Annual/Termination Reports:

[06/25/2008] [02/08/2010]

Report Information

Participants

Zhihua Jiang (Washington State University);
Joe Cassady (NC State University);
Deb Hamernik (USDA-CSREES);
Cathy Ernst (Michigan State University);
Joan Lunney (ARS- BARC);
Chris Tuggle (Iowa State University);
Max Rothschild (Iowa State University);
Jack Dekkers (Iowa State University);
Romdhane Rekaya (University of Georgia);
Rick Barb (ARS-USDA);
Le Ann Blomberg (BARC-USDA);
Bert E Stromberg Jr (University of Minnesota)

Brief Summary of Minutes

8:00 am Dr. Joan K Lunney elcomed everyone to NC1037 annual meeting. As chair, Dr. Lunney presided over the sessions.

8:15 am Business meeting and Election of NC1037 officers. A motion regarding the selection of officers for 2008 was approved. Dr. Jiang (Chair), Dr. Rekaya (Vice-Chair) and Ohio representative (secretary).

8:30 am Dr. Jiang suggested Seattle (Washington State) as location for 2009 meeting. After some discussions, no decision was made. Also there have been some discussions regarding the schedule of the meeting for 2009. Two options were looked at. Regular schedule or at the same time as PAG-2009.

8:50 am Dr. Rothschild , Iowa State University, gave an update on swine sequencing & SNP chip plans. He indicates that a purchase order has to be placed by August 22, 2008 where money will be committed but there is no guaranty on number of chips. He also indicated that an amount of $100 to $110K is already available. After some discussions, it was clear that some policies-rules are needed for the best use of such money. Drs. Rothschild, Hamernik, and Ernst agreed to form a committee to set some rules.

9:30 am Break

10:00 am Updates on USDA bovine genome research

- Dr. Zimin gave an update on the assembly of the cow genome
o He showed interest for collaboration on the pig genome assembly
o Dr. Rothschild and Dr. Cassady suggested being in touch with Dr. Zimin for potential collaboration with the pig genome
- Dr. Steven Schroeder from the Bovine Functional Genomics Laboratory (BFGL), BARC, gave an update on the cattle gene atlas
- Dr. Matukumalli, BFGL, BARC gave some results on the application of BovineSNP50 for CNVs and genome-wide associations.
- Dr. Paul VanRaden from Animal Improvement Programs Laboratory presented an application of Genomic selection in dairy cattle.
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12:00 pm Lunch break

1:00 pm NC1037 Station Reports

Chris Tuggle (Iowa state university)
Jack Dekkers (Iowa State University)
Max Rothschild (Iowa State University)
Joe Cassady (North Carolina State University)
Rick Barb and Romdhane Rekaya (ARS- University of Georgia)
Cathy Ernst (Michigan State University)
Le Ann Blomberg (BARC-USDA)
Jiang (Washington State University)

3:45 pm Administrative Reports:
Deb Hamernik, CSREES, NPL, Animal Physiology;
Bert Stromberg, Administrative Advisor;
Max Rothschild, National Swine Genome Coordinator





Thursday May 15, 2008

8:00 am Review of NC1037 objectives/station reports

1. Discussion of major areas of research in objective 1: Reproduction, growth and development, sow longevity, bone strength and behavior

2. Discussion of major areas of research in objective 2: genetic mechanisms controlling animal health

10:15 am Collaboration and possibility for collaboration
- Meat Quality: potential collaboration between Iowa and Michigan.
- Growth and Development: Potential collaboration between BARC and Michigan on fetal and neonatal development and between BARC and North Carolina on pre-weaning survival trial with Smithfield, Inc.
- Feed efficiency/Intake: Extending the already existing collaboration between Georgia and Iowa on gene expression data analysis, follow up with the MSH/NPY treatment and the used of RFI resources at IA.
- Reproduction: Potential collaboration between BARC and Iowa on comparing data for early embryonic development
- Behavior: Possibility of joint analysis of chute scores (standardization of scoring systems)

11:15 am Update on PRRS CAP project by J. Lunney
- Great potential for collaboration between NC1037 members
- Important issue for the industry
- Discussion of the potential use of $100K as matching fund

11:45 am Dr. Hamernik suggested adding impact statements to station reports as well as some discussions on CRIS reporting and station reports

11:51 am Meeting adjourned at 11:51 a.m.

