). Two sites to check for more information on the project and to subscribe to future emailings regarding this project are: www.plantgenome.agtec.uga.edu/register and the Cotton Portal at http://gossypium.info.

6. State Reports
Given limited time, state reports were not given at this time. An email soliciting reports and publications will be sent out in the next few weeks. These will be necessary to put together the 2004 Annual Report.

7. The next S-304 Meeting will take place in conjunction with the 2004 Breeder Tour tentatively scheduled for the 2nd full week in September in the Southeast.

8. Nominations/vote for new secretary
There were no volunteer from those in attendance so nominees will be solicited over the next few weeks and voted on as appropriate

Elections for the following posts were held and officers selected to serve for 2005 were:
Chair John Yu
Vice-chair Peng Chee
Secretary To be determined at next annual meeting

NEW BUSINESS
Multistate Research Project (MRP) S-304 was scheduled to expire September 30, 2005. A request was e-mailed soliciting input regarding the continuation of participation in research efforts as a MRP or as a SSR (Southern Coordinating Committee), formerly known as SRIEG (Southern Research Information Exchange Group). All comments received were supportive of developing a new MRP. The development committee (P. Chee, G. Myers, W. Smith, and John Yu) drafted a pre-proposal and submitted a request for a new MSR. A request for extension was e-mailed to the Executive Director of the Southern Association of Agricultural Experiment Station (SAES) Directors who recommended that MRP S-304 be extended for one year, CSRESS concurred and approved the extension until September 30, 2006. A one year extension will allow for the development of a full proposal for the new MRP. Inputs for the new proposal will be solicited at the next meeting of S-304 participants.

