Duration: 11/01/2007 to 09/30/2013

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Sustained, profitable cotton production (Gossypium hirsutum L. and G. barbadense L.) in the U.S. is under increasing pressure from a number of sources. Foremost among these is the competition that natural fibers are facing from synthetic fibers for the manufacture of yarns and textiles. Nearly as significant is a fundamental shift that has taken place in the market for cotton lint, viz. a viz. from a primarily domestically consumed product to one in which nearly two-thirds of U.S. production must compete successfully on the world market with cotton lint produced by overseas countries. To remain competitive with synthetic fibers and with other cotton producing countries, further improvements in the genetic potential for yield and fiber quality are needed.

Failure to address the needs of our producers and their customers will lead to a marginalization of cotton production in the U.S. and the loss of one of our most important agricultural exports. This loss would be exacerbated since the infrastructure of the cotton industry cannot be reapportioned like the grain industry. Cotton is the leading textile fiber and second most important oilseed in the world. Ranked second in world cotton production, the U. S. grows about 14 million acres of cotton per year, with acreage in all southern states, from Virginia to California and from Kansas and Missouri to the lower Rio Grande Valley of Texas. The U.S. cotton industry is a $25 billion/yr industry and generates over 400,000 domestic jobs that are critically needed in farm-based communities. Clearly, the cotton crop is a significant contributor to the U.S. economy, but especially to that of rural America.

Analyses of historical cotton yield data indicate that genetic gain or progress in increasing yield has declined over the past several years (Meredith 2006). There is not a consensus as to the underlying cause of this decline in genetic gain potential. Previous responses to this reduction in progress included the 5 to 10 yr delay often seen as a common feature in conventional plant breeding efforts and the decline in publicly funded research for the development of improved cotton germplasm and cultivars. Such research in the past has had a significant, positive effect on cotton improvement in both the public and private sectors. Germplasm development efforts are often long-term and have little profit potential and thus not attractive to the private sector. Policy, funding, and regulatory changes over the last decade have also had an impact on the development of improved cotton cultivars/germplasm. Many of the efforts devoted by public institutions such as State Agricultural Experiment Stations and the USDA-ARS to develop cotton cultivars have been suspended and emphasis placed on germplasm improvement and characterization, redirected to other research initiatives, or the positions have been eliminated as the result of budgetary constraints. While germplasm development within the public sector will have future positive impacts on cotton cultivar development, it continues to limit the availability of elite improved genetic material for direct use in the short term. Regulatory changes and legal protection of intellectual property continue to restrict the free exchange of germplasm necessary for swift future improvement.

A third suggestion is that the focus of the cottonseed industry on the addition of highly beneficial transgenic traits, such as Bt and herbicide-resistance, have come at a cost in research time and effort on the overall improvement of yield and fiber quality of new cotton cultivars. Also, the increased reliance of the seed market on private breeding activities and the merging of those firms with other agricultural support companies may leave the cotton industry vulnerable to the financial stability of a small number of commercial breeding programs.

Whatever the underlying causes, genetic improvement is the best choice for increasing yield and improving fiber quality, and thus enhancing profitability for producers, manufacturers, marketers, etc. The challenges that face the cotton industry transcend state boundaries and can be most economically and efficiently addressed by linking the public research institutions (federal and state) with their multidisciplinary skills, and in partnership with private cotton researchers through a multi-state research project.

Continued genetic gain in all economic aspects of cotton production will require the utilization of both applied and molecular genetic approaches focused on identification of genes responsible for traits of interest, characterization of and use of exotic germplasm to expand the genetic base from which genetic gain is possible, and the incorporation of genes coding for traits of interest into phenotypic constructs where desirable epistatic interactions are maximized. These approaches follow current, progressive research techniques that are being used in cotton and other species.

Related, Current and Previous Work

The preceding MultiState Project (S-304) made progress on all of its objectives but additional work remains. Previous projects, S-258, S-77, and initially S-1 as well as S-304, have impacted every area of the genetic improvement of cotton. The Terminal Report for the S-304 MultiState Project can be found in Appendix A. No other cotton multistate project concerning the genetic improvement of cotton is currently found in the National Information Management and Support System (NIMSS) that is maintained by the University of Maryland.

A basic measure of success is the elite germplasm that was shared and exploited as part of the S-304 project. Contributions were made by and to both public and private cotton breeding programs. The new released elite germplasm lines and varieties include; from the USDA-ARS, Florence, SC: PD 94045 (Upland cotton germplasm lines); from the University of Georgia: GA96-211, GA98028, GA 98033, and GA98066 (Upland cotton germplasm lines) with GA 161 (an Upland cultivar); from the USDA-ARS in cooperation with the University of Arizona: 93252, 93260, 94217, 94218, and 94220 (G. barbadense germplasm lines); from Texas A&M University: TAM 94L-25, TAM 94J-3, TAM 94WE-37s, TAM 96WD-69s, TAM 98D-99ne, TAM 96WD-18, and TAM 98D-102 (Upland cotton germplasm lines) with Tamcot 22 (an Upland cultivar); from Texas Agricultural Experiment Station-MAR: CD3HG2CABS-1-91, CD3HGCBU8S-1-91, LBCBHGDPIS1-91, CUBQHGRPIS-1-92, PD23CD3HGS-1-93, CBD3HGDPIH-1-91, LBCHUD3HGH-1-91, CD3HGCULBH-1-91, CDRCIQCUBH-2-92, CDARCILBCH-1-92, and CUBQHGRPIH-1-92 (Upland cotton germplasm lines); from the University of Arkansas: Arkot 8712 (Upland cotton germplasm line); and from Mississippi State University: MISCOT 8806 and MISCOT 8839 (Upland cultivars). Additional germplasm lines and cultivars will be released in the near future that are directly related to S-304 activities. Publicly developed germplasm lines such as these are necessary more today than ever given the legal entanglements generated by private industry (and public Agricultural Experiment Stations in some cases) in efforts to gain intellectual property rights and thus reduce the free movement of germplasm among cultivar developers.
Acquisitions of valuable and unique new cotton germplasm from plant explorations have been conducted in more than 20 nations. These and significant contributions from exchanges with Brazil, the Peoples Republic of China, India, and Zimbabwe as well as Russia and Uzbekistan have been made to the USDA Plant Germplasm Collection. These germplasms are available for exploitation by the cotton research community world wide without restrictions. Conservation of our genetic resources is an important aspect of previous Multistate Projects and must be continued to insure that valuable genes are not lost from the species.