Accomplishments

Objective 1. Further understand the dynamic genetic mechanisms that influence production efficiency and quality of pork.<br /> <br /> Genetic improvement of production efficiency and pork quality using traditional selection programs. Iowa State University reported a six-generation selection experiment for intramuscular fat (IMF) based on the average EBV estimated using real-time ultrasound. Of the 149 pigs harvested in generation six, the station found that line LS means for tenth rib backfat and loin muscle area were 16.63 mm and 45.45 cm2 in the control line, and 24.22 mm and 38.02 cm2 in the select line (P < 0.01), respectively. Analysis of STAGES data evaluated on all 621 pigs in generation six revealed significant differences between lines for days to 114 kg, backfat, and loin muscle area. Results through generation six indicate that selection for IMF resulted in slower growth, more tenth-rib backfat, and less LMA. Chemical analysis of a loin sample from pigs harvested revealed a significant phenotypic response in IMF (2.41% in the control line vs. 4.53% in the select line) similar to the difference between lines for IMF EBV. Line LS means for pigs harvested in generation six for 24 h Hunter L and Minolta were 47.00 and 22.17 in the control line, and 49.42 and 24.49 in the select line (P < 0.001), respectively. Subjective measures of marbling were significantly different between lines (2.50 in the control line vs. 4.89 in the select line). Evaluation of correlated response in litter traits after selection for IMF showed that dams in the control line farrowed litters that were 1.22 kg heavier at birth. Individual piglets in control line litters were 0.11 kg (P < 0.05) heavier at birth when compared to piglets farrowed by select line dams. Iowa State University also carried out a selection experiment for residual feed intake (RFI) in Yorkshire pigs, which produced generation 6 in summer 2008. Analysis of feed intake and growth curves showed that differences in RFI between the two lines occur after ~60 kg body weight. The slightly lower ADG observed in the select line also occured primarily after ~60 kg.<br /> <br /> <br /> Selection for litter size continues at the Nebraska State University. Two selection lines (Lines 2 and 45) and two contemporary control lines (Lines 1 and 6) have been maintained in the Station for 27 generations. Line 2 was derived from an Index line that had undergone 11 generations of selection for ovulation rate and embryo survival. This selection was followed by three generations of selection for total born per litter, six generations of selection for number of live pigs per litter, and seven generations of number of live pigs per litter and within litter selection for growth rate and backfat thickness. Line 1 has been randomly selected. The Station report indicated that selection lines 2 and 45 farrowed 5 additional fully formed pigs per litter than their respective controls, but also had greater incidence of stillborn piglets so that the difference in number of live pigs per litter is approximately 4 pigs per litter. Recent selection for growth is causing lines to differentiate in weight and backfat, but not in loin eye area. Improvement of growth appears to be greater in Line 45 than in Line 2. <br /> <br /> <br /> North Carolina State University has started a divergent selection for response to the backtest to study pig behavior, the extent to which it is genetically controlled, and its relationship with economically important traits. During their previous work the Station estimated the heritability of the backtest to be approximately 0.40. The long term goal will be to monitor correlated responses to selection for high and low total time spent struggling during the backtest. Between 7 and 21 days of age each pig will be evaluated using the backtest. A pig will be placed on a padded table in a supine position for 60 s and gently restrained. The experimenters right hand will be placed loosely on the pigs thorax with the right foreleg between the index and middle finger. The hind legs will be held with experimenters left hand and stretched and moved downward to begin the test and the hand will remain loosely on the hind legs throughout the test. Each bout of struggling with at least one hind leg will be recorded as an escape attempt. The number of escape attempts, duration of escape behavior, and latency to the first escape attempt will be recorded. It is expected that this test will lead to a better understanding of the relationship between pig behavior, growth, reproduction, and health. <br /> <br /> <br /> North Carolina Agricultural And Technical State University has recently received a SARE Grant entitled A Multi-Disciplinary Approach to Improve the Environmental Performance of Niche Pork Production Systems and Marketability of Heritage Swine Breeds. This project will investigate niche pork production systems that address market demands and natural resource conservation concerns, with a specific focus on maximizing vegetative ground cover and nutrient distribution in pastures and understanding marketability of heritage breeds produced in alternative production systems. Consumer interest in heritage breed pork continues to rise; howeve,r little is known about taste characteristics and production potential in alternative systems. The Station will also collaborate with an animal nutritionist in the department to develop a collaborative team that will integrate quantitative and molecular technologies for genetic improvement of pigs. The approach will utilize genomic science and bioinformatics tools to aid in the selection of pigs best fitted for outdoor swine production systems, by evaluating production characteristics such as, nutrient utilization, disease resistance and increased litter weights.