Accomplishments

OBJECTIVE 1 - To acquire, curate, characterize, and evaluate the species, races, and genetic types of Gossypium (cotton). <br /> <br /> The 196 Uzbekistan accessions were evaluated in the field for root-knot nematode resistance. The gall score average for the resistant check was 1.63 and for the susceptible check was 4.16 which is in line with expectations and previous ratings of these plants in other trials. As expected, a large majority of the Uzbekistan lines (157) were susceptible (gall score >=3) to highly susceptible (gall score = 5). Thirty one lines were moderately resistant (gall score >2 but <3). Eight lines could be classified as resistant with two of these (SA2654 and SA2791) being rated as more resistant than the resistant check (Stoneville LA887). <br /> <br /> Yield and fiber data was collected on 189 accessions from Uzbekistan. Lint yield for the accessions ranged from 129 to 739 lbs/a compared to 750 lbs/a for the check (PSC 355). Lint percent values for accessions ranged from 18.2% to 40.7% compared to 40.1% for the check. Most accessions performed poorly in terms of agronomic traits, however, a few accessions were identified with a competitive yield. Several accessions were used as parental material. Previously collected descriptor data will be submitted to the GRIN database<br /> <br /> The Cotton Cytogenetics Group (Stelly) is utilizing interspecific germplasm introgression (IGI) to expand the baseline genetic variability in cotton, and making it available to cultivar breeding programs. The Cotton Improvement Laboratory (Smith and Thaxton) strives to utilize such IGI lines as well as other sources to produce germplasm having improved quality, better yield potential, and resistance to biotic stresses such as seed/seedling diseases and abiotic stresses such as temperature and drought. G. barbadense, G. tomentosum and G. mustelinum carry genes that could improve agronomic traits in Upland cotton, even though they themselves perform poorly. In the G. tomentosum, individuals in segregating populations possessed superior fiber quality traits relative to the recurrent upland parent. The G. mustelinum populations also contained improved fiber quality phenotypes in an Upland background. Recent (2004) germplasm lines released because of their fiber quality package exhibited fiber length in the 35 and 36 staple range, fiber bundle strength as high as 36 g/tex, and 4.0 to 4.5 mic.<br /> <br /> Russell Kohel visited Uzbekistan and 800 Uzbek accessions were received for evaluation on an ARS-Uzbek project. These materials are being increased in Mexico, and they will be evaluated in Texas and Mississippi. Seed of 3,687 accessions were distributed from the Cotton Germplasm Collection to 85 domestic users and 44 accessions were distributed to 5 international users. These included governmental and commercial users.<br /> <br /> A. An 11-day survey (funded by USDA) was conducted in Mexico (Nov. 9-20, 2004) for two Gossypium species whose status was unknown. During this survey it was determined that Gossypium trilobum is a threatened species, whereas G. turneri, although it has a restricted distribution, is stable for the moment. New seed collections were made of both species. <br /> <br /> B. Several morphological traits were maintained and further characterized. <br /> Short fruiting branch. Twenty-eight selections of open-pollinated plants with the short fruiting branch phenotype made in 2003 were each planted to 50' progeny rows for evaluation and re-selection. New open-pollinated selections were made of individual plants with consistency of phenotype and good yield potential. This phenotype originated as a transgressive segregate from a A1xD2-1xAD1 trispecies hybrid. <br /> <br /> Glabrous thick leaf. Fifty-five rows (50'/row) were planted from seeds of plants grown the previous year and evaluated for chlorophyll content with a Spad meter. The two or three plants in each row with the highest chlorophyll content were self-pollinated and seed harvested at the end of the season. Phenotypic parameters including leaf thickness, specific chlorophyll content, photosynthesis, etc. will be measured next year. This phenotype originated as a segregate from a A1xD2-1xAD1 trispecies hybrid and was probably donated by the D2-1 species. <br /> <br /> Qualitative Traits in Cotton: Red-calyx, red anther, hairy anther, green fiber, brown fiber. Selected plants with good phenotypic expression of each of the qualitative traits listed were self-pollinated to maintain genetically stabilized homozygous lines. It was determined that the red calyx trait (introgressed from G. herbaceum) was pleiotropic with red petal spot but, as demonstrated previously, the red anther trait (D genome origin) is not associated petal spot. Selections based on yield potential were also made from these genetic lines. The hairy anther trait originated from a cross between G. hirsutum with the pilose trait and G. barbadense. For this trait to be expressed the pilose gene must be present, but all plants with pilose do not express the hairy anther trait. <br /> <br /> C. Species diversity. Three projects are concerned with evaluation of genetic diversity among taxa.<br /> <br /> Genetic diversity of Caribbean cotton. As a result of a survey and collection of wild cotton in Florida, a project was initiated to determine the genetic diversity of the cotton around the Caribbean basin and, if possible, determine the origin of the Florida wild cotton. Seeds of more than 50 accessions of G. hirsutum collected near the coast of numerous island nations around the Caribbean were obtained and these, along with the collections from Florida were germinated and are growing in pots in the greenhouse. DNA for molecular analysis has been extracted from some of these. <br /> <br /> Diversity of the Gossypium species of the G genome. The objective of this project is to determine the diversity of G. australe, G. bickii and G. nelsonii and determine if hybridization between these species occurs in natural populations. In initial results the diversity of G. australe accessions from across Australia was measured with approximately 50 AFLP markers. This limited data set shows that accessions from Western Australia are significantly different from eastern (Queensland) accessions at the molecular level. <br /> <br /> Diversity among arborescent D-genome species. Diversity among the species with in section Erioxylum represented in germplasm collected in 2002, was measured by AFLP. <br /> <br /> DNA content of the Gossypium genus. Estimates of the nuclear DNA contents of the species in Gossypium are highly variable within a species, or have not been made. This information has significance in relation to molecular maps of the genomes, and in evolutionary understanding of the genus. Work was completed on the project to obtain an accurate estimation of the DNA content of a majority of the known Gossypium species based on flow cytometry. It was also determined that barley, when used as an internal standard, as conventionally recommended, gives an erroneously high estimation of the DNA content of cotton. Three external standards (rice, maize, & barley) were included in each run and a standard curve was constructed to assure accuracy of the results. <br /> <br /> Epigenetics of wide hybridization in cotton. Aspects of epigenetic responses in wide-hybrid introgression were examined. Reports for other plant species indicate that when dissimilar genomes are combined via hybridization, genome structure and normal gene expression patterns are disrupted. To investigate these issues in cotton, we assembled a panel of DNA composed of G. davidsonii, G. anomalum, and subsequent hybrids (non-doubled and doubled through F2) between these species. This panel was screened with SSR primers to assess the conservation of repetitive fractions of these genomes. Additionally, nuclear DNA contents for the lineage were measured. Complete genome conservation was observed for 20 SSR primer pairs. For the DNA content, a small reduction in genome size was observed in the G. davidsonii x G. anomalum F1 hybrid but no other epigenetic phenomena were observed through the F2 generation. <br /> <br /> Gossypium barbadense 3-79 chromosome substitution lines (CS-B lines) were evaluated directly and in the form of F2 progeny performance. <br /> <br /> A set of 434 Gossypium hirsutum L. landraces of Mexico from the USDA-ARS Cotton Germplasm Collection was planted at Shafter, CA for phenotypic and genetic characterization of variability. Commonly used phenotypic characters were scored for each accession and tissue was bulked of each accession for DNA extraction. Preliminary results showed that significant variation still exists in the collection from the data collection. Diversity between and within accessions was the highest for accessions collected within the states of Guerrero, Yucatan, Oaxaca, Veracruz and Chiapas. The use of molecular markers is expected to reveal more variation not evident in the physical traits, and will become a valuable tool in the maintenance and utility of the diversity of the germplasm collection.<br /> <br /> Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans race 4 isolate has been identified in California soils. Disease expression of this race has been most severe in Pima cotton fields, but also has the capability to infect many Acala and Upland cotton varieties to a high degree depending upon inoculum levels. In order to assess the U.S. cotton gene pool and study the resistance inheritance of FOV race 4, in 2003 and 2004 more than 150 Pima and Acala/Upland commercial and experimental varieties, and improved germplasm were evaluated in known infested fields and in inoculated greenhouse assays. Preliminary results showed that most commercial Pima varieties grown in California were observed to be more susceptible to FOV race 4 (stand loss, stunting, etc) than any Upland cottons (G. hirsutum). However, tested Acala and non-Acala Upland cotton varieties were still infected by FOV race 4 at levels where plants would be expected to reproduce the fungus and expand inoculum. Highly resistant germplasm to FOV race 4 were identified on Pima for inoculum levels tested (field and greenhouse). Development of highly resistant germplasm and genetic mapping populations are ongoing in order to further study FOV resistance and its heritability.<br /> <br /> OBJECTIVE 2 - To develop, maintain, and distribute molecular genetic, genetic, and cytogenetic tools for the evaluation and enhancement of cotton germplasm. <br /> <br /> Alloplasmic lines (AD3, AD4, AD5, A2, C1, D3-d, D8, E1) in the G. barbadense semigamy (Se) nuclear background were maintained. A partial set of molecular markers were developed to distinguish among the various alloplasmic lines based on chloroplast DNA markers. Markers to distinguish among A- type cytoplasms have not been identified. <br /> <br /> D8-R lines that had previously been backcrossed to various elite cotton cultivars to improve their agronomic quality were self-pollinated to increase available seeds for evaluation. Reciprocal crosses were made between four elite cotton cultivars and the original D8 restorer containing the cytoplasm of G. trilobum and Rf2 and between the elite cultivars and B411R with the G. harknessii cytoplasm and RF1. The effect of cytoplasm was determined in replicated field trials at Las Cruces, NM. The D8 cytoplasm caused about a 20% reduction in yield whereas no detectable yield loss was associated with the D2 cytoplasm. <br /> <br /> Additional quantitative trait loci (QTL) were added to the intraspecific AFLP map of Gossypium hirsutum. Loci added were for yield and the within boll yield components: bolls per plant, number of fiber per seed, average weight per fiber, and number of seeds per boll. The number of QTL identified by composite interval mapping were 2, 1, 2, 2, and 0, respectively. An additional 2 markers were identified using interval mapping and 40 using single point analysis [AES-LA]. Using G. tomentosum chromosome substitution lines of G. hirsutum, AFLP linkage groups were able to be assigned to some of the monosomic and monotelodisomic genetic stocks. In the end, 53 AFLP markers were assigned to chromosomes and/or chromosome arms. At least one AFLP marker was assigned to each of 16 different chromosomes and 50 markers were localized to different chromosome arms. Nine of 53 common AFLP markers were found between the aneuploid stocks and the intraspecific cross used to develop the AFLP map. This allowed 8 linkage groups to be assigned to 6 different chromosomes <br /> <br /> In cooperation with Cotton Inc and cotton programs across the Cotton Belt, ARS in College Station, Texas, assembled, maintained, and distributed a standard germplasm panel of 12 diverse cotton genotypes for systematic evaluation of molecular genetic markers. We filled in the requests of the community for the permanent mapping population of 191 TM-1 x 3-79 RI lines. We also delivered 192 pairs of SSR primers that were developed from TM-1 BAC clones. Genetic mapping of SSR markers from this and other sources was conducted in the RI population. In cooperation with Texas A&M University, we assembled 5,000 physical contigs from 100,000 TM-1 BAC fingerprints. <br /> <br /> Interspecific germplasm developed in the Cotton Improvement Laboratory with G. barbadense, G. tomentosum and G. mustelinum are being distributed to the molecular geneticist for evaluation.<br /> <br /> In 2004, an intraspecific Gossypium barbadense RIL population of 144 F6.8 lines (PS-6/89590) was characterized for yield, fiber, and agronomic properties in replicated tests in California, Arizona, and New Mexico. An introgressed G. hirsutum RIL population of 98 lines (NM24016/TM-1) was increased for public seed distribution. <br /> <br /> Molecular marker technology has progressed rapidly in the 1990s with the construction of the first genetic map of cotton published in 1994. Our lab has collaborated with Dr. Andrew Paterson to expand the cotton map to include over 2500 loci. This high-density genetic map, which covers all 26 chromosomes of the tetraploid cotton genome, provides new insights into the structure, function, and evolution of the cotton genome. A majority of the loci was from RFLPs, although a few came from PCR based technology such as SSRs or STS. Data was also presented that shows the feasibility of converting the mapped loci into a Single Nucleotide Polymorphism (SNP) detection system that is better suited for use in marker-assisted breeding.<br /> <br /> To add to knowledge of gene expression during cotton fiber development, a cDNA library (prepared from Gossypium hirsutum cv Delta Pine 90) biased toward genes expressed at 20 DPA compared to 6 DPA was constructed and sequenced in collaboration with Curt Wilkerson, Michigan State University. In this case where plants were growing under fairly cool conditions, 20 DPA represented a very early stage of secondary wall deposition. From 9,121 high quality EST sequences (GenBank Accession numbers CO490611  CO499850; called G.h.fbr-sw ESTs), 3,420 unigenes were assembled within this one library, and the sequences were contributed to a comprehensive assembly of cotton ESTs, (J. Udall and J. Wendel, Iowa State University, and coworkers, http://agcol.arizona.edu/pave/cotton/. in which the library was called GH_SCW). About 15% of the translated G.h.fbr-sw ESTs had no significant match to the Arabidopsis proteome, and 150 had no similarity to proteins in the Non-redundant database. Such genes are indicative of processes that make the cotton fiber distinctive. Based on the comprehensive assembly including primary and secondary wall fiber genes, cotton fiber expresses genes with significant similarity (<E-10) to 7,457 Arabidopsis genes, or >25% of the proteome of this model plant. Of these, 600 were sequenced only from the secondary wall stage of fiber development. The G.h.fbr-sw library was not sequenced to completion, indicating that this is a minimal estimate of the uniqueness of secondary-wall-specific expression in cotton fiber. Therefore, secondary wall deposition in cotton fiber is accomplished through a substantial number of genes that are apparently uniquely expressed at that stage, as well as a large complement of expressed genes that are shared with the primary wall stage. These novel secondary wall sequences add to the growing platform for functional genomics of cotton fiber. The support of the NSF Plant Genome Program and Cotton Incorporated, Cary, NC is gratefully acknowledged.