Distribution of acquired accessions impacts germplasm and varietal improvement in all areas of cotton production worldwide. In total, 16,773 accessions were distributed to cotton researchers in the U. S. and other nations between 2001 and 2004 in response to 405 seed requests. Approximately 6,000 accessions maintained in the U.S. Cotton Germplasm Working Collection were increased by seed propagation, both to assure their preservation and to make sufficient quantities of seed available to others. More than 1,100 of the increased accessions were recent acquisitions from Uzbekistan and Russia. More than 1,000 G. hirsutum and G. barbadense accessions were utilized by participants in S-304 in identification of GRIN descriptors, yield potential, and insect, nematode, and disease resistance. Given that most of the cotton germplasm accessions have not been adequately evaluated, such activities within the extant accessions are a priority in this project.

Diversity is necessary as the foundation of genetic improvement. Geomorphological data with genetic fingerprinting is needed to understand the relationships between cotton lines and the population structure of the Gossypium species. The cotton around the Caribbean basin was evaluated for its genetic diversity and to determine the origin of the Florida wild cotton. The genetic diversity of the Gossypium species of the G genome, indicate that accessions from Western Australia are significantly different from eastern (Queensland) accessions. Genetic characterization of almost 300 different American and Russian cotton types reveal the genetic similarities and differences between these cottons of widely differing origin. Genetic diversity among almost 500 landraces was assessed to find that SSR marker data was more helpful than the morphological data in characterizing the diversity of the landraces according to their origin of collection. Diversity of these Mexican landraces was highest for accessions collected within the states of Guerrero, Yucatan, Oaxaca, Veracruz and Chiapas. Genetic diversity of 346 obsolete and current germplasm lines were clustered into three main groups which were typified by the Texas A&M University MAR program, the USDA-ARS Pee Dee program, and the Acala type. Information from diversity research will be useful to breeders as they identify parents for use in crosses to maximize genetic diversity in their crossing programs which will remain as the foundation of this collaboration of information.

Genetic maps of the cotton genome have been developed that provide a solid basis for future cotton improvement efforts. The molecular marker linkage maps that have been assembled for G. hirsutum and G. barbadense are not fully saturated even though there are some that have attained 26 linkage groups (Rong et al. 2004). These maps need to be more completely saturated and additional, new maps are needed to extend the utility of linkage maps since each segregating population is novel.

During the period of the past project, cooperators have constructed components of an integrated genetic and physical map of the cotton genome. Cytogenetic tools provided a set of 17 chromosome substitution backcross lines (BCnF1) that are genetically identical except that each differs by the replacement of a specific homologous pair of chromosomes from Pima 3-79 (G. barbadense) into Upland cotton (G. hirsutum). The interspecific backcrossed chromosome substitution lines provide unique opportunities to detect the effect of the group of genes that a specific chromosome carries and thus aid cotton genome mapping programs. It is also a novel resource to plant 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. The set (26) needs to be completed to help finish the integration of the physical and molecular maps. Development of new chromosome substitution series for G. tomentosum and G. mustelinum will also be of great value.

More markers are needed in a system that provide polymorphisms within the populations to be studied, that are inexpensive, and have high throughput; all are necessary for effective breeding. A standardized 12-cotton DNA genotype panel, foundation for systematic screening of cotton DNA markers, was developed to assist in the development and mapping of additional cotton SSR markers (Blenda et al., 2006) including those recently derived from TM-1 BAC libraries. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage.

Even though over 1,000 SSR cotton primers have been developed from positive BAC clones and another 1,000 SSR cotton primers are being designed from small-insert genomic clones, more are needed. Also, the feasibility of using the Single Nucleotide Polymorphism (SNP) detection system (Koebner and Summers 2003) has been shown in other allopolyploids and is better suited for use in intraspecific marker-assisted breeding. Preliminary work has been completed in cotton and further work will be given a higher priority. Another method to develop markers uses techniques to screen differentially expressed genes. This has detected significant variation within the functional genes in cotton fiber quality which in turn will provide functional polymorphisms so we can select for the actual genes of these important characters.

Intraspecific and interspecific QTL mapping (Guo et al. 2003, Zhang et al. 2003, Mei et al. 2004, Chee et al. 2005a, Chee et al. 2005b, Draye et al. 2005) using the available markers for traits such as fiber quality have given a starting point for Marker Assisted Selection (MAS). These and new mapping populations are required to bring us realistically to the attractive benefits that MAS brings in stacking multiple genes needed to enhance the value of the new cultivars. Some of these interspecific populations from G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii are also useful to develop near-isogenic introgression lines that can be used to extract useful traits. Many synthetic tetraploids, from hybrids made between the A genome (G. arboreum) accessions and D genome species (G. trilobum, G. raimondii and G. aridum) as well as crosses of G. herbaceum x G. aridum, G. davidsonii x G. anomalum and G. hirsutum x G. laxum, have been developed that are also available to obtain novel traits. A new synthetic hybrid, made from cross-pollinations of G. arboreum with a 2(ADD) genetic stock to make trispecies hybrids with 2(AD) genomic constituencies, was backcrossed to an elite line of upland cotton to begin development of an introgression population.

Efforts to better utilize the available germplasm led to the conversion of race stocks of G. hirsutum to eliminate photoperiodism by a conversion program using backcrossing. This program needs to continue in order to make all of the photosensitive G. hirsutum Race Stocks photoinsensitive and thus more easily available to plant breeders world wide. Other segregating populations are being developed as a basic component of breeding as well as investigating academic questions within the breeding effort such as general- and specific-combining ability, and the relationship between genetic relatedness (as determined by molecular analyses) and yield, fiber, and agronomic data.

Even more distant introgression from the quarternary gene pool such as Bt cotton must be supported. A first step is to work toward developing a genotype-independent transformation technology to modify cotton cultivars. Not being able to transform any desired genotype is a bottleneck in providing elite trangenic cultivars to the growers and must be overcome. One of several approaches included an effort to increase the number of genotypes that can be genetically modified by increasing the alleles for regeneration potential in the cotton gene pool. Concurrently, elite breeding lines developed by the UGA cotton breeding program were found to have enhanced somatic embryogenesis, the basis of successful transformation (Sakhanokho et al. 2004). Additional improvements to callus induction medium increased the range of genotypes that can be transformed and regenerated as well as technical refinements that reduce the time needed to regenerate transformed plants to 6-8 months (Wilkins et al. 2004).