<br /> <br /> <br /> Quantitative genomics of production efficiency and pork quality using genome scans and candidate gene approaches. Iowa State University has nearly completed a QTL study using the Berkshire x Yorkshire population. The group found QTL on many chromosomes with special emphasis on chromosomes 1, 17 and 18. From there, the station started to find the underlying genes responsible. Fine mapping of QTL on chromosomes 17 and 18 has continued with the addition of >45 genes in the relevant region on chromosome 17 and >10 on chromosome 18 and increasing the marker density to the linkage map. The Station also used comparative studies to examine candidate genes affecting longevity through reproduction and leg soundness. These include genes in the IGF pathway and genes associated with stress and muscle and bone pathways. Over 100 new genes have been mapped and analyses revealed that some of these genes have effects varying from 0.1 to nearly 1 parity more on average and also affect growth, reproduction and longevity. A NPB funded project is underway to look at 2000 sows (1000 old, 1000 young) to examine the effects of genes on leg traits. The group has identified over 100 genes, mapped 75 new ones and identified several genes that have large effects on many leg action and conformation traits. Using commercial populations they are also examining genes on chromosomes 2 and 12 for effects of scrotal hernia and have found several interesting associations.<br /> <br /> <br /> At Michigan State University, a Duroc x Pietrain resource population has been developed to map quantitative trait loci (QTL) affecting carcass composition and pork quality. In the report, they focused their work on confirmation of QTL on pig chromosome 6 by incorporation of marker genotype data for an additional 452 F2 pigs into the QTL analysis. A total of 962 F2 pigs were genotyped for the SSC6 markers S0087, SW122, SW1881 and SW322. Other SSC6 markers genotyped for the original genome scan (510 F2 pigs) included S0099, SW2406, SW2525, S0220 and SW2419. Data were analyzed with line cross least squares regression interval mapping methods using sex and litter as fixed effects and carcass weight or harvest age as covariates. QTL significant at the 5% chromosome-wise level were found for 24 h carcass temperature, Boston shoulder weight and marbling score. These results confirmed previously identified QTL and included four new QTL (carcass weight, first rib backfat, Boston shoulder weight and belly weight). <br /> <br /> <br /> Michigan State University has also targeted porcine insulin-like growth factor binding protein 2 (IGFBP2) for its association with economically important traits in pigs. For this study, 417 F2 pigs from their Duroc x Pietrain resource population were genotyped and the IGFBP2 was placed on SSC15 at 78.0 cM in a region previously found to contain significant QTL affecting meat color and tenderness. Pigs from litters segregating both alleles (N=226 F2 pigs) were used to determine potential associations between IGFBP2 genotype and growth, carcass and meat quality traits. Genotype effects (P<0.05) were found for loin muscle area (LMA) at 10, 19 and 22 wk of age, ADG, carcass length, ham wt, loin wt, 10th rib carcass LMA, 45 min pH, pH decline from 45 min to 24 h postmortem, CIE L*, CIE a*, subjective color score, Warner-Bratzler shear force, sensory panel muscle fiber tenderness and sensory panel overall tenderness. <br /> <br /> <br /> At Nebraska State University, fine mapping of QTL identified in previous scans was accomplished by using phenotypic and genotypic data from pigs of several generations. Phenotypic data were collected for birth weight (BWT, n = 1422), weaning weight (WWT, n = 1311), age at puberty (AP, n = 669), ovulation rate (OR, n = 797), number of fully formed pigs (FF, n = 841), number of pigs born alive (BA, n = 841), number of mummified pigs (MUM, n = 841), number of nipples (NN, n = 1434), incidence of pigs with splaylegs (n = 458), and number of stillborn pigs (SB, n = 841). Age at puberty was recorded in gilts of Lines 1 and 2 from Generation 2 through Generation 15 and in gilts of Lines 4, 5, and 6 through Generation 16. Ovulation rate was recorded in gilts of Lines 1 and 2 through Generation 11, and in gilts of Lines 4, 5, and 6 through Generation 16. Number of fully formed pigs, MUM, SB, BA were recorded in gilts within 24 h of parturition each generation.