<br /> <br /> A germplasm release was made of 17 chromosome substitution backcross lines, each being quasi-isogenic to TM-1, but substituted for one chromosome or one chromosome arm of the non-photoperiodic G. barbadense line 3-79. Development was advanced for new chromosome substitution series for G. tomentosum and G. mustelinum Various BCnF1 chromosome substitution stocks from these programs and DNAs were distributed. DNAs of G. barbadense chromosome substitution BCnF1 stocks were created and distributed to several genome-mapping labs. Backcross-mediated chromosome substitution with 3-79 into TM-1 was advanced for more recently discovered G. hirsutum hypoaneuploids. Prospectively new G. hirsutum hypoaneuploids continue to be identified and tested. The identification of a new monosomic G. hirsutum was reported, H21. <br /> <br /> An expressed sequence tag (EST) database, developed from a diploid cotton species (Gossypium arboreum L.) (http://cfgc.ucdavis.edu), contains ~14,000 non-redundant sequences from 7-10 dpa (days post anthesis) fiber transcripts and their homologous gene functions, was used to develop microsatellite markers. A total of 1232 EST-derived microsatellite (MUSS and MUCS) primer pairs were designed and tested for PCR amplification. Based on PCR amplification, the transferability of the microsatellite markers was high in that 83% of the primer pairs successfully amplified products from eight Gossypium species, including both diploid (A and D) and tetraploid accessions and cultivars (total 23 entries). High interspecific transferability can be due to the sequence conservation of the gene-coding region of the genome. Polymorphic PCR-amplified DNA fragments among species of cotton were observed for 311 (62.7 %) MUSS and 251 (48.0%) MUCS, while 457 (44.6 %) were monomorphic. Between G. hirsutum L. and G. barbadense L., 202 markers were polymorphic, while the polymorphism within these two tetraploid species was low - 1.4 % and 1.5 %, respectively (Table 1). Locations of 40 microsatellite markers were delimited to 19 cotton chromosomes and/or 17 chromosome arms by hypo-aneuploid deficiency analysis. Polymorphic markers between G. hirsutum and barbadense showed segnificant sequence similarity to genes or putative genes with known function including endo-²-1,4-glucanses, Cytochrome P450-like protein, expansin, RING zinc finger protein, and ABC transporter, which are related to fiber. PIC values ranged from 0.12 to 0.74. Analysis of relationship among 23 accessions generated three major clusters which grouped separately the different species. Besides being of value for genome analysis per se, the origin of these SSR markers from fiber-derived ESTs and their demonstrated portability, suggest that they may also be useful for marker-assisted selection in breeding of fiber quality-related genes. This information will be useful to other geneticist working with cottons and will facilitate future efforts to map the cotton genome. Funding for this project was provided by Cotton Inc. These microsatellite markers are made public through the Cotton Microsatellite Database (CMD), http://www.mainlab.clemson.edu/cmd/projects/muss/index.shtml <br /> <br /> To exploit the cotton sequence in the public domain, simple and complex SSRs derived from fiber ESTs were identified as potential DNA markers for genetic mapping and screening germplasm collections. The SSR candidate list is posted on the labs web page (http://cfgc.ucdavis.edu). Several groups are working from this list, and new fiber loci have been mapped, increasing the number of fiber genes on the molecular map. The discovery of cotton SSRs was recently expanded to screen the new global assembly of cotton ESTs (Udall et al., 2005). Mapping of fiber mutants identified new fiber QTLs and characterized new fiber loci as candidate genes for functional analysis.<br /> <br /> OBJECTIVE 3 - To adapt and develop methodologies to evaluate, modify, and utilize cotton germplasm. <br /> <br /> The CIL (Texas) evaluated the use of early generation testing (EGT) methods to predict advanced strain performance at College Station (CS) and Weslaco (WS), TX based on lint yield, lint percent, micronaire, fiber length, fiber strength, fiber elongation, and fiber uniformity. Associations (P=.05) were present for fiber length and fiber strength. At WS, F2 EGT lint yield data were associated with the number of plants and strains selected through the F6 generation, yet no associations were found for fiber quality characteristics. Lack of consistent r values across generations and locations suggest a large environmental influence on both lint yield and fiber quality parameters.<br /> <br /> Twenty-one F2 populations were developed from diallel crosses involving seven Upland cottons, TM-1, 7235, SG125, Fibermax 832, CAMD-E, MD51, and DPL50. The populations were grown in the ARS field plot in College Station, Texas, for measurements of fiber properties and isolation of genomic DNA from individual F2 plants. We continued to develop molecular descriptors with portable PCR-based DNA markers that will be at foundation of germplasm characterization.<br /> <br /> In 2004, an investigation was initiated to determine the relationship between genetic relatedness (as determined by molecular analyses) and general combining and specific combining ability in U.S. and foreign Gossypium barbadense cultivars. Yield, fiber, and agronomic data were obtained from replicated tests of diallel F1 lines at Maricopa, AZ and Las Cruces, NM. <br /> <br /> The limited number of regenerable cotton varieties has not only exacerbated the narrow genetic base of commercial cotton varieties, but also remains a major obstacle for the routine use of gene transformation for cotton improvement. Our lab has initiated a project to evaluate elite breeding lines developed by the UGA cotton breeding program for somatic embryogenesis. The results showed that somatic embryogenic ability is present in several elite lines. The line with the greatest embryo production, GA98033, was released in 2004 as public germplasm line. GA98033 combines high yield potential, acceptable fiber quality, resistance to fusarium wilt and conducive to plant regeneration through tissue culture somatic embryogenesis. Therefore, in additional to being useful to breeders as a parental source with high yield potential and acceptable fiber quality, GA98033 can potentially be useful to molecular biologists as a recipient of transgenic traits.<br /> <br /> Expression profiling using cotton fiber long oligonucleotide microarrays revealed major and minor developmental switches that control fiber growth and development. Using this developmental framework as the foundation, comparative genomics studies identified genes deemed of pivotal importance to fiber development, and as molecular determinants of fiber traits. A list of candidate genes has been generated for functional analysis and to develop into molecular markers for genetic mapping. Cotton fiber chips are distributed to the cotton community on a cost recovery basis<br /> <br /> OBJECTIVE 4 - Germplasm enhancement for biotic and abiotic stress resistance and agronomic traits. <br /> <br /> Diploid hybrids were made between the A genome (G. arboreum) accessions and D genome species (G. trilobum, G. raimondii and G. aridum). These need to be doubled to convert these to allotetraploids and restore fertility for crossing with cotton. One hybrid (A2 x D8) had doubled sectors after colchicine treatment and a flower was obtained with some fertile pollen. This was crossed as male to AD1 cotton and two plants were obtained. Prior to boll maturity the two F1 plants died with symptoms similar to that shown by lethal gene complementation, but four BC1 embryos were obtained by rescue culture. One of the plants died with symptoms similar to the trispecies hybrid, whereas the other three matured, developed bolls and yielded BC2F1 and BC1F2 seeds. The death of the tri-species hybrids and one of the BC1 plants suggests that a genetic lethal complementation was present. As a part of the project to enhance the secondary germplasm pool we developed a trispecies hybrids with a D3-compatible AD1: (B1 x D3-d x AD1). These hybrids were self-pollinated and also backcrossed to the same AD1 to produce F2 and BC1 seeds. These will be evaluated for trait segregation in 2005. New synthetic hybrids were made from cross-pollinations of G. arboreum with a 2(ADD) genetic stock to make trispecies hybrids with 2(AD) genomic constituencies. One of these was backcrossed to an elite line of upland cotton to begin development of an introgression population. <br /> <br /> Cotton improvement laboratory is an aggressive plant breeding program headquartered at the flagship campus of Texas A&M University centers around improving the genetic variability, yield potential, agronomic performance, and fiber quality of germplasm or cultivars adapted to Texas while enhancing resistance to biotic pests, such as insects, nematodes, and diseases, and abiotic stresses such as drought. The CIL developed and released of four germplasm lines and one new cultivar in 2004. These were TAM 96WD-18, TAM 96WD-69s, TAM 98D-99ne, and TAM 98D-102. TAM 96WD-18 and TAM 98D-102 have excellent fiber packages and competitive agronomic performance, while TAM 96WD-69s is a glabrous genotype expressing a measurable level of fleahopper resistance and TAM 98D-99ne carries the nectariless trait in a good agronomic background for central and south Texas. Tamcot 22 was released as a conventional cultivar.<br /> <br /> The CIL (Smith and Thaxton), collaboratively with Dr. Jim Starr, Plant Pathologist, has developed an interspecific population that is segregating for both root-knot and reniform (a problem in the LRGV) nematode resistance. The donor parent for reniform resistance is a G. barbadense. Additional efforts (Stelly) are underway to introgress the high level of resistance found in G. longicalyx. <br /> <br /> Converted race stocks have been in our basic breeding program with a number of advanced strains and segregating populations developed. Breeding programs have been evaluating the BC2F2 populations for yield and fiber quality. The race stocks are being screened for resistance to cotton fleahopper, silverleaf whitefly, nematode resistance. <br /> <br /> A project is underway to simultaneously improve G. hirsutum germplasm for fiber quality and heat tolerance. In 2003, 90 lines selected for heat adaptation and fiber quality at Maricopa, AZ were evaluated in non-replicated tests at Tifton, GA, Maricopa, AZ, and Shafter, CA. In 2004, 16 of these lines - along with check cultivars - were evaluated in replicated tests at the above locations. On the basis of their yield and fiber performance, three of the 16 lines have been selected for public release in 2005. The project continues, incorporating fiber quality traits from Gossypium barbadense introgression sources, as well as from Acala sources. In 2004, selection was made within F3 populations of two way or double crosses, thus incorporating two sources of fiber improvement and two sources of heat adaptation within each segregating population. <br /> <br /> The nectariless trait in cotton has been well documented as a host plant resistance trait through a reduction in tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois). Changes in insect management technology (boll weevil eradication and transgenic Bt cotton) have allowed TPB to become a key pest. Improved methods of managing TPB in cotton are needed to fully exploit the potential benefits of the new insect management environment in cotton production. Over 400 nectariless progeny rows (F3 to F10) where grown in 2003 and the top performing entries selected for evaluation under plant bug infested conditions. A wide range of germplasm was represented in this material including obsolete varieties, breeding lines, and nectariless isolines. A field evaluation of TPB resistance in lines of nectariless cotton was established in 2004 on Delta Branch Experiment Station, Stoneville, Mississippi. Approximately 90 nectariless progeny rows were selected for evaluation in 2004 for yield and fiber quality when grown under plant bug infested and controlled (split-plot design) conditions and compared to a conventional nectaried commercial check variety. TPB infestation and damage data (insect counts, square shed, and bloom injury) and crop production data (square and bloom production, and yield) were evaluated by calculating ratios of data for infested/controlled plots and ranking the ratios from those inferring greatest resistance to those inferring least resistance to TPB. The top performing entries (upper 50 percent) have been selected for repeating the evaluation in 2005. Reduction in fiber quality due to plant bugs was minimal. The nectariless trait, however, appears to have conferred a yield advantage for a number of entries. A second year of testing will help determine if testing under plant bug infested vs. controlled conditions is useful in discriminating among susceptible and more tolerant genotypes. <br /> <br /> Using the African species G. longicalyx as the immunity source, euploid reniform nematode-immune BC3F1, BC4F1, and BC5F1 G. hirsutum backcross segregates were identified. Their tissue was sampled for nuclear genomic DNA preparation, and some were backcrossed and inbred. Preliminary co-segregation analysis was initiated for markers. <br /> <br /> Genome-wide introgression efforts from G. tomentosum, G. mustelinum, G. longicalyx and G. armourianum were advanced 1-2 generations. Generation means analysis field evaluation experiments conducted for G. tomentosum and G. mustelinum introgression products. <br /> <br /> Improved methods in cotton transformation were published, and a pipeline for high-throughput cotton transformation to test gene function, and determine the impact of ectopic expression on fiber traits has been developed.<br /> <br /> OBJECTIVE 5  To refine and develop cotton breeding and variety testing methodologies and techniques. <br /> <br /> The ability of the program GGEbiplot to identify the best environments for selection (discriminating environments) was evaluated. Results corroborated historical anecdotal information on the best environments for selection. <br /> <br /> During 2004, we grew approximately 2000 F3:4 lines (pedigree method) and approximately 200 F3:4 lines from single-seed descent populations. Based on fiber data from individual F3 plants collected the previous year, a selection index was applied to the pedigree lines based on a combination of upper quartile length of fibers (inches, by fiber weight) (UQL), short fiber content (count) (SFC) and lint weight seed-1 (LWS). From each population the best 50 F4 rows from F3 plants with the highest UQL, lowest SFC, and highest LWS were selected. One hundred ninety-five F4 lines derived from the single-seed descent populations were also harvested without selection. This leaves us with a minimum of 300 lines derived by pedigree and 195 lines derived by SSD for future evaluation. We will begin yield-testing of these lines to compare effects of inbreeding method on estimates of genetic variance, heritability, and mean performance for a variety of fiber quality, yield, and yield-related traits.<br /> <br /> Update information on genetic relationships.<br /> Pedigree information has not been updated since the 1997 publication.<br /> Genetic uniformity has been examined since the introduction of transgenic cultivars and it was found that the level of diversity in the field was not compromised. Fiber strength has increased since 1980 and the sources of fiber strength genes were determined to come from two public breeding programs <br /> <br /> Quantify advantages and disadvantages of divergent variety development strategies. SSD v. Pedigree . David Weaver ( Auburn) has completed growing F3-derived F4 populations ( 6 different ones) this past summer. F5 progeny rows will be grown next summer and selected rows will be yield tested the following summer.<br /> <br /> Develop guidelines for efficient and discriminating genotype evaluation.<br /> Visual selection versus yield measurement. This work was performed by David Caldwell, Gerald Myers, Ted Wallace, Fred Bourland, and Daryl Bowman. There is a positive correlation between visual ratings and seed cotton yield suggesting a viable option for breeders.<br /> <br /> Compare spatial designs for efficiency; compare lattice designs with randomized, complete block designs. Work has been done by Wayne Smith and others and needs to be compiled.<br /> <br /> Compare post-mortem analyses- NNA, Trend, Lattice. Data are available and needs to be compiled.<br /> <br /> Evaluate the need to incorporate systems testing in variety trials for transgenic technologies. Interactions by varieties with technologies were not detected indicating that the relative ranking of cultivars within system (transgenic) should remain the same. However, the systems may need to be tested with cultivars to reveal true yield potential for the growers. <br /> <br /> Investigate the consequences of forward crossing of transgenic parents. This may best be evaluated over the long term by the private sector.<br /> <br /> OBJECTIVE 6 - To develop cotton bioinformatic systems. <br /> <br /> PEG-induced gene expression in cotton roots (Hendrix) The objective of this study was to develop a gene expression model of drought tolerance in cotton based on responses of the drought tolerant cultivar Siokra L23 to osmotic shock induced by polyethylene glycol (PEG). A PEG-induced phenotype was described for the plants based on time-course measurements of photosynthesis and leaf temperature. A gene expression profile was then developed from root RNA extractions taken at 0, 1, 4, 24, and 96 h after stress initiation utilizing cDNA-AFLP and cotton-fiber-based microarray chips. Siokra L23 progressed through two phases of PEG-induced stress that we designated response (0 to 48 h) and recovery (48 to 96 h). Forty-eight and 363 PEG-responsive genes were identified in the cDNA-AFLP and microarray analysis, respectively. Global gene expression profiles revealed an adaptation to the stress after 96 h. Functional categories played distinct roles in the response and recovery phases. The expression profiles of aquaporins suggested that osmotic adjustment occurred between 4 and 24 h. Sucrose synthase and several genes in the glycolytic pathway supported the hypothesis that sucrose was a solute involved in this osmotic adjustment. The expression patterns observed in this study provide insight into the mechanisms by which Siokra L23 responds to osmotic shock.<br /> <br /> ARS in College Station, Texas, re-organized CottonDB data classes and updated them with new information including cotton germplasm, variety trial, SSR clones and primers, BAC clones and fingerprints, and DNA sequences. Some bioinformatic tools were incorporated into CottonDB for sequence blast and integration of genome maps. <br /> <br /> The Cotton Functional Database has been expanded and improved to be more user friendly, allowing access and manipulation of expression-related data that is now linked to clones, constructs, ESTs, genes, and SSRs. These databases will be linked to the genetic map via the Cotton Portal. Expression data in the public domain can be downloaded into a MIAMI-compliant database for view by the community.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br />