Genotypes with drought and heat resistance and resistance to pests must be identified and incorporated into lines with high yield and fiber quality potential. This must be accomplished to reduce risks and production costs in order to increase grower profit. We also have to react when new disease races emerge to find and introduce new resistance genes. Such is happening now as we look for highly resistant germplasm to FOV race 4 and develop genetic mapping populations to further study FOV resistance for this race and its heritability. It is also possible that new technologies and methodologies may unbalance the crop production scheme that is presently in place. With the success of Bt cotton, plant bug infestations is an example of an achievement creating new challenges. Obsolete cultivars, breeding lines, and nectariless isolines (F3 to F10) were grown under plant bug infested conditions. Even though the reduction in fiber quality due to plant bugs was minimal, the nectariless trait appeared to have conferred a yield advantage for a number of entries.

Nematode resistance is highly coveted because these pests are hidden underground and not directly visible. Researchers in Georgia, Mississippi, and Texas are looking for tightly linked markers to the resistance genes. Screening for nematode resistance is difficult and tedious so searching for molecular markers linked to resistance is a high priority. In Mississippi, several sequences homologous to fungal wilt resistance genes have also been cloned and are being further characterized since RKN resistant isolines are also known to show resistance to fungal wilt. Converted race stocks from within G. hirsutum are being used successfully to develop advanced strains and segregating populations with resistance to nematodes as well as screening for resistance to seed-seedling disease, cotton fleahopper, and silverleaf whitefly. Resistance sources for a second serious nematode pest, reniform nematodes, are coming from complex interspecific hybridization efforts using G. tomentosum, G. mustelinum, G. longicalyx and G. armourianum. Integrating resistance for both of these nematodes, plants from a cross of M315 (root-knot resistant) and TX 110 (putatively reniform resistant) have been screened and resistant candidates identified for resistance to both nematodes.

While looking for desired traits such as increased yield, improved fiber quality, and enhanced resistance to abiotic and biotic stresses, improving breeding efficiency and effectiveness continues to be important. Evaluating the visual rating of yield showed a positive correlation between visual ratings and seed cotton yield (Bowman et al. 2004). Since some high-yielding genotypes are occasionally not visually chosen even though high-yielding genotypes are identified, placement of checks and use of the grid system should reduce the chances of eliminating these better lines. In cotton breeding, recent efforts to improve yield have focused increasingly on breeding for the improvement of specific yield components; notable among these is the number of fiber/seed and weight of fiber per seed. Further research on yield and fiber quality components will bring great advancement in selecting for increased yield and improved fiber quality. Characterization of traits that are not primary to yield and fiber quality such as the variability for bract trichomes will continue to be valuable to assess cultivars for improved performance in ginning. Methods to manipulate populations have been compared such as investigating the genetic gain from using the pedigree vs. the Single Seed Descent (SSD) plant breeding approach.

Numerous, essential yield tests to elucidate the cultivars of choice throughout the cotton belts are always taking place. Nothing can take the place of these tests; however it may be that the efficiency in selecting the best genetic material could be improved. A comparison of experimental design efficiency between Lattice and Randomized Complete Block is being analyzed. Nearest Neighbor Analysis (NNA), ANOVA, and TREND analyses were compared across five states on various trials, but each gave different results with no one design best overall. More work is required to determine the effectiveness of our statistical analyses. Improvement may also be accomplished by the use of early generation testing (EGT) methods. However, tests to predict advanced strain performance based on EGT of lint yield, lint percent, and fiber quality (micronaire, fiber length, fiber strength, fiber elongation, and fiber uniformity) lack consistent r values across generations and locations which suggest that a large environmental influence on both lint yield and fiber quality parameters exists (Jones and Smith 2006). Further refinements may be valuable.

Proper parental selection, a key step in breeding, is critical to continued progress for increased yield, enhanced fiber quality, and profitability in our new cultivars. Pedigree information has been updated and includes 283 new upland and 10 new Pima cultivars. Using this new information, genetic uniformity measured as Coefficient of Parentage (COP) has not increased since the introduction of transgenic varieties (Bowman et al. 2003). However, COP is not highly correlated to genetic uniformity based on molecular markers (Van Becelaere et al. 2005).

Practical interaction in cotton breeding between transgenic and conventional cotton leaves a lot of questions in keeping the two genetics separate. One third of the publicly developed strains in the 2002 Regional Breeders Testing Network were found to be an admixture with the RR transgene. Frequency of transgenes ranged from 0.230% to 1.892%. As this was only one of several possible transgenes (BG, BXN, LL), observed frequencies are conservative as an estimate for overall admixture. The USA and European Union have proposed a 1% tolerance level for transgene mixture. Suggestions have been provided for screening publicly developed germplasm prior to release or exchange to limit the improper distribution of patented genes. Since cross-pollination earlier in breeding would be more problematic, transgene screening utilizing test strips in an early generation, followed by screening prior to the first sizable seed increase is suggested. Transgene screening in combination with extra precautions against mechanical mixing and outcrossing should greatly reduce the presence of transgenes in publicly developed germplasm. Monitoring this problem must be maintained.

Another difficulty in working with cultivars that have transgenic technologies is the suggestion to separately test the cultivars of each transgenic system. Interaction of the cultivars with the transgenic systems was not detected indicating that the relative ranking of cultivars within systems should remain the same and may simplify field testing. However regarding main effects, cultivars need to be tested with the systems to reveal true yield potential for the growers.

Theoretical aspects of forward crossing were examined with such factors as relevance of transgenes, speed of market demand, capability of removing transgenes, genetic background, access to transgenes, and many other factors justifying whether one should forward cross. Backcrossing transgenes does have its advantages.

With all the breadth of data that this and the previous project develop, bioinformatic systems must be improved and maintained to drive our progress. A number of web-accessed databases have been developed to provide access to the data that has been gathered. This is a noteworthy aspect of the collaboration within the previous multi-state project. All of these sites have proven value and should be expanded and improved to be more user friendly.

Significant contributions to the CottonDB, http://www.cottondb.org, have been accomplished through addition of new information and reorganization. Data will contribute to the identification and exploitation of genetic variability at the molecular level for greatly improved efficacy in cotton germplasm improvement. Data from the Cotton Germplasm Collection is included in the GRIN database as well as in the CottonDB. The data classes were reorganized and updated with new information including cotton germplasm, cultivar trial, SSR clones and primers, BAC clones and fingerprints, and DNA sequences. Bioinformatic tools were incorporated into CottonDB for sequence blast and integration of genome maps. The USDA-ARS, College Station, TX also hosts the website of the International Cotton Genome Initiative, http://icgi.tamu.edu.