<br /> <br /> <br /> The Ohio State University has maintained both purebred Berkshire and Landrace populations of swine, which are available to evaluate the influence of pure and reciprocal crossbred lines on growth, carcass, and fresh and cooked pork quality traits of the loin, belly and ham. Data collected in previous years, including full pedigree and well defined contemporary groups are in place and DNA samples from all parent and progeny are available for use in collaborative gene, QTL discovery and or verification studies. The Station encouraged all interested collaborators within NC-1037 to inquire about potential collaboration opportunities. Litters of purebred and crossbred animals are produced in four farrowing groups annually with the ability to produce up to 60 litters per group. Specific aims of future generations will be discovery of mechanisms influencing variation in loin tenderness, a trait likely to have the greatest impact on consumer assessment of pork palatability and overall desirability.<br /> <br /> <br /> Washington State University has worked on the porcine mitochondrial transcription factor A (TFAM). The group determined both full-length cDNA and promoter sequences of the porcine TFAM gene, which were then used for comparative characterization of the TFAM gene with other species. Using Radiation Hybrid mapping the Station assigned this gene to porcine chromosome 14 (SSC14). A G557A substitution in intron 1 of porcine TFAM gene was detected and genotyped on a total of 252 animals, including 165 from seven Chinese and 87 from five Western pig breeds. Bayesian analysis via MCMC (Markov chain Monte Carlo) revealed that these two groups of pigs were well separated at this locus during the breed history; 95% of the posterior difference of TFAM allelic frequency between these two pig groups was greater than zero. As there are marked differences in fatness and lean meat production between Western and Chinese pig breeds, the TFAM gene deserves further investigation in order to evaluate its phenotypic effect on fat deposition and carcass traits in commercial pig populations. Washington Station has also worked on comparative assembly of Sus scrofa chromosome. The Station assigned more than 1,200 clones to their orthologous regions on human chromosomes 6, 9, 14, 15 and 18, which are consistent with the current comparative relationship between these two species. On the other hand, porcine chromosome 1 might have some small regions orthologous to human chromosomes 1, 10, 11 and 20. The comparative analysis provides information on candidate genes for QTL identified on the pig chromosome.<br /> <br /> <br /> Transcriptomics of production efficiency and pork quality using microarray analysis and real time PCR. University of Georgia has used transcriptional profiling to identify genetic mechanisms that respond to alpha-MSH, a MC3/4-R agonist. Three MC4R genotypes (2 homozygous and the heterozygous for MC4R) were selected from the UGA swine herd (PIC composite). Thirty-six pigs (6 per genotype per treatment) were randomly assigned to one of the following treatments: ICV administration of 150 ul 0.9% saline, or 10 µg NDP-MSH (agonist) in 150 ul of 0.9% saline. Feed intake was measure at 12 and 24 hous after treatment (time 0). All pigs were sacrificed 24 hours post-injection and hypothalamus, liver and middle layer of back fat was collected and mRNA was hybridized to 24,123 probe set Affymetrix Porcine Genome Arrays. The group found that MSH suppressed (P< 0.04) feed intake in all animals at 12 and 24 hr after treatment regardless of genotype with no treatment x genotype interaction detected (P > 0.8). There were 5070, 253 and 282 genes that were differentially expressed (P<0.07) in adipose, liver and hypothalamic tissue, respectively after central administration of MSH. The report concluded that the MC4R genotype did not effect the feeding behavior reponse to MSH but the greatest response to MSH was observed in adipose tissue gene expression. <br /> <br /> <br /> Iowa State University has worked on a USDA-NRICGP funded project to determine the genes expressed in both the endometrium and embryo/conceptus during the elongation and implantation phase of reproduction in both the Yorkshire and the Meishan breeds. using Affymetrix Genechip transcript profiling analysis. The endometrial results were analyzed and 47 genes were tested by Q-PCR across several contrasts; approximately 85% of expression patterns across > 200 pairwise comparisons were confirmed. Conceptus data analyzed in conjunction with similar data collected at Oklahoma State University determined that a joint analysis improves the power to detect differentially expressed genes. An analysis of the OSU data on embryonic gene expression during the critical time of elongation has been submitted for publication. In addition to the selection experiment for residual feed intake described above, Iowa State University also performed gene expression profiling for this project and initial analysis of gene expression data has been completed. <br /> <br /> <br /> Michigan State University has evaluated the new Swine Protein-Annotated Oligonucleotide Microarray (http://www.pigoligoarray.org) by analyzing transcriptional profiles for longissimus dorsi muscle (LD), liver, brain and uterine endothelium (UE). The extent of non-specific hybridization was evaluated by comparing intensities of 60 negative control oligonucleotides to background intensity and by estimating the distribution of intensities of non-control oligonucleotides. The study indicated that increasing temperature appreciably improved overall specificity while hybridizations performed at 40 °C showed unacceptable levels of