Publications

Abdurakhmonov, I, Abdullaev, A, Rizaeva, S, Buriev, Z., Adylova, A, Abdukarimov, A, Saha, S, Kohel, R, Yu, J, Pepper, A, 2004. Evaluation of G. hirsutum exotic accessions from Uzbek cotton germplasm collection for further molecular mapping purposes. Proc Beltwide Cotton Improvement Conference. January 5-9, 2004. San Antonio, TX<br /> <br /> Akash, M., G.O. Myers, B. Jiang and B.E. Moser. 2004. Multiple imputation for missing data in molecular genetic studies. p. 1203. In: Proc. Beltwide Cotton Conf, San Antonio, TX. 5-9 Jan. 2004. Natl. Cotton Counc. Am., Memphis, TN.<br /> <br /> Akash, M.W. and G.O. Myers. 2004. QTL mapping of agronomic and fiber quality traits in cotton using AFLPs. p. 1056. . In: Proc. Beltwide Cotton Conf, San Antonio, TX. 5-9 Jan. 2004. Natl. Cotton Counc. Am., Memphis, TN.<br /> <br /> Alabady, M.S., Ulloa, M., Park, Y.H., Sickler, B.A., Wilkins, T.A., Stelly, D., Cantrell, R.G. 2004. Cotton (gossypium arboreum l.) fiber est-derived compound sequence repeat (CSR) used to develop pcr based markers.. ASA-CSSA-SSSA Annual Meeting.<br /> <br /> Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, Main D, Wood T, Leslie A, Wing RA, Wilkins TA (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Molec Biol 54:911-929<br /> <br /> Baral, J.B., Yingzhi Lu, J.-F. Zhang, C.-D Feng, and J.McD. Stewart. 2004. High resolution mapping of fertility restorer genes for cytoplasmic male sterility in cotton. Pp. 1057-1060. In: Proc. Beltwide Conf. Conf., National Cotton Council, Memphis, TN. <br /> <br /> Biddle, K. D., G. L. Hodnett, and D. M. Stelly. 2004. Gametophytic inheritance and developmental biology of semigamous apomixis in Gossypium barbadense. Plant & Animal Genomes XII Conference, January 10-14, 2004, San Diego. http://www.intl-pag.org/12/abstracts/P7b_PAG12_884.html <br /> <br /> Blanche, S.B., G.O. Myers and D. Caldwell. 2004. Stability measures in cotton: where do we stand? p. 1064. In: Proc. Beltwide Cotton Conf, San Antonio, TX. 5-9 Jan. 2004. Natl. Cotton Counc. Am., Memphis, TN.<br /> <br /> Bowman, D.T., and O.A. Gutierrez. 2003. Sources of fiber strength in the U.S. Upland cotton crop from 1980-2000. J. Cotton Sci. 7:86-94.<br /> <br /> Bowman, D.T., F.M. Bourland, G.O. Myers, T.P. Wallace and D. Caldwell. 2004. Visual selection for yield in cotton breeding programs. J. Cotton Sci. 8(2):62-68.<br /> <br /> Bowman, D.T., O.L. May, and J.B. Creech. 2003. Genetic uniformity of the U.S. Upland cotton crop since the introduction of transgenic cottons. Crop Sci. 43: 515-518.<br /> <br /> Braden, C. C.W. Smith and P. Thaxton, 2004. Determining gin variability for HVI and AFIS data. In: D. J. Herber and D. A. Richters (eds.) Proc. Beltwide Cotton Conf., Nat'l. Cotton Council of Am., Memphis, TN.<br /> <br /> Burke, T., and J.McD. Stewart. 2004. Development of molecular markers to distinguish cytop[lasm substitution lines of cotton. Pp. 23-28. In: D.M. Oosterhuis (ed.). Summaries of Arkansas Cotton Research 2003. Ark. Agri. Exp. Sta., Research Series 521.<br /> <br /> Chee, P.W., J. Rong, D. Williams-Coplin, S.R. Schulze, and A.H. Paterson. 2004. EST derived PCR-based markers for functional gene homologues in cotton. Genome 47:449-462.<br /> <br /> Feng, C., and J.McD. Stewart. 2004. A cDNA-AFLP profile of cotton genes in response to drought stress. Pp. 176-182. In: D.M. Oosterhuis (ed.). Summaries of Arkansas Cotton Research 2003. Ark. Agri. Exp. Sta., Research Series 521.<br /> <br /> Feng, C.D., J.McD. Stewart, and J.F. Zhang. 2004. STS markers linked to the Rf 1 fertility restorer gene of cotton. Theoretical and Applied Genetics Online First: DOI: 10.1007/s00122-004-1817-3.<br /> <br /> Frelichowski, J.E., Ulloa, M. 2005. Germplasm evaluation of cotton accessions from the U.S. cotton germplasm collection, USDA-ARS (Landraces of Mexico). National Cotton Council Beltwide Cotton Conference. pp. 1020-1024.<br /> <br /> Frelichowski, J.E., Ulloa, M., Tomkins, J.P., Palmer, M., Main, D., Stelly, D., Cantrell, R.G. 2004. New bac-end derived microsatellite markers in cotton (Gossypium hirsutum L.) Acala 'Maxxa'. ASA-CSSA-SSSA Annual Meeting Abstracts.<br /> <br /> Gao, W., Z. J. Chen, J. Z. Yu, D. Raska, R. J. Kohel, J. E. Womack, and D. M. Stelly. 2004. Wide-cross whole-genome radiation hybrid (WWRH) mapping of cotton (Gossypium hirsutum L.). Genetics 167 (3): 1317-1329.<br /> <br /> Haigler, C.H., Zhang, D., Wilkerson, C.G. 2005. Biotechnological improvement of cotton fiber maturity. Physiologia Plantarum 124: 285-294<br /> <br /> Halfmann, R. A., D. M. Stelly, and D. H. Young. 2004. Towards improved cell cycle manipulation and chromosome doubling methods in Gossypium. Proc. Beltwide Cotton Proc. Res. Conf., Jan. 5-9, 2004 San Antonio, Texas. <br /> <br /> Halfmann, R. A., D. M. Stelly, and D. H. Young. 2004. Towards improved cell cycle manipulation and chromosome doubling methods in Gossypium. Plant & Animal Genomes XII Conference, January 10-14, 2004, San Diego. http://www.intl-pag.org/12/abstracts/P04_PAG12_89.html <br /> <br /> <br /> He, L., Du, C., Covaleda, L., Xu, Z., Robinson, A. F., Yu, J. Z., Kohel, R. J., Zhang, H. -B. 2004. Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploidy cotton (Gossypium hirsutum L.) MPMI 17:1234-1241.<br /> <br /> Hendrix BL, Stewart JMcD, Wilkins TA (2005) Gene expression in developing fibers as a model for water-deficit stress in cotton. Plant Phsyiol: In Review<br /> <br /> Hendrix, B.L., and J.McD. Stewart. 2004. Examination of the role of fungal cell wall degrading enzymes in plant fungal resistance. Pp. 173-175. In: D.M. Oosterhuis (ed.). Summaries of Arkansas Cotton Research 2003. Ark. Agri. Exp. Sta., Research Series 521.<br /> <br /> Hutmacher, B., Davis, M.R., Ulloa, M., Wright, S., Munk, D.S., Vargas, R.N., Roberts, B.A., Marsh, B.H., Keeley, M.P., Kim, Y., Percy, R.G. 2005. Fusarium in acala and pima cotton: symptoms and disease development.. National Cotton Council Beltwide Cotton Conference. pp. 245-246.<br /> <br /> Ibrokhim, A, Buriev, Z. T., Rizaeva, S. M., Ernazarova, Z., Abdullaev, A. A., Abdusattor, A., Kohel, R. J., Yu, J. Z., Pepper, A. E., Saha, S. 2004. Evaluation of fiber quality and other agronomic traits of G. hirsutum accessions from Uzbek cotton germplasm. Proc 2nd International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India. October 10-13, 2004. p88<br /> <br /> Kakani, V. G., K.R. Reddy, S. Koti, T.P. Wallace, P.V. Vara Prasad, V.R. Reddy and D. Zhao. 2005. Differences in in vitro pollen germination and pollen tube growth of cotton cultivars in response to high temperatures. Annals of Botany 96(1):59-67.<br /> <br /> Karaca, M., S. Saha, F. Callahan, J.N. Jenkins, J.R. Read, and R.G. Percy. Molecular and cytological characterization of a cytoplasmic-specific mutant in pima cotton (Gossypium barbadense L.). Euphytica 139:187-197. 2004.<br /> <br /> Kohel, R. J., Yu, J. Z. 2004. Permanent recombinant inbred mapping population for cotton genome research. Proc 2nd International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India. October 10-13, 2004. p44<br /> <br /> Kohel, R. J., Cui, P., Hoffman, S. M., Yu, J. Z. 2004. SSR genotyping of 191 recombinant inbred cotton lines that were derived from the TM-1 x 3-79 cross. Proceedings of the International Annual Meetings of ASA-CSSA-SSSA. Seattle, WA. <br /> <br /> Lee, J. J., O. S. Hassan, W. Gao, R. J. Kohel, X-Y. Chen, D. M. Stelly, and Z. J. Chen. 2004. Microarray and AFLP-cDNA display analyses of gene expression in cotton fiberless mutants. Plant & Animal Genomes XII Conference, January 10-14, 2004, San Diego. http://www.intl-pag.org/12/abstracts/W19_PAG12_71.html <br /> <br /> <br /> Lu, Y., J. Zhang, R.G. Percy, and R.G. Cantrell. An intregrated SSR-STS-SRAP-RAPD genetic map using recombinant inbred line population in tetraploid cotton. Proc. Beltwide Cotton Conf. p.1156-1161. 2004<br /> <br /> Mauney, J.R., J. McD. Stewart, and M. Jones. 2004. Onset and progression of the Hollow Seed (Seed Rot) malady of South Carolina . Pp. 1967-1969. In: Proc. Beltwide Cotton conferences, National Cotton Council. Memphis, TN.<br /> <br /> May, O.L., F. M. Bourland, and R. L. Nichols. 2003. Challenges in testing transgenic and nontransgenic cotton cultivars. Crop Sci. 43: 1594-1601.<br /> <br /> May, O.L., P.W. Chee, and H. Sakhanokho. 2004. Registration of GA98033 upland cotton germplasm line. Crop Sci. 44:2278-2279.<br /> <br /> Meek, C.R., D.M. Oosterhuis, and J.McD. Stewart. 2004. Physiological and molecular responses of common cotton cultivars under water-deficient conditions. Pp. 1475-1485. In A. Swanepoel (ed.) Cotton Production for the New Millennium. World Cotton Research Conference-3. Agricultural Research Council, Institute for Industrial Crops, Pretoria, RSA.<br /> <br /> Mei, M., N. H. Syed, W. Gao, P. M. Thaxton, C. W. Smith, D. M. Stelly and Z. J. Chen. 2004. Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280291.<br /> <br /> Myers, G.O., M.W. Akash and B. Jiang. 2004. An intraspecific AFLP map of G. hirsutum. International Cotton Genome Inititative, 2004 Workshop, 10-13 Oct. 2004. Hyderabad, India.<br /> <br /> Owens, B. F and T. P. Wallace. 2004. Comparison of Methods for Estimating Fibers Per Seed. P. 1114. In Proc. Beltwide Cotton Prod. Res. Conf., San Antonio, TX. 5-9 Jan. 2004. Natl. Cotton Counc. Am., Memphis Tn.<br /> <br /> Palmer, M.B., Main, D., Frelichowski, J.E., Tomkins, J.P., Ulloa, M. 2004. High-throughput development of new molecular markers for cotton.. National Cotton Council Beltwide Cotton Conference. p. 1131.<br /> <br /> Park Y-H, Alabady MS, Sickler BA, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shihy OM, Cantrell RG, Ulloa M (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line (RIL) cotton population. Molec Gen Genomics: In Press<br /> <br /> Park, Y.H., Ulloa, M. 2004. PCR-mediated recombination generated from allotetraploid cotton DNA using microsatellite markers.. ASA-CSSA-SSSA Annual Meeting.<br /> <br /> Paterson, A.H., R.K Boman, S.M. Brown, P.W. Chee, J.R. Gannaway, A.R. Gingle, O.L. May, and C.W. Smith. 2004. Reducing the genetic vulnerability of cotton. Crop Sci. 44:1900-1901.<br /> <br /> Percy, R.G. Comparison of bulk F2 performance testing and pedigree selection in thirty Pima cotton populations. J.Cotton Sci. 7:170-178. 2003.