In collaboration with Cotton Incorporated, the standardized 12-cotton DNA genotype panel was established as the foundation of the Cotton Microsatellite Database (CMD), http://www.mainlab.clemson.edu/cmd/, for a systematic screening of cotton DNA markers developed by participants from the cotton community. At present it contains sequence, primer, mapping and homology data for nine cotton microsatellite projects (BNL, CIR, CM, JESPR, MGHES MUSB, MUSS/MUCS, NAU, and TMB). This provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp. The Cotton Functional Database, http://cfg.ucdavis.edu/microarrary.asp, at UC-Davis, Davis, CA allows access and manipulation of expression-related data that are now linked to clones, constructs, ESTs, genes, and SSRs. The Regional Breeders Testing Network (RBTN) provides a means for testing advanced breeding lines over a wide range of environments and also serves as vehicle for germplasm exchange among participants. The RBTN (http://cottonrbtn.com) has posted on its website the analyses for 2002, 2003, and 2004 with plans underway to include yield stability. The RBTN presently includes test sites in NC, GA, AL, MS, AR, LA, and TX. Other Cotton bioinformatics advances over the duration of the project include the development of The Cotton Portal, http://gossypium.info (which consist of various websites that provide query and display capabilities for performance trials, genetic maps, and comparative maps) and the Cotton Fiber Genomics Project, http://cottongenomics.tamu.edu).

FUTURE RESEARCH NEEDS

The results from S-304 established a solid basis for further research on the utilization of genetic resources to improve cotton. Current and additional germplasm accessions need to be evaluated and characterized for potential usefulness. Although considerable progress was made during the past five years, additional research is needed to develop new molecular tools to understand and manipulate our cotton germplasm. As additional sequencing of the cotton genome is completed and the sequencing data made available, research is needed to mine the data for useful genes. Enhancement of germplasm and cultivars through introgression and recombination for input and output traits must continue so that our industry remains competitive and profitable. This regional project needs to continue to provide both germplasm and methodology that will allow cotton breeders to address the needs for producers, industry, and the consumer by ensuring that this knowledge is available and disseminated on the internet web sites.

Objectives

1. Acquisition, curation, characterization, and evaluation of cotton germplasm for the improvement of cotton
   
2. Understanding and manipulating the cotton genomes through traditional, cytogenetic, and molecular approaches.
   
3. Enhancing the profitability of cotton through germplasm enhancement, cultivar development, pest and disease resistance, and improved output traits.
   
4. Improvement of cotton bioinformatic systems and tools
   

Methods

Objective 1: Acquisition, curation, characterization, and evaluation of cotton germplasm for the improvement of cotton (GA -Chee, TX - Hague, TX - Smith, TX-Starr, AL - Weaver, etc., and with cooperation from USDA-ARS: Kohel, Percy, John Yu) Curating Gossypium accessions involves the coordinated efforts of researchers with a diverse set of skills. Acquisition may occur through plant exploration, the negotiated exchange of germplasm between international institutions, or the careful development of novel genetic combinations. Public and private sectors will acquire and contribute significant genetic material to the U.S. National Cotton Germplasm Collection which is comprised of the germplasm collected as seed during various expeditions, along with materials obtained as donations and exchanges with other germplasm banks around the world. The Collection, located in the USDA-ARS facility at College Station, TX, is a part of the National Plant Germplasm System (NPGS), and personnel in this ARS unit under the directive of Dr. Kohel (and after November 1, Dr. Richard Percy) are responsible for the acquisition, maintenance (including multiplication and preservation), and distribution of those germplasm resources. Data on the materials maintained is accessible through the Germplasm Resources Information Network (GRIN) [http://www.ars-grin.gov/npgs] and CottonDB [http://www.cottondb.org]. Multiple accessions of most of the 49 recognized Gossypium species are maintained as seed. The collection will be expanded and maintained as five subcollections representing different categories of germplasm by collaborative efforts of researchers across the cotton belt. Duplicate seed lots will be stored in the working collection at the Crop Germplasm Research Unit, College Station, TX, and in the base collection at the National Seed Storage Laboratory, Ft. Collins, CO. The collection consists of five subcategories: 1.OBSOLETE CULTIVARS (VARIETIES): Released cultivars, with rare exceptions, of G. hirsutum that are no longer commercially popular as well as recent releases that are not protected under PVP. Entries in this collection carry an "SA" number designation. 2.LANDRACE COLLECTION: Wild, feral, and "dooryard" (few or single plants, usually grown for home use) seed of G. hirsutum. Of these, 25% have been classified according to geographic-morphological races; palmeri, richmondi, punctatum, latifolium, marie-galante, morilli, and yucatanense. These are identified with a "TX-" designation. 3.G. barbadense COLLECTION: All germplasm is maintained with a "GB-" designation and includes cultivars (old and recent), dooryard, and wild accessions. 4.ASIATIC COLLECTION: Cultivated and wild A-genome cotton G. herbaceum and G. arboreum in this collection carry an "A1-" and "A2-"designation, respectively. 5.WILD SPECIES COLLECTION: currently, multiple accessions of three wild tetraploid species and 38 wild diploid species. We will continue the exchange of collections with other domestic and international germplasm collections. The new and present cotton germplasm will be characterized and evaluated by public and private sectors and then documented as part of the bioinformatic systems that are also in development and part of this proposal. Given that a small percentage of cotton germplasm types have been adequately explored, evaluation of the extant germplasm is a priority. More accessions must be characterized and evaluated for information ranging from GRIN descriptors and yield, to disease and pest resistance, to tolerance of abiotic and biotic stresses. With nearly 10,000 accessions currently in the US cotton collection, the agronomic, physiological, pest, fiber, and molecular attributes of them cannot be determined by any one research program. Multi-state cooperation is needed to provide accurate, precise characterization and to coordinate activities on evaluation of a significant number of unique accessions with potentially useful genes. This project, through its annual meetings will provide a mechanism to approach the characterization of accessions in the germplasm bank systematically and ensure that duplicate efforts are mimimized. Additionally, recently proposed enhancements to the GRIN descriptor list (which includes cross references to data in other international cotton germplasm databases) will provide a more unified framework for incorporating data on the accessions, including molecular data. Institutions and individuals who have prior experience and commitment to these activities are: Chee  UGA and Yu  ARS, TX: genetic diversity based on DNA markers; Weaver  Auburn, Starr  Texas A&M, and Stewart  UAR: root knot and reniform nematode resistance; Myers  LSU, Smith, Hague and Gannaway  Texas A&M, Wallace and Thaxton  MSU: fiber quality (AFIS and HVI). Seed increases to support proposed activities of Objective 1 will be made at three locations. Germplasm stocks will be increased at the Cotton Winter Nursery, Tecoman, Colima, Mexico. Wild species will be increased in greenhouses at College Station, TX. Distribution of seed will be made from the working collection (USDA-ARS, TX). Objective 2: Understanding and exploiting the cotton genome through traditional, cytogenetic, and molecular approaches (GA - Chee, TX - Stelly, AR - Stewart, MS - Turley, TX - Magill, NM - Zhang, etc., and with cooperation from USDA-ARS: John Yu) The cotton genome is complex and requires the best efforts of research institutions across the U.S. to be fully utilized for the benefit of domestic producers. Traditional plant genetics research (e.g. mating designs, variance component estimation, heritability calculations, and inheritance studies) have made significant historical progress that has provided a scientific basis for germplasm and cultivar development efforts. Advances in genetic research methodology have made possible the dissection and analysis of plant genomes at the molecular level. Cytogenetic investigations to help understand the gross and fine structure of chromosomes provide a critical link in the development of a unified genetic map. Additional efforts will be placed in developing new linkage maps for novel crosses and placing more markers on the present research populations. This project will help by providing a forum for research coordination and discussion which will foster increased collaborative efforts among laboratories in development of additional molecular markers and marker systems for a more complete saturation across the genome, increased refinement of the present genetic maps, and for a greater utility in breeding. Project participants will focus their efforts on using the SSR marker system because of their ease in use and greater polymorphic potential than previous systems that makes them more suitable for breeding elite lines. A common panel of publicly available SSRs will be compiled and shared among participating laboratories for use in various genetic and QTL mapping experiments. The standardized 12-cotton DNA genotype panel from S-304, foundation for systematic screening of cotton DNA markers, was developed to assist in the development and mapping of additional cotton markers. The newly produced portable markers will be screened against this panel to provide a common starting point in genetic analysis and to identify a core marker set (highly polymorphic) so that a common point of interaction can be generated among multiple mapping populations. Continued development of portable markers such as RFLPs, RAPDs, AFLPs, SSRs, SNPs, and CAPs must continue, but not to exclude any additional subsequent systems. A web-distributed, group-approved, standardized nomenclature for cotton molecular markers, ESTs, cDNAs, etc. which includes embedded information as to lab source and/or developer will be established. Development of cytogenetic stocks has not been completed to mark all of the G. hirsutum chromosomes by hypoaneuploidy. Those that have been developed and the other stocks in the Cotton Cytogenetic Collection will be maintained by Stelly lab (TX) which has committed itself to making these available to the community. Additional chromosome-doubled derivatives of interspecific F1 hybrids along with chromosome and chromatin substitution lines of the primary and secondary gene pool will be developed and placed in the Cotton Cytogenetic Collection. These can be used as points of targeted introgression so the evaluation of traits, markers, genes, expression, and linkage groups has great value. Genetic diversity will be enhanced by these chromosome/chromatin substitution lines and other chromatin substitution lines developed using methodologies such as the Advanced Backcross QTL system (Tanksley & Nelson 1996). Both cytogenetic and molecular genetic systems will provide new combinations as well as introgressing both the tetraploid and diploid into the primary gene pool. Specifically, Chee (GA) will coordinate the effort to create new gene combinations by introgression using tetraploid cottons G. barbadense and G mustelinum, Stelly (TX) and Stewart (AR) will develop populations from diploid cottons G.arboreum and G. longicalyx. These interspecific populations, which will be made available to other team members, represent a central part of developing MAS using DNA markers linked to QTLs and qualitative genetic traits. Developing isoline series of these introgressions will maximize their utility. Additional research using molecular fingerprinting on the genetic population structure of Gossypium will provide further understanding on the relationships among the individual lines and accessions in the collection. Cytogenetic/physical maps and molecular genetic/linkage maps have been integrated but we must refine and synthesize the existing and new linkage, physical, and cytogenetic maps into a more complete, valuable consensus map. To support these activities, the Yu (USDA-ARS, TX) and Zhang lab (NM) will each develop and distribute RIL mapping populations that are important components of this consensus map. Of further interest is to establish a comparative map with Arabidopsis, especially with regard to conserved sequences, regions of macro- and micro-synteny, and relative rearrangement. Utilizing a plant system approach to discover potential genes within the germplasm collection by screening differentially expressed genes in cotton has proven to be successful. Further efforts will provide functional polymorphisms to select actual genes of important characters as well as a valuable resource to develop additional markers. Arabidopsis ESTs will be evaluated against ESTs from the cotton germplasm collection and the information from the cotton BAC library to look at cotton functional