<br /> <br /> Percy, R.G., J. Zhang, and R. Cantrell. Characterization of a population of introgressed recombinant inbred lines for agronomic and fiber quality traits. Proc. Beltwide Cotton Conf. p.1055. 2004.<br /> <br /> Percy, R.G., L. May, M. Ulloa, and R. Cantrell. A project to develop broadly adapted, heat tolerant, high fiber quality germplasm. Proc. Beltwide Cotton Conf. p. 1148. 2004.<br /> <br /> Robinson, F. A., A. A. Bell, N. Dinghe and D. Stelly. 2004. Status report on introgression of reniform nematode resistance from Gossypium longicalyx. Proc. Beltwide Cotton Proc. Res. Conf., Jan. 5-9, 2004 San Antonio, Texas. <br /> <br /> Rong J, Pierce GJ, Waghmare VN, Rogers CJ, Desai A, Chee PW, May OL, Gannaway JR, Wendel JF, Wilkins TA, Paterson AH (2005) Genetic mapping and comparative analysis of seven mutants related to seedborne fiber development in cotton. Theor Appl Genet: In Press <br /> <br /> Rong, J., C. Abbey, J.E. Bowers, C.L. Brubaker, C. Chang, P.W. Chee, T.A. Delmonte, X. Ding, J.J. Garza, B.S. Marler, C. Park, G.J. Pierce, K.M. Rainey, V.K. Rastogi, S.R. Schulze, N.L. Trolinder, J.F. Wendel, T.A. Wilkins, D. Williams-Coplin, R.A. Wing, R.J. Wright, X. Zhao, L. Zhu, and A.H. Paterson. 2004. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389-417. <br /> <br /> Saha. S., J. Wu, J.N. Jenkins, J.C. McCarty, Jr., O.A. Gutierrez, D. M. Stelly, R. G. Percy, and D. A. Raska. 2004. Effect of Chromosome Substitutions from Gossypium barbadense L. 3-79 into G. hirsutum L. TM-1 on Agronomic and Fiber Traits. J. Cotton Sci. 8:162169. http://www.cotton.org/journal/2004-08/3/162.cfm<br /> <br /> Sakhanokho, H.F., P. Ozias-Akins, O.L. May, and P.W. Chee. 2004. Induction of somatic embryogenesis and plant regeneration in select Georgia and Pee Dee cotton (Gossypium hirsutum L.) lines. Crop Sci. 44:2199-2205.<br /> <br /> Scheffler, B, Taliercio, E, Scheffler, J, Yu, J. Z. 2004. Molecular markers run on a test panel: a data source for the cotton community. Proc 2nd International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India. October 10-13, 2004. p45<br /> <br /> <br /> <br /> Stelly, D. M., S. Saha, D. A. Raska, J. Wu, J. Jenkins, J. C. McCarty, O. A. Gutierrez, R. G. Percy, B. Gardunia, and N. Dighe. 2004. Chromosome-specific resources for germplasm introgression and genomics in Gossypium. Plant & Animal Genomes XII Conference, January 10-14, 2004, San Diego. http://www.intl-pag.org/12/abstracts/W42_PAG12_187.html <br /> <br /> Stelly, D.M. and S. Saha. 2004. Organizing cotton genomics through physical mapping. Proc. Beltwide Cotton Proc. Res. Conf., Jan. 5-9, 2004 San Antonio, Texas. <br /> <br /> Stelly, D. M., Gao, W., Todd, S., Chen, Z. J., Yu, J. Z. 2004. Wide-cross whole-genome radiation hybrid (WWRH) resources for cotton genomics. Proc 2nd International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India. October 10-13, 2004. p25<br /> <br /> Stelly, David. 2004. Aneuploid mapping in polyploids. Encyclopedia of Plant and Crop Science. Marcell Dekker, Inc.<br /> <br /> Stewart, J.McD. and C.-D. Feng. 2004. Utilization of exotic cotton germplasm resources to increase genetic diversity. Pp. 193-197. In A. Swanepoel (ed.) Cotton Production for the New Millennium. World Cotton Research Conference-3. Agricultural Research Council, Institute for Industrial Crops, Pretoria, RSA.<br /> <br /> Thaxton, P. M. and C. W. Smith. Registration of TAM 98D-102 and TAM 98D-99ne Upland Cotton Germplasm Lines with High Fiber Strength. Crop Sci. accepted.<br /> <br /> Thaxton, P. M. and C. W. Smith. 2004. Plant Variety Protection for Tamcot 22. Technology Licensing Office.<br /> <br /> Thaxton, P. M. and C. W. Smith. 2004. Notice of Release of Tamcot 22 Upland Cotton Cultivar, Texas Agricultural Experiment Station. Approved for release, 2004. <br /> <br /> Thaxton, P. M. and C. W. Smith. 2004. Registration of TAM 96WD-18 Upland Cotton Germplasm Line With Improved Fiber Length and Strength. Crop Sci. accepted.<br /> <br /> Thaxton, P. M. and C. W. Smith. 2004. Registration of TAM 96WD-69s Glabrous Upland Cotton Germplasm Line. Crop Sci. accepted.<br /> <br /> Thaxton, P. M. and C. W. Smith. 2004. Registration of Tamcot 22 High Yielding Upland Cotton Cultivar. Crop Sci. accepted.<br /> <br /> Udall JA, Swanson J, Haller K, Rapp RA, Sparks M, Hatfield J, Yu Y, Wu Y, Llewellyn DJ, Dennis E, Arpat AB, Sickler BA, Wilkins TA, Guo J, Chen X, Taliercio E, Turley R, Dowd C, Mcfadden H, Klueva N, Payton P, Allen R, Zhang D, Haigler C, Wilkerson C, Suo J, Schulze S, Pierce M, Essenberg M, Kim H, Kudrna D, Soderlund C, Wing R, Paterson AH, Wendel JF (2005) A global assembly of ESTs. Genome Res: In Review.<br /> <br /> Ulloa M, Park Y-H, Sicker TA, Wilkins T. 2004. Development and characterization of fiber EST-Derived microsatellite in cotton (Gossypium spp). National Cotton Council Beltwide Cotton Conference. p. 1187-1191.<br /> <br /> Ulloa, M., Hutmacher, R., Davis, M., Percy, R.G., Mcguire, M.R., Marsh, B. 2005. Breeding for fusarium wilt (fov) race 4 resistance in cotton.. National Cotton Council Beltwide Cotton Conference. p. 901.<br /> <br /> Ulloa, M., Park, Y.H., Alabady, M.S., Stewart, J.M., Wilkins, T. 2004. Orgins of allelic diversity and genic regions revealed by microsatellite est markers in cotton.. ASA-CSSA-SSSA Annual Meeting.<br /> <br /> Ulloa, M., Stewart, J., Garcia-C, E.A., Godoy-A, S., Gaytan-M, A., Acosta-N, S. (in press). Cotton genetic resources in the western states of Mexico: in situ conservation status and germplasm collection for ex situ preservation. Genetic Resources and Crop Evolution.<br /> <br /> Ulloa, M., Stewart, J.M., Park, Y.H., Frelichowski, J.E. 2004. Evaluation of germplasm with microsatellites.. International Cotton Genome Initiative Workshop. INDIA.<br /> <br /> Ulloa, M., Stewart, J.M., Park, Y.H., Murillo, P.N., Gaytan, A.M., Acosta, S.N. 2004. Comparison Of Geographical And Genetic Diversity Revealed By Microsatellites For The Arborescent (D Genome) Gossypium Species From Western States Of Mexico.. ASA-CSSA-SSSA Annual Meeting.<br /> <br /> Wallace, T.P., B.F. Owens and G.O. Myers. 2004. Evaluation of Uzbeckistan and California accessions: characterization for GRIN. p.1045. In: Proc. Beltwide Cotton Conf, San Antonio, TX. 5-9 Jan. 2004. Natl. Cotton Counc. Am., Memphis, TN.<br /> <br /> Wallace, T.P., B.W. White and J.E. Hollowell. 2005. Registration of MISCOT 8839 Cotton. Crop Sci. 45:1167-1168.<br /> <br /> West, J., P. M. Thaxton and C.W. Smith, 2004. Screening Race Stocks for Resistance to Rhizoctonia solani In: D. J. Herber and D. A. Richters (eds.) Proc. Beltwide Cotton Conf., Nat'l. Cotton Council of Am., Memphis, TN.<br /> <br /> Wilkins TA, Arpat AB (2004) The cotton fiber transcriptome. Physiol Plantarum 124:295-300<br /> <br /> Wilkins TA, Mishra R, Trolinder NL (2004) Agrobacterium-mediated transformation and regeneration of cotton. J Food Agric Environ 2:179-187<br /> <br /> <br /> <br /> <br /> Xu Z, Yu JZ, Covaleda L, Dong J, Lee M-K, Ding K, Kohel RJ, Zhang H-B 2004. Toward an integrated physical and genetic map of the cultivated cotton genome: physical map contig assembling and anchoring to its subgenomes. Proc 12th International Conference on Plant and Animal Genome Research. January 10-14, 2004. San Diego, CA<br /> <br /> Yu, J and Zhang, T 2004. Towards an international collaboration on cotton structural genomics. (Invitational) Proc Beltwide Cotton Research Conferences. January 5-9, 2004. San Antonio, TX<br /> <br /> Yu, J, Cantrell, R, Kohel, R, Saha, S, Tomkins, J, Pepper, A, Ulloa, M, Scheffler, J, Stelly, D, Main, D, Palmer, M, Jones, D 2004. Establishment of the standardized cotton microsatellite database (CMD) panel. Proc Beltwide Cotton Improvement Conference. January 5-9, 2004. San Antonio, TX<br /> <br /> Yu, J. Z. 2004. A standard panel of Gossypium genotypes established for systematic characterization of cotton microsatellite markers. Plant Breeding News Edition 148, an electronic newsletter of applied plant breeding sponsored Food and Agriculture Organization of the United Nations<br /> <br /> Yu, J. Z., Kohel, R. J., Zhang, H-B., Xu, Z., Dong, J. 2004. Integrated physical mapping of the cotton genome. Proc 2nd International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India. October 10-13, 2004. p24<br /> <br /> Yu, J. Z. 2004. A minimal tiling path for maximal genome coverage: International collaboration on the global BAC sequencing platform. (Invitational) Proc 2nd International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India. October 10-13, 2004. p168 <br /> <br /> Yu, J. Z., Kohel, R. J., Zhang, H-B., Xu, Z., Dong, J., Lee, M., Cui, P., Covaleda, L. 2004. Integrative Physical Mapping of the Cotton Genome and Its Synteny with Arabidopsis. Proc ASA-CSSA-SSSA International Annual Meetings, Seattle, WA, October 31-November 4, 2004 <br /> <br /> Yu, J. Z., R. J. Kohel, H-B. Zhang, D. M. Stelly, Z. Xu, J. Dong, L. Covaleda, M-K. Lee, G. R. Lazo, and P. Gupta. 2004. Toward an integrated physical and genetic map of the cultivated allotetraploid cotton genome. Plant & Animal Genomes XII Conference, January 10-14, 2004, San Diego. http://www.intl-pag.org/12/abstracts/W32_PAG12_147.html <br /> <br /> Zhang and J.McD. Stewart 2004. Identification of molecular markers linked to the fertility restorer genes for CMS-D8 in cotton. Crop Sci. 44:1209-1217.<br /> <br /> Zhang J.-F., and J. McD. Stewart. 2004. Semigamy gene is associated with chlorophyll reduction in cotton. Crop Sci. 44:2054-2062.<br /> <br /> Zhang, J.-F., G. Mara-Koosham, Y.Z. Lu, and J.McD. Stewart. 2004. Comparative molecular analysis of mitochondrial genome in two cytoplasmic male sterile systems of cotton. Pp. 1178-1182. In: Proc. Beltwide Cotton conferences, National Cotton Council. Memphis, TN.<br /> <br /> Zhang, T., Shen, X., Guo, W, Yu, J. Z., Kohel, R. J. 2004. Molecular mapping of QTLs for fiber qualities in Upland cotton using SSR markers. Proc 2nd International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India. October 10-13, 2004. p33<br /> <br /> Zumba, J.X. and G.O. Myers. 2004. Evaluation of Shafter collection cotton (Gossypium spp.) for agronomic and fiber traits. p. 2008. In: Proc. Beltwide Cotton Conf, San Antonio, TX. 5-9 Jan. 2004. Natl. Cotton Counc. Am., Memphis, TN.<br /> <br />