genomics. Exploring and expandin the utility of microarrays for comparative analyses of genotypes, physiological/ developmental stages, organs, tissues, and cell types to efficiently speed along the understanding of cotton genomics is a research area envisioned during this projects tenure. Tissue culture and transformation technologies are advancing but further improvements are yet possible in developing genotype-independent transformation technologies. Stacking alleles for regeneration potential in the cotton gene pool, finding enhanced somatic embryogenesis within current elite cultivars, and improving callus induction techniques are some of the methods that still have further potential (GA). Objective 3: Enhancing the profitability of cotton through germplasm enhancement, cultivar development, pest and disease resistance, and improved output traits (NC - Bowman, AR - Bourland, GA - Chee, TX - Hague, NC - Jones, TX - Knutsons, LA - Myers, TX - Smith, TX - Starr, MS - Thaxton, AL - Weaver, , MS - Wallace, NM - Zhang, etc., and with cooperation from USDA-ARS: John Yu) Germplasm enhancement efforts have become increasingly dependent upon the incorporation of new genetic diversity into usable backgrounds. In the case of exotic germplasm, we will use advanced crossing schemes and other introgression techniques to improve productivity potential and quality characteristics. Cultivar development research must increasingly use expanded testing and statistical techniques, e.g. spatial and genotype x environment analyses, to effectively identify stable, high yielding cultivars.. Improving output traits will require coordinated research efforts using a variety of techniques such as continued application of the Regional Breeders Testing Network (RBTN) (http://cottonrbtn.com). Thirteen breeding/genetics programs in North Carolina, South Carolina, Georgia, Alabama, Mississippi, Louisiana, Arkansas, Texas, and Arizona are now participating in the RBTN. The correlation of fiber properties to yarn performance is also being conducted by the members of the RBTN in collaboration with Cotton Incorporated (Cary, NC). Several public programs (USDA-ARS-AZ, CA and SC; LA, MS, GA) along with Cotton Incorporated are working to increase the heat tolerance of cotton with joint release of elite germplasm planned. This and similar coordinated efforts will remain important and serve as a measure of success. Development of populations from both interspecific and intraspecific gene pools will continue to be essential to develop cotton germplasms. Members of this Multi-State Project will develop new populations and test methodologies to manipulate these populations with our present technologies utilize recombination and to decrease linkage drag in order to improve germplasm lines and cultivars. Methodologies useful in effectively selecting valuable traits introgressed from more distant gene pools such as the tetraploid and diploid Gossypium species will also be explored. Investigations to understand basic genetic questions that are directly useful in efficiently generating valuable parents will be initiated such as the relationship of the measures of general- and specific-combining ability with the genetic structure of the cotton germplasm pools. Biotechnological innovations combined with germplasm evaluations will become important tools to surmount current and newly identified pests and to overcome abiotic and biotic stresses MAS will begin to be significantly employed using the QTL markers that have been previously found and those that will be located in further research from within this proposal. While traditional phenotypic selection will continue to be important, researchers in several of the states involved in this project are looking into the development of selection indices that better correlate with end product (yarn and fabric) performance with important germplasm lines being developed for the wider cotton industry. This project will provide an additional mechanism for breeding programs and genetic research laboratories to work together to combine DNA markers and phenotypic screening approaches to provide greater efficiencies in selecting breeding lines with traits that are extremely tedious, time-consuming and expensive to manipulate. Initial focus will likely be on pathogenic soil nematodes (root-knot and reniform) with some additional efforts on fiber quality, heat tolerance, and drought resistance. For example, in the Chee (GA), Yu (USDA-ARS, TX), and Zhang (NM) labs, the focus will include a core of quality measures, specifically length, strength, fineness, elongation, length uniformity, and short fiber content, while in Starr (TX), Stewart (AR), Stelly (TX) and Weaver (AL) lab, the focus will be on pests resistance such as root-knot and reniform nematodes. Another approach is to re-examine how we achieve genetic gains, both in terms of methodology used to develop and evaluate new genotypes and in terms of the values of critical genetic parameters such as heritability. Genetic parameters are a function of the genetic populations they describe, so when genetic populations change, the genetic parameters of such traits as heritability of lint percentage and fiber quality of the population change. Many genetic parameters have been determined, but these studies were done some time ago and values may not apply to genetic populations currently in use. With the advent of new technology, such as greatly increased, readily available computer power, it may be feasible to utilize more sophisticated experimental design and data analysis than in the past. Design and analysis beyond the traditional ways may allow breeders to identify superior genotypes more accurately and dependably. Project participants will re-examine breeding methodologies and protocols for different post harvest analyses to compare overall effectiveness in the light of statistical advancements. A preliminary study at the Delta Research and Extension Center indicated a moderate positive correlation between early generation performance and performance of descendent pure lines (Barut, 1998). However, tests to predict advanced strain performance based on EGT of lint yield, lint percent, and fiber quality (micronaire, fiber length, fiber strength, fiber elongation, and fiber uniformity) lacked consistent r values across generations and locations which suggest that a large environmental influence on both lint yield and fiber quality parameters exists (Jones & Smith, 2006). Smith (TX) will further study this issue in cooperation with other breeders. Even though visual rating of yield showed a positive correlation to seed cotton yield, additional fine-tuning is possible. Since some high-yielding genotypes are occasionally chosen that do not have a high visual rating, placement of checks and use of the grid system will be researched to reduce the chances of eliminating these better lines. Given that selection for yield per se has resulted in shifts among yield components (Bridge et al., 1971), integration of a visual rating with specific yield components not associated with the strong visual whiteness of the lint of open bolls may provide a superior index and save time in selecting elite breeding lines. Further selection will be prioritized for yield components with a relatively low environmental main effect/high genotypic main effect. The main effects and genotype by environment interaction of these traits will be reassessed and then corroborated across regional breeding programs. This aspect will be led by the Myers (LA), but with data from other participating breeders across the cotton belt. Objective 4: Improvement of cotton bioinformatic systems and tools (LA - Myers, TX - Jing Yu, MS - Wallace, etc., and with cooperation from USDA-ARS: Kohel, John Yu) Bioinformatics is playing an increasingly critical role in crop improvement. Keeping track of all the data that is increasingly been gathered requires a dedicated effort. Updates and improvements of bioinformatics systems will serve the cotton research community with greater efficiency. In addition to maintaining data from various types of cotton research, long-term management and coordination beyond the life of an individual grant is needed to sustain the utilization of the information and resources from the cotton germplasm and genome project. The CottonDB, http://www.cottondb.org, which is housed in and maintained by the USDA-ARS in College Station, TX, will continue to be the keystone for documenting cotton genetic information. New data will continually be added along with improvements in the presentation and organization of the site. Data in the CottonDB from the Cotton Germplasm Collection will be included in the GRIN database. In addition, participants engaged in objective 2 in this project will submit data to contribute to the identification and exploitation of genetic variability at the molecular level for greatly improved efficacy in cotton germplasm improvement. Additional bioinformatic tools will be incorporated into CottonDB. The available annual reports of the previous cotton multi-state projects will be organized and archived as historical documentation for posterity in Adobe Acrobat PDF files. Jing Yu will coordinate the CottonDB web resources activities. Utilizing the standardized 12-cotton DNA genotype panel will be a foundation of the Cotton Microsatellite Database (CMD), http://www.mainlab.clemson.edu/cmd/, for a systematic screening of all cotton DNA markers developed by participants from the cotton community. The collection of all publicly available cotton SSR markers will be placed into a readily accessible web-enabled database to provide a more efficient utilization of microsatellite resources. These resources are available to the participants of this project as well as the general cotton research community. Other cotton bioinformatic websites such as The Cotton Portal, http://gossypium.info (which consist of various websites that provide query and display capabilities for performance trials, genetic maps, and comparative maps) will be improved as the bioinformatics field advances. The Cotton Functional Database, http://cfg.ucdavis.edu/microarrary.asp, will be expanded as additional items such as clones, constructs, ESTs, genes, and SSRs are input. It will be improved to be more user friendly, allowing access and manipulation of expression-related data. The Regional Breeders Testing Network (RBTN) will offer a means for testing advanced breeding lines over a wide range of environments and also serve as vehicle for germplasm exchange among participants. The RBTN (http://cottonrbtn.com) will post on its website the analyses for all the years in existence with additional analyses such as yield stability.

Measurement of Progress and Results

Outputs

• For Objective 1: More readily available cotton germplasm useful as a resource in developing improved cultivars. Systematic and expanded characterization of the germplasm accessions for standard agronomic GRIN descriptors and opportunistic screening for resistance to abiotic and biotic stresses; genetic materials which include seed and DNA stocks that are developed during the course of this project will be delivered to the appropriate clients: growers, researchers, or other interested parties
• For Objective 2: New traditional, cytogenetic, and molecular tools and the associated information that will be used to find, manipulate, and transfer genes for the traits required for improved cultivars. Development and refinement of the molecular and cytogenetic inter- and intra-specific maps; development of more portable markers in systems with high throughput potential; developing genotype-independent transformation technologies; utilizing a plant system approach to discover potential genes within the germplasm collection; genetic materials, which include genomic clones and primer sequences that are developed during the course of this project will be delivered to the appropriate client.
• For Objective 3: Novel genetic diversity that will provide traits to improve the profitability of cotton agriculture by improving performance and quality as well as decreasing the negative impact of such things like pests and diseases. Greatly enhanced genetic diversity of domesticated cotton derived from both the primary and secondary gene pools; reassessed traditional breeding designs and analytical methodologies while reviewing breeding techniques used with other species; continuing to develop breeding populations while developing protocols to utilize Marker-Assisted Breeding genetic materials which include elite breeding lines and cultivars that are developed during the course of this project will be delivered to the appropriate client.
• For Objective 4: More easily accessible database on genetic/breeding research in cotton to speed the development of both intermediary goals and final products such as improved cultivars deemed useful by the U.S. cotton industry. Development and improvement of the bioinformatic resources that provide timely access to the data developed by this project.

Outcomes or Projected Impacts

• Initial outcomes include the development of the tools necessary to understand the genetics of cotton and its germplasm, which will allow us to more effectively manipulate the germplasm as a resource. The development of knowledge, tools, and basic genetic resources will have strong impacts in research steps that are initially somewhat removed from directly impacting the cotton industry. Success in achieving these objectives will ultimately have a positive impact on viability of the cotton industry via lower costs and higher quality from new cultivars which in turn will improve the profitability of U.S. cotton by making it more competitive against synthetic fibers and within the world market.

Milestones

(2008): Completion of the physical cytogenetic map prior to integration of the physical and linkage map. Most of what we learn in one objective can be applied to other objectives in serial or in parallel with the harvest of the basic facts, a common trait in investigating such in a rich research area.

Projected Participation

View Appendix E: Participation

Outreach Plan

The release of the elite germplasm lines and cultivars will be published in the Journal of Plant Registration (CSSA). Characterization and evaluation of germplasm accessions will be placed on-line using the new GRIN descriptor list via CottonDB. All cotton DNA markers will be placed on-line in the CMD. The RBTN web site hosts a U.S. meta-environmental trial analysis for public breeder to help address issues of yield and stability. The information will be reported within appropriate media including the annual MultiState project reviews, web-sites, refereed journals; popular articles; presentations and posters in state, national, and international meetings and conferences; breeder tours; producer workshops; and field days but not excluding other suitable means of communication. The collaborative nature of the research will be emphasized via such output as web sites, regional bulletins, multi-authored journal articles, joint germplasm releases, etc.

Organization/Governance

The regional technical committee plans and coordinates research and performs other functions as specified in the "Manual for Cooperative Regional Research." The membership of the regional technical committee will include representatives from each participating Land Grant Institution USDA-ARS, and private industry. Appointments will be made by the appropriate administrator. The committee will also have an administrative advisor as appointed by the SAES and a CSREES representative; both of these positions will be nonvoting. Each participating public or private research group will have one vote. All voting members of the technical committee will be eligible to hold office. Regional technical committee offices will consist of a chair, a vice-chair, and a secretary. An executive committee, composed of current office holders, will conduct necessary business between annual meetings in consultation with the administrative advisor.

The regional technical committee will meet annually to summarize and critically evaluate progress, discuss results, and to plan data analyses, activities, reports, and publications. Notices for all meetings will be sent to participants. Meeting notices will also be sent by the administrative advisor to appropriate administrators. The chair will be responsible for compiling an annual report. The secretary will be responsible for preparing and distributing the minutes of meetings.

The scientific cooperators involved in this effort have developed an RRP that addresses key issues through a plan that orchestrates diverse genetic and breeding research efforts at multiple sites. Success of any major crop genetic improvement program, whether public or private, requires such multidisciplinary teamwork, extensive resources (sustained financial support, personnel, and facilities) and time. While many of the participating AES and ARS programs serve state and regional needs in an idiosyncratic manner, they also comprise a large part of the national public effort. Each group brings to the table unique research capabilities, technologies, and/or germplasm resources. This RRP builds on past interagency collaborations (S-304, S-258, S-77, S-1, and others) for the common good of the nation and offers greater success for each of the RRPs respective state components. So as to avoid redundancy, extend the ramifications, and reduce cost, the RRP will take advantage, where possible, of external research components in the U.S. and elsewhere that are not official participants in the group effort.

Literature Cited

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 Mol. Biol. 54:911-929.

Barut A. 1998. Early generation bulk testing for predicting F4:5 line performance in cotton. M.S. thesis. Miss. State Univ., Starkville.

Blenda A., J. Scheffler, B. Scheffler, M. Palmer, J.-M. Lacape, J. Z. Yu, C. Jesudurai, S. Jung, S. Muthukumar, P. Yellambalase, S. Ficklin, M. Staton, R. Eshelman, M. Ulloa, S. Saha, B. Burr, S. Liu, T. Zhang, D. Fang, A. Pepper, S. Kumpatla, J. Jacobs, J. Tomkins, R. Cantrell, and D. Main. 2006. CMD: A Cotton Microsatellite Database resource for Gossypium genomics. BMC Genomics 7:132 doi:10.1186/1471-2164-7-132.

Bourland FM, Johnson JT, Jones DC. 2005. Registration of Arkot 8712 germplasm line of cotton. Crop Sci. 45: 1173-1174.

Bowman DT, Bourland FM, Myers GO, Wallace TP, Caldwell WD. 2004. Visual selection for yield in cotton breeding programs. J. Cotton Sci. 8(2):62-68.