Impact Statements

1. Significant progress was demonstrated in the development of genetic resources for cotton during the reporting period. Recently acquired accessions that have been characterized and interspecifc germplasm introgression lines will provide new sources of variability in efforts to expand the genetic base of cultivated cotton and may contribute to immediate needs in the area of fiber quality and nematode resistance. Efforts directed towards measuring genetic diversity will help aid in the identific

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Accomplishments

OBJECTIVE 1 - To acquire, curate, characterize, and evaluate the species, races, and genetic types of Gossypium (cotton). <br /> <br /> The 196 Uzbekistan accessions were evaluated in the field for root-knot nematode resistance. The gall score average for the resistant check was 1.63 and for the susceptible check was 4.16 which is in line with expectations and previous ratings of these plants in other trials. As expected, a large majority of the Uzbekistan lines (157) were susceptible (gall score >=3) to highly susceptible (gall score = 5). Thirty one lines were moderately resistant (gall score >2 but <3). Eight lines could be classified as resistant with two of these (SA2654 and SA2791) being rated as more resistant than the resistant check (Stoneville LA887). <br /> <br /> Yield and fiber data was collected on 189 accessions from Uzbekistan. Lint yield for the accessions ranged from 129 to 739 lbs/a compared to 750 lbs/a for the check (PSC 355). Lint percent values for accessions ranged from 18.2% to 40.7% compared to 40.1% for the check. Most accessions performed poorly in terms of agronomic traits, however, a few accessions were identified with a competitive yield. Several accessions were used as parental material. Previously collected descriptor data will be submitted to the GRIN database. <br /> <br /> The Cotton Cytogenetics Group (Stelly) is utilizing interspecific germplasm introgression (IGI) to expand the baseline genetic variability in cotton, and making it available to cultivar breeding programs. The Cotton Improvement Laboratory (Smith and Thaxton) strives to utilize such IGI lines as well as other sources to produce germplasm having improved quality, better yield potential, and resistance to biotic stresses such as seed/seedling diseases and abiotic stresses such as temperature and drought. G. barbadense, G. tomentosum and G. mustelinum carry genes that could improve agronomic traits in Upland cotton, even though they themselves perform poorly. In the G. tomentosum, individuals in segregating populations possessed superior fiber quality traits relative to the recurrent upland parent. The G. mustelinum populations also contained improved fiber quality phenotypes in an Upland background. Recent (2004) germplasm lines released because of their fiber quality package exhibited fiber length in the 35 and 36 staple range, fiber bundle strength as high as 36 g/tex, and 4.0 to 4.5 mic.<br /> <br /> Russell Kohel visited Uzbekistan and 800 Uzbek accessions were received for evaluation on an ARS-Uzbek project. These materials are being increased in Mexico, and they will be evaluated in Texas and Mississippi. Seed of 3,687 accessions were distributed from the Cotton Germplasm Collection to 85 domestic users and 44 accessions were distributed to 5 international users. These included governmental and commercial users.<br /> <br /> A. An 11-day survey (funded by USDA) was conducted in Mexico (Nov. 9-20, 2004) for two Gossypium species whose status was unknown. During this survey it was determined that Gossypium trilobum is a threatened species, whereas G. turneri, although it has a restricted distribution, is stable for the moment. New seed collections were made of both species. <br /> <br /> B. Several morphological traits were maintained and further characterized. <br /> Short fruiting branch. Twenty-eight selections of open-pollinated plants with the short fruiting branch phenotype made in 2003 were each planted to 50' progeny rows for evaluation and re-selection. New open-pollinated selections were made of individual plants with consistency of phenotype and good yield potential. This phenotype originated as a transgressive segregate from a A1xD2-1xAD1 trispecies hybrid. <br /> <br /> Glabrous thick leaf. Fifty-five rows (50'/row) were planted from seeds of plants grown the previous year and evaluated for chlorophyll content with a Spad meter. The two or three plants in each row with the highest chlorophyll content were self-pollinated and seed harvested at the end of the season. Phenotypic parameters including leaf thickness, specific chlorophyll content, photosynthesis, etc. will be measured next year. This phenotype originated as a segregate from a A1xD2-1xAD1 trispecies hybrid and was probably donated by the D2-1 species. <br /> <br /> Qualitative Traits in Cotton: Red-calyx, red anther, hairy anther, green fiber, brown fiber. Selected plants with good phenotypic expression of each of the qualitative traits listed were self-pollinated to maintain genetically stabilized homozygous lines. It was determined that the red calyx trait (introgressed from G. herbaceum) was pleiotropic with red petal spot but, as demonstrated previously, the red anther trait (D genome origin) is not associated petal spot. Selections based on yield potential were also made from these genetic lines. The hairy anther trait originated from a cross between G. hirsutum with the pilose trait and G. barbadense. For this trait to be expressed the pilose gene must be present, but all plants with pilose do not express the hairy anther trait. <br /> <br /> C. Species diversity. Three projects are concerned with evaluation of genetic diversity among taxa.<br /> <br /> Genetic diversity of Caribbean cotton. As a result of a survey and collection of wild cotton in Florida, a project was initiated to determine the genetic diversity of the cotton around the Caribbean basin and, if possible, determine the origin of the Florida wild cotton. Seeds of more than 50 accessions of G. hirsutum collected near the coast of numerous island nations around the Caribbean were obtained and these, along with the collections from Florida were germinated and are growing in pots in the greenhouse. DNA for molecular analysis has been extracted from some of these. <br /> <br /> Diversity of the Gossypium species of the G genome. The objective of this project is to determine the diversity of G. australe, G. bickii and G. nelsonii and determine if hybridization between these species occurs in natural populations. In initial results the diversity of G. australe accessions from across Australia was measured with approximately 50 AFLP markers. This limited data set shows that accessions from Western Australia are significantly different from eastern (Queensland) accessions at the molecular level. <br /> <br /> Diversity among arborescent D-genome species. Diversity among the species with in section Erioxylum represented in germplasm collected in 2002, was measured by AFLP. A manuscript reporting the results is in preparation. <br /> <br /> DNA content of the Gossypium genus. Estimates of the nuclear DNA contents of the species in Gossypium are highly variable within a species, or have not been made. This information has significance in relation to molecular maps of the genomes, and in evolutionary understanding of the genus. Work was completed on the project to obtain an accurate estimation of the DNA content of a majority of the known Gossypium species based on flow cytometry. It was also determined that barley, when used as an internal standard, as conventionally recommended, gives an erroneously high estimation of the DNA content of cotton. Three external standards (rice, maize, & barley) were included in each run and a standard curve was constructed to assure accuracy of the results. A manuscript was submitted and accepted for publication. <br /> <br /> Epigenetics of wide hybridization in cotton. Aspects of epigenetic responses in wide-hybrid introgression were examined. Reports for other plant species indicate that when dissimilar genomes are combined via hybridization, genome structure and normal gene expression patterns are disrupted. To investigate these issues in cotton, we assembled a panel of DNA composed of G. davidsonii, G. anomalum, and subsequent hybrids (non-doubled and doubled through F2) between these species. This panel was screened with SSR primers to assess the conservation of repetitive fractions of these genomes. Additionally, nuclear DNA contents for the lineage were measured. Complete genome conservation was observed for 20 SSR primer pairs. For the DNA content, a small reduction in genome size was observed in the G. davidsonii x G. anomalum F1 hybrid but no other epigenetic phenomena were observed through the F2 generation. <br /> <br /> Gossypium barbadense 3-79 chromosome substitution lines (CS-B lines) were evaluated directly and in the form of F2 progeny performance. <br /> <br /> A set of 434 Gossypium hirsutum L. landraces of Mexico from the USDA-ARS Cotton Germplasm Collection was planted at Shafter, CA for phenotypic and genetic characterization of variability. Commonly used phenotypic characters were scored for each accession and tissue was bulked of each accession for DNA extraction. Preliminary results showed that significant variation still exists in the collection from the data collection. Diversity between and within accessions was the highest for accessions collected within the states of Guerrero, Yucatan, Oaxaca, Veracruz and Chiapas. The use of molecular markers is expected to reveal more variation not evident in the physical traits, and will become a valuable tool in the maintenance and utility of the diversity of the germplasm collection.<br /> <br /> Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans race 4 isolate has been identified in California soils. Disease expression of this race has been most severe in Pima cotton fields, but also has the capability to infect many Acala and Upland cotton varieties to a high degree depending upon inoculum levels. In order to assess the U.S. cotton gene pool and study the resistance inheritance of FOV race 4, in 2003 and 2004 more than 150 Pima and Acala/Upland commercial and experimental varieties, and improved germplasm were evaluated in known infested fields and in inoculated greenhouse assays. Preliminary results showed that most commercial Pima varieties grown in California were observed to be more susceptible to FOV race 4 (stand loss, stunting, etc) than any Upland cottons (G. hirsutum). However, tested Acala and non-Acala Upland cotton varieties were still infected by FOV race 4 at levels where plants would be expected to reproduce the fungus and expand inoculum. Highly resistant germplasm to FOV race 4 were identified on Pima for inoculum levels tested (field and greenhouse). Development of highly resistant germplasm and genetic mapping populations are ongoing in order to further study FOV resistance and its heritability.<br /> <br /> OBJECTIVE 2 - To develop, maintain, and distribute molecular genetic, genetic, and cytogenetic tools for the evaluation and enhancement of cotton germplasm. Report submitted by J.M. Stewart <br /> <br /> Alloplasmic lines (AD3, AD4, AD5, A2, C1, D3-d, D8, E1) in the G. barbadense semigamy (Se) nuclear background were maintained. A partial set of molecular markers were developed to distinguish among the various alloplasmic lines based on chloroplast DNA markers. Markers to distinguish among A- type cytoplasms have not been identified. <br /> <br /> D8-R lines that had previously been backcrossed to various elite cotton cultivars to improve their agronomic quality were self-pollinated to increase available seeds for evaluation. Reciprocal crosses were made between four elite cotton cultivars and the original D8 restorer containing the cytoplasm of G. trilobum and Rf2 and between the elite cultivars and B411R with the G. harknessii cytoplasm and RF1. The effect of cytoplasm was determined in replicated field trials at Las Cruces, NM. The D8 cytoplasm caused about a 20% reduction in yield whereas no detectable yield loss was associated with the D2 cytoplasm. <br /> <br /> Additional quantitative trait loci (QTL) were added to the intraspecific AFLP map of Gossypium hirsutum. Loci added were for yield and the within boll yield components: bolls per plant, number of fiber per seed, average weight per fiber, and number of seeds per boll. The number of QTL identified by composite interval mapping were 2, 1, 2, 2, and 0, respectively. An additional 2 markers were identified using interval mapping and 40 using single point analysis [AES-LA]. Using G. tomentosum chromosome substitution lines of G. hirsutum, AFLP linkage groups were able to be assigned to some of the monosomic and monotelodisomic genetic stocks. In the end, 53 AFLP markers were assigned to chromosomes and/or chromosome arms. At least one AFLP marker was assigned to each of 16 different chromosomes and 50 markers were localized to different chromosome arms. Nine of 53 common AFLP markers were found between the aneuploid stocks and the intraspecific cross used to develop the AFLP map. This allowed 8 linkage groups to be assigned to 6 different chromosomes <br /> <br /> In cooperation with Cotton Inc and cotton programs across the Cotton Belt, ARS in College Station, Texas, assembled, maintained, and distributed a standard germplasm panel of 12 diverse cotton genotypes for systematic evaluation of molecular genetic markers. We filled in the requests of the community for the permanent mapping population of 191 TM-1 x 3-79 RI lines. We also delivered 192 pairs of SSR primers that were developed from TM-1 BAC clones. Genetic mapping of SSR markers from this and other sources was conducted in the RI population. In cooperation with Texas A&M University, we assembled 5,000 physical contigs from 100,000 TM-1 BAC fingerprints. <br /> <br /> Interspecific germplasm developed in the Cotton Improvement Laboratory with G. barbadense, G. tomentosum and G. mustelinum are being distributed to the molecular geneticist for evaluation.<br /> <br /> In 2004, an intraspecific Gossypium barbadense RIL population of 144 F6.8 lines (PS-6/89590) was characterized for yield, fiber, and agronomic properties in replicated tests in California, Arizona, and New Mexico. An introgressed G. hirsutum RIL population of 98 lines (NM24016/TM-1) was increased for public seed distribution. <br /> <br /> Molecular marker technology has progressed rapidly in the 1990s with the construction of the first genetic map of cotton published in 1994. Our lab has collaborated with Dr. Andrew Paterson to expand the cotton map to include over 2500 loci. This high-density genetic map, which covers all 26 chromosomes of the tetraploid cotton genome, provides new insights into the structure, function, and evolution of the cotton genome. A majority of the loci was from RFLPs, although a few came from PCR based technology such as SSRs or STS. Data was also presented that shows the feasibility of converting the mapped loci into a Single Nucleotide Polymorphism (SNP) detection system that is better suited for use in marker-assisted breeding.<br /> <br /> To add to knowledge of gene expression during cotton fiber development, a cDNA library (prepared from Gossypium hirsutum cv Delta Pine 90) biased toward genes expressed at 20 DPA compared to 6 DPA was constructed and sequenced in collaboration with Curt Wilkerson, Michigan State University. In this case where plants were growing under fairly cool conditions, 20 DPA represented a very early stage of secondary wall deposition. From 9,121 high quality EST sequences (GenBank Accession numbers CO490611  CO499850; called G.h.fbr-sw ESTs), 3,420 unigenes were assembled within this one library, and the sequences were contributed to a comprehensive assembly of cotton ESTs, (J. Udall and J. Wendel, Iowa State University, and coworkers, http://agcol.arizona.edu/pave/cotton/. in which the library was called GH_SCW). About 15% of the translated G.h.fbr-sw ESTs had no significant match to the Arabidopsis proteome, and 150 had no similarity to proteins in the Non-redundant database. Such genes are indicative of processes that make the cotton fiber distinctive. Based on the comprehensive assembly including primary and secondary wall fiber genes, cotton fiber expresses genes with significant similarity (<E-10) to 7,457 Arabidopsis genes, or >25% of the proteome of this model plant. Of these, 600 were sequenced only from the secondary wall stage of fiber development. The G.h.fbr-sw library was not sequenced to completion, indicating that this is a minimal estimate of the uniqueness of secondary-wall-specific expression in cotton fiber. Therefore, secondary wall deposition in cotton fiber is accomplished through a substantial number of genes that are apparently uniquely expressed at that stage, as well as a large complement of expressed genes that are shared with the primary wall stage. These novel secondary wall sequences add to the growing platform for functional genomics of cotton fiber. The support of the NSF Plant Genome Program and Cotton Incorporated, Cary, NC is gratefully acknowledged.