Bowman DT, May OL, Creech JB. 2003. Genetic uniformity of the U.S. Upland cotton crop since the introduction of transgenic cottons. Crop Sci. 43: 515-518.

Bridge RR, Meredith Jr WR, Chism JF. 1971. Comparative performance of obsolete and current varieties of upland cotton. Crop Sci. 11:29-32.

Chee P, Draye X, Jiang C-X, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH. 2005a. Molecular dissection of phenotypic variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: I. Fiber Elongation. Theor. Appl. Genet. 111:757-763

Chee P, Draye X, Jiang C-X, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH. 2005b. Molecular dissection of phenotypic variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: III. Fiber Length. Theor. Appl. Genet. 111:772-781.

Draye X, Chee P, Jiang C-X, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH. 2005. Molecular dissection of phenotypic variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: II. Fiber Fineness. Theor. Appl. Genet. 111:764-771.

Guo WZ, Zhang TZ, Shen XL, Yu JZ, Kohel RJ. 2003. Development of SCAR marker linked to a major QTL for high fiber strength and its molecular marker assisted selection in Upland cotton. Crop Sci. 43:2252-2256.

May OL. 2001. Registration of PD94045 germplasm line of Upland cotton. Crop Sci. 41:279-280.

May OL. 2004. Registration of GA98028 Upland cotton germplasm line. Crop Sci. 44:1882-1883.

May OL, Cantrell RG, Jones DC. 2005. Registration of GA98066 Upland cotton germplasm line. Crop Sci. 45:1175-1176.

May OL, Chee PW, Sakhanokho H. 2004. Registration of GA98033 Upland cotton germplasm line. Crop Sci. 44:2278-2279.

May OL, Davis RF, Baker SH. 2001. Registration of GA 161 cotton. Crop Sci. 41:1995-1996.

May OL, Davis RF, Baker SH. 2004. Registration of GA96-211 Upland cotton germplasm line. Crop Sci. 44:700-701.

Mei M, Syed NH, Gao W, Thaxton PM, Smith CW, Stelly DM, Chen ZJ. 2004. Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor. Appl. Genet. 108:280291.

Haigler CH, Zhang D, Wilkerson CG. 2005. Biotechnological improvement of cotton fiber maturity. Physiologia Plantarum 124:285-294.

Jones DG and Smith CW. 2006. Early Generation Testing in Upland Cotton. Crop Sci. 46:1-5.

Koebner RMD and Summers RW. 2003. 21st century wheat breeding: plot selection or plate detection? Trends in Biotechnology 21:59-63.

Kohel RJ, Stelly DM, Yu J. 2002. Tests of six cotton (Gossypium hirsutum L.) mutants for association with aneuploids. J. Heredity 93:130-132.

Liu S, Saha S, Stelly D, Burr B, Cantrell RG. 2000. The use of cotton aneuploid for the chromosomal assignment of microsatellite loci. J. Heredity 91:326-332.

Meredith WR. 2006. Obsolete conventional vs. modern transgenic cultivar performance evaluations. 2006 Beltwide Cotton Conferences, San Antonio, Texas - January 3 - 6, 2006.

Park YH, Alabady MS, Ulloa M, Sickler B, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shihy OM, Cantrell RG. 2005. Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population, Molecular Genetics and Genomics. 274(4): 428 - 441.

Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS, Park C, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin D, Wing RA, Wright RJ, Zhao X, Zhu L, Paterson AH. 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.

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 seed fiber development in cotton. Theor. Appl. Genet. 111(6):1137-1146.

Saha S, Wu J, Jenkins JN, McCarty Jr JC., Gutierrez OA, Stelly DM, Percy RG, Raska DA. 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.

Sakhanokho,HF, Ozias-Akins P, May OL, Chee PW. 2004. Induction of somatic embryogenesis and plant regeneration in select Georgia and Pee Dee cotton (Gossypium hirsutum L.) lines. Crop Sci. 44:2199-2205.

Smith CW. 2003a. Registration of TAM 94L-25 and TAM 94J-3 germplasm lines of upland cotton with improved fiber length. Crop Sci. 43: 742-743.

Smith CW. 2003b. Registration of TAM 94WE-37s smooth-leaf germplasm line of upland cotton with improved fiber length. Crop Sci. 43: 743-744.

Stelly D. 2004. Aneuploid mapping in polyploids. Encyclopedia of Plant and Crop Science. Marcell Dekker, Inc. Tanksley SD, Nelson JC. 1996. Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92: 191-203

Thaxton PM, El-Zik KM. 2003. Registration of eleven multi-adversity resistant (MAR-7A) germplasm lines of upland cotton. Crop Sci. 43: 741-742.

Thaxton PM, Smith CW, Cantrell R. 2005a. Registration of Tamcot 22 high-yielding upland cotton cultivar. Crop Sci. 45: 1165-1166.

Thaxton PM, Smith CW, Cantrell R. 2005b. Registration of TAM 98D-102 and TAM 98D-99ne Upland Cotton Germplasm Lines with High Fiber Strength. Crop Sci. 45: 1668.

Thaxton PM, Smith CW, Cantrell R. 2005c. Registration of TAM 96WD-18 Upland Cotton Germplasm Line with Improved Fiber Length and Strength. Crop Sci.45: 1172.

Thaxton PM, Smith CW, Cantrell R. 2005d. Registration of TAM 96WD-69s Glabrous Upland Cotton Germplasm Line. Crop Sci. 45: 1172-1173.

Van Becelaere G, Lubbers EL, Paterson AH, Chee PW. 2005. Pedigree- vs. DNA Marker-Based Genetic Similarity Estimates in Cotton. Crop Sci. 45:22812287
Wallace TP, White BW, Hollowell JE. 2002. Registration of MISCOT 8806 Cotton. Crop Sci. 42: 2216-2217.

Wallace TP, White BW, Hollowell JE. 2005. Registration of MISCOT 8839 Cotton. Crop Sci. 45:1167-1168.

Wilkins TA, Arpat AB. 2005. The cotton fiber transcriptome. Physiol Plantarum 124(3):295-300.

Wilkins TA, Mishra R, Trolinder NL. 2004. Agrobacterium-mediated transformation and regeneration of cotton. J Food Agric Environ 2:179-187

Zhang TZ, Yuan YL, Yu JZ, Guo WZ, Kohel RJ. 2003. Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor. Appl. Genet. 106:262-268.

Attachments

Land Grant Participating States/Institutions

AL, GA, LA, MS, NM, OK, TX

Non Land Grant Participating States/Institutions

Cotton Incorporated