<br /> <br /> A germplasm release was made of 17 chromosome substitution backcross lines, each being quasi-isogenic to TM-1, but substituted for one chromosome or one chromosome arm of the non-photoperiodic G. barbadense line 3-79. Development was advanced for new chromosome substitution series for G. tomentosum and G. mustelinum Various BCnF1 chromosome substitution stocks from these programs and DNAs were distributed. DNAs of G. barbadense chromosome substitution BCnF1 stocks were created and distributed to several genome-mapping labs. Backcross-mediated chromosome substitution with 3-79 into TM-1 was advanced for more recently discovered G. hirsutum hypoaneuploids. Prospectively new G. hirsutum hypoaneuploids continue to be identified and tested. The identification of a new monosomic G. hirsutum was reported, H21. <br /> <br /> An expressed sequence tag (EST) database, developed from a diploid cotton species (Gossypium arboreum L.) (http://cfgc.ucdavis.edu), contains ~14,000 non-redundant sequences from 7-10 dpa (days post anthesis) fiber transcripts and their homologous gene functions, was used to develop microsatellite markers. A total of 1232 EST-derived microsatellite (MUSS and MUCS) primer pairs were designed and tested for PCR amplification. Based on PCR amplification, the transferability of the microsatellite markers was high in that 83% of the primer pairs successfully amplified products from eight Gossypium species, including both diploid (A and D) and tetraploid accessions and cultivars (total 23 entries). High interspecific transferability can be due to the sequence conservation of the gene-coding region of the genome. Polymorphic PCR-amplified DNA fragments among species of cotton were observed for 311 (62.7 %) MUSS and 251 (48.0%) MUCS, while 457 (44.6 %) were monomorphic. Between G. hirsutum L. and G. barbadense L., 202 markers were polymorphic, while the polymorphism within these two tetraploid species was low - 1.4 % and 1.5 %, respectively (Table 1). Locations of 40 microsatellite markers were delimited to 19 cotton chromosomes and/or 17 chromosome arms by hypo-aneuploid deficiency analysis. Polymorphic markers between G. hirsutum and barbadense showed segnificant sequence similarity to genes or putative genes with known function including endo-²-1,4-glucanses, Cytochrome P450-like protein, expansin, RING zinc finger protein, and ABC transporter, which are related to fiber. PIC values ranged from 0.12 to 0.74. Analysis of relationship among 23 accessions generated three major clusters which grouped separately the different species. Besides being of value for genome analysis per se, the origin of these SSR markers from fiber-derived ESTs and their demonstrated portability, suggest that they may also be useful for marker-assisted selection in breeding of fiber quality-related genes. This information will be useful to other geneticist working with cottons and will facilitate future efforts to map the cotton genome. Funding for this project was provided by Cotton Inc. These microsatellite markers are made public through the Cotton Microsatellite Database (CMD), http://www.mainlab.clemson.edu/cmd/projects/muss/index.shtml <br /> <br /> To exploit the cotton sequence in the public domain, simple and complex SSRs derived from fiber ESTs were identified as potential DNA markers for genetic mapping and screening germplasm collections. The SSR candidate list is posted on the labs web page (http://cfgc.ucdavis.edu). Several groups are working from this list, and new fiber loci have been mapped, increasing the number of fiber genes on the molecular map. The discovery of cotton SSRs was recently expanded to screen the new global assembly of cotton ESTs (Udall et al., 2005). Mapping of fiber mutants identified new fiber QTLs and characterized new fiber loci as candidate genes for functional analysis.<br /> <br /> OBJECTIVE 3 - To adapt and develop methodologies to evaluate, modify, and utilize cotton germplasm. <br /> <br /> The CIL (Texas) evaluated the use of early generation testing (EGT) methods to predict advanced strain performance at College Station (CS) and Weslaco (WS), TX based on lint yield, lint percent, micronaire, fiber length, fiber strength, fiber elongation, and fiber uniformity. Associations (P=.05) were present for fiber length and fiber strength. At WS, F2 EGT lint yield data were associated with the number of plants and strains selected through the F6 generation, yet no associations were found for fiber quality characteristics. Lack of consistent r values across generations and locations suggest a large environmental influence on both lint yield and fiber quality parameters.<br /> <br /> Twenty-one F2 populations were developed from diallel crosses involving seven Upland cottons, TM-1, 7235, SG125, Fibermax 832, CAMD-E, MD51, and DPL50. The populations were grown in the ARS field plot in College Station, Texas, for measurements of fiber properties and isolation of genomic DNA from individual F2 plants. We continued to develop molecular descriptors with portable PCR-based DNA markers that will be at foundation of germplasm characterization.<br /> <br /> In 2004, an investigation was initiated to determine the relationship between genetic relatedness (as determined by molecular analyses) and general combining and specific combining ability in U.S. and foreign Gossypium barbadense cultivars. Yield, fiber, and agronomic data were obtained from replicated tests of diallel F1 lines at Maricopa, AZ and Las Cruces, NM. <br /> <br /> The limited number of regenerable cotton varieties has not only exacerbated the narrow genetic base of commercial cotton varieties, but also remains a major obstacle for the routine use of gene transformation for cotton improvement. Our lab has initiated a project to evaluate elite breeding lines developed by the UGA cotton breeding program for somatic embryogenesis. The results showed that somatic embryogenic ability is present in several elite lines. The line with the greatest embryo production, GA98033, was released in 2004 as public germplasm line. GA98033 combines high yield potential, acceptable fiber quality, resistance to fusarium wilt and conducive to plant regeneration through tissue culture somatic embryogenesis. Therefore, in additional to being useful to breeders as a parental source with high yield potential and acceptable fiber quality, GA98033 can potentially be useful to molecular biologists as a recipient of transgenic traits.<br /> <br /> Expression profiling using cotton fiber long oligonucleotide microarrays revealed major and minor developmental switches that control fiber growth and development. Using this developmental framework as the foundation, comparative genomics studies identified genes deemed of pivotal importance to fiber development, and as molecular determinants of fiber traits. A list of candidate genes has been generated for functional analysis and to develop into molecular markers for genetic mapping. Cotton fiber chips are distributed to the cotton community on a cost recovery basis<br /> <br /> Diploid hybrids were made between the A genome (G. arboreum) accessions and D genome species (G. trilobum, G. raimondii and G. aridum). These need to be doubled to convert these to allotetraploids and restore fertility for crossing with cotton. One hybrid (A2 x D8) had doubled sectors after colchicine treatment and a flower was obtained with some fertile pollen. This was crossed as male to AD1 cotton and two plants were obtained. Prior to boll maturity the two F1 plants died with symptoms similar to that shown by lethal gene complementation, but four BC1 embryos were obtained by rescue culture. One of the plants died with symptoms similar to the trispecies hybrid, whereas the other three matured, developed bolls and yielded BC2F1 and BC1F2 seeds. The death of the tri-species hybrids and one of the BC1 plants suggests that a genetic lethal complementation was present. As a part of the project to enhance the secondary germplasm pool we developed a trispecies hybrids with a D3-compatible AD1: (B1 x D3-d x AD1). These hybrids were self-pollinated and also backcrossed to the same AD1 to produce F2 and BC1 seeds. These will be evaluated for trait segregation in 2005. New synthetic hybrids were made from cross-pollinations of G. arboreum with a 2(ADD) genetic stock to make trispecies hybrids with 2(AD) genomic constituencies. One of these was backcrossed to an elite line of upland cotton to begin development of an introgression population. <br /> <br /> OBJECTIVE 4 - Germplasm enhancement for biotic and abiotic stress resistance and agronomic traits. <br /> <br /> Cotton improvement laboratory is an aggressive plant breeding program headquartered at the flagship campus of Texas A&M University centers around improving the genetic variability, yield potential, agronomic performance, and fiber quality of germplasm or cultivars adapted to Texas while enhancing resistance to biotic pests, such as insects, nematodes, and diseases, and abiotic stresses such as drought. The CIL developed and released of four germplasm lines and one new cultivar in 2004. These were TAM 96WD-18, TAM 96WD-69s, TAM 98D-99ne, and TAM 98D-102. TAM 96WD-18 and TAM 98D-102 have excellent fiber packages and competitive agronomic performance, while TAM 96WD-69s is a glabrous genotype expressing a measurable level of fleahopper resistance and TAM 98D-99ne carries the nectariless trait in a good agronomic background for central and south Texas. Tamcot 22 was released as a conventional cultivar.<br /> <br /> The CIL (Smith and Thaxton), collaboratively with Dr. Jim Starr, Plant Pathologist, has developed an interspecific population that is segregating for both root-knot and reniform (a problem in the LRGV) nematode resistance. The donor parent for reniform resistance is a G. barbadense. Additional efforts (Stelly) are underway to introgress the high level of resistance found in G. longicalyx. <br /> <br /> Converted race stocks have been in our basic breeding program with a number of advanced strains and segregating populations developed. Breeding programs (Thaxton, Smith and May) have been evaluating the BC2F2 populations for yield and fiber quality. The race stocks are being screened for resistance to cotton fleahopper (Knutson), silverleaf whitefly (Harris), nematode resistance (Starr).<br /> <br /> A project is underway to simultaneously improve G. hirsutum germplasm for fiber quality and heat tolerance. In 2003, 90 lines selected for heat adaptation and fiber quality at Maricopa, AZ were evaluated in non-replicated tests at Tifton, GA, Maricopa, AZ, and Shafter, CA. In 2004, 16 of these lines - along with check cultivars - were evaluated in replicated tests at the above locations. On the basis of their yield and fiber performance, three of the 16 lines have been selected for public release in 2005. The project continues, incorporating fiber quality traits from Gossypium barbadense introgression sources, as well as from Acala sources. In 2004, selection was made within F3 populations of two way or double crosses, thus incorporating two sources of fiber improvement and two sources of heat adaptation within each segregating population. <br /> <br /> The nectariless trait in cotton has been well documented as a host plant resistance trait through a reduction in tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois). Changes in insect management technology (boll weevil eradication and transgenic Bt cotton) have allowed TPB to become a key pest. Improved methods of managing TPB in cotton are needed to fully exploit the potential benefits of the new insect management environment in cotton production. Over 400 nectariless progeny rows (F3 to F10) where grown in 2003 and the top performing entries selected for evaluation under plant bug infested conditions. A wide range of germplasm was represented in this material including obsolete varieties, breeding lines, and nectariless isolines. A field evaluation of TPB resistance in lines of nectariless cotton was established in 2004 on Delta Branch Experiment Station, Stoneville, Mississippi. Approximately 90 nectariless progeny rows were selected for evaluation in 2004 for yield and fiber quality when grown under plant bug infested and controlled (split-plot design) conditions and compared to a conventional nectaried commercial check variety. TPB infestation and damage data (insect counts, square shed, and bloom injury) and crop production data (square and bloom production, and yield) were evaluated by calculating ratios of data for infested/controlled plots and ranking the ratios from those inferring greatest resistance to those inferring least resistance to TPB. The top performing entries (upper 50 percent) have been selected for repeating the evaluation in 2005. Reduction in fiber quality due to plant bugs was minimal. The nectariless trait, however, appears to have conferred a yield advantage for a number of entries. A second year of testing will help determine if testing under plant bug infested vs. controlled conditions is useful in discriminating among susceptible and more tolerant genotypes. <br /> <br /> Using the African species G. longicalyx as the immunity source, euploid reniform nematode-immune BC3F1, BC4F1, and BC5F1 G. hirsutum backcross segregates were identified. Their tissue was sampled for nuclear genomic DNA preparation, and some were backcrossed and inbred. Preliminary co-segregation analysis was initiated for markers. <br /> <br /> Genome-wide introgression efforts from G. tomentosum, G. mustelinum, G. longicalyx and G. armourianum were advanced 1-2 generations. Generation means analysis field evaluation experiments conducted for G. tomentosum and G. mustelinum introgression products. <br /> <br /> Improved methods in cotton transformation were published, and a pipeline for high-throughput cotton transformation to test gene function, and determine the impact of ectopic expression on fiber traits has been developed.<br /> <br /> OBJECTIVE 5  To refine and develop cotton breeding and variety testing methodologies and techniques. <br /> <br /> The ability of the program GGEbiplot to identify the best environments for selection (discriminating environments) was evaluated. Results corroborated historical anecdotal information on the best environments for selection. <br /> <br /> During 2004, we grew approximately 2000 F3:4 lines (pedigree method) and approximately 200 F3:4 lines from single-seed descent populations. Based on fiber data from individual F3 plants collected the previous year, a selection index was applied to the pedigree lines based on a combination of upper quartile length of fibers (inches, by fiber weight) (UQL), short fiber content (count) (SFC) and lint weight seed-1 (LWS). From each population the best 50 F4 rows from F3 plants with the highest UQL, lowest SFC, and highest LWS were selected. One hundred ninety-five F4 lines derived from the single-seed descent populations were also harvested without selection. This leaves us with a minimum of 300 lines derived by pedigree and 195 lines derived by SSD for future evaluation. We will begin yield-testing of these lines to compare effects of inbreeding method on estimates of genetic variance, heritability, and mean performance for a variety of fiber quality, yield, and yield-related traits.<br /> <br /> Update information on genetic relationships. Pedigree information has not been updated since the 1997 publication. Genetic uniformity has been examined since the introduction of transgenic cultivars and it was found that the level of diversity in the field was not compromised. Fiber strength has increased since 1980 and the sources of fiber strength genes were determined to come from two public breeding programs (<br /> <br /> Quantify advantages and disadvantages of divergent variety development strategies. SSD v. Pedigree . David Weaver ( Auburn) has completed growing F3-derived F4 populations ( 6 different ones) this past summer. F5 progeny rows will be grown next summer and selected rows will be yield tested the following summer.<br /> <br /> Using 20 populations compare unselected bulk populations for ability to select superior pure lines. This is not being conducted at this time.<br /> <br /> Determine relationship of lint yield, lint percentage, and fiber quality in single plants in succeeding generations. No reports on this.<br /> <br /> Develop guidelines for efficient and discriminating genotype evaluation.<br /> Visual selection versus yield measurement. This work was performed by David Caldwell, Gerald Myers, Ted Wallace, Fred Bourland, and Daryl Bowman. There is a positive correlation between visual ratings and seed cotton yield suggesting a viable option for breeders.<br /> <br /> Compare spatial designs for efficiency; compare lattice designs with randomized, complete block designs. Work has been done by Wayne Smith and others and needs to be compiled.<br /> <br /> Evaluate the need to incorporate systems testing in variety trials for transgenic technologies. Interactions by varieties with technologies were not detected indicating that the relative ranking of cultivars within system (transgenic) should remain the same. However, the systems may need to be tested with cultivars to reveal true yield potential for the growers. <br /> <br /> Investigate the consequences of forward crossing of transgenic parents. This may best be evaluated over the long term by the private sector.<br /> <br /> OBJECTIVE 6 - To develop cotton bioinformatic systems. <br /> <br /> PEG-induced gene expression in cotton roots (Hendrix) The objective of this study was to develop a gene expression model of drought tolerance in cotton based on responses of the drought tolerant cultivar Siokra L23 to osmotic shock induced by polyethylene glycol (PEG). A PEG-induced phenotype was described for the plants based on time-course measurements of photosynthesis and leaf temperature. A gene expression profile was then developed from root RNA extractions taken at 0, 1, 4, 24, and 96 h after stress initiation utilizing cDNA-AFLP and cotton-fiber-based microarray chips. Siokra L23 progressed through two phases of PEG-induced stress that we designated response (0 to 48 h) and recovery (48 to 96 h). Forty-eight and 363 PEG-responsive genes were identified in the cDNA-AFLP and microarray analysis, respectively. Global gene expression profiles revealed an adaptation to the stress after 96 h. Functional categories played distinct roles in the response and recovery phases. The expression profiles of aquaporins suggested that osmotic adjustment occurred between 4 and 24 h. Sucrose synthase and several genes in the glycolytic pathway supported the hypothesis that sucrose was a solute involved in this osmotic adjustment. The expression patterns observed in this study provide insight into the mechanisms by which Siokra L23 responds to osmotic shock.<br /> <br /> ARS in College Station, Texas, re-organized CottonDB data classes and updated them with new information including cotton germplasm, variety trial, SSR clones and primers, BAC clones and fingerprints, and DNA sequences. Some bioinformatic tools were incorporated into CottonDB for sequence blast and integration of genome maps. <br /> <br /> The Cotton Functional Database has been expanded and improved to be more user friendly, allowing access and manipulation of expression-related data that is now linked to clones, constructs, ESTs, genes, and SSRs. These databases will be linked to the genetic map via the Cotton Portal. Expression data in the public domain can be downloaded into a MIAMI-compliant database for view by the community.<br />

Publications

Frelichowski, J.E., Ulloa, M. 2005. Germplasm evaluation of cotton accessions from the U.S. cotton germplasm collection, USDA-ARS (Landraces of Mexico). National Cotton Council Beltwide Cotton Conference. pp. 1020-1024.<br /> <br /> Haigler, C.H., Zhang, D., Wilkerson, C.G. 2005. Biotechnological improvement of cotton fiber maturity. Physiologia Plantarum 124: 285-294<br /> <br /> Hendrix BL, Stewart JMcD, Wilkins TA (2005) Gene expression in developing fibers as a model for water-deficit stress in cotton. Plant Phsyiol: In Review<br /> <br /> Hutmacher, B., Davis, M.R., Ulloa, M., Wright, S., Munk, D.S., Vargas, R.N., Roberts, B.A., Marsh, B.H., Keeley, M.P., Kim, Y., Percy, R.G. 2005. Fusarium in acala and pima cotton: symptoms and disease development.. National Cotton Council Beltwide Cotton Conference. pp. 245-246.<br /> <br /> Kakani, V. G., K.R. Reddy, S. Koti, T.P. Wallace, P.V. Vara Prasad, V.R. Reddy and D. Zhao. 2005. Differences in in vitro pollen germination and pollen tube growth of cotton cultivars in response to high temperatures. Annals of Botany 96(1):59-67.<br /> <br /> Park Y-H, Alabady MS, Sickler BA, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shihy OM, Cantrell RG, Ulloa M (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line (RIL) cotton population. Molec Gen Genomics: In Press<br /> <br /> Rong J, Pierce GJ, Waghmare VN, Rogers CJ, Desai A, Chee PW, May OL, Gannaway JR, Wendel JF, Wilkins TA, Paterson AH (2005) Genetic mapping and comparative analysis of seven mutants related to seedborne fiber development in cotton. Theor Appl Genet: In Press <br /> <br /> Udall JA, Swanson J, Haller K, Rapp RA, Sparks M, Hatfield J, Yu Y, Wu Y, Llewellyn DJ, Dennis E, Arpat AB, Sickler BA, Wilkins TA, Guo J, Chen X, Taliercio E, Turley R, Dowd C, Mcfadden H, Klueva N, Payton P, Allen R, Zhang D, Haigler C, Wilkerson C, Suo J, Schulze S, Pierce M, Essenberg M, Kim H, Kudrna D, Soderlund C, Wing R, Paterson AH, Wendel JF (2005) A global assembly of ESTs. Genome Res: In Review.<br /> <br /> Ulloa, M., Hutmacher, R., Davis, M., Percy, R.G., Mcguire, M.R., Marsh, B. 2005. Breeding for fusarium wilt (fov) race 4 resistance in cotton.. National Cotton Council Beltwide Cotton Conference. p. 901.<br /> <br /> Wallace, T.P., B.W. White and J.E. Hollowell. 2005. Registration of MISCOT 8839 Cotton. Crop Sci. 45:1167-1168.<br /> <br />

Impact Statements

1. Significant progress was demonstrated in the development of genetic resources for cotton during the reporting period. Recently acquired accessions that have been characterized and interspecifc germplasm introgression lines will provide new sources of variability in efforts to expand the genetic base of cultivated cotton and may contribute to immediate needs in the area of fiber quality and nematode resistance. Efforts directed towards measuring genetic diversity will help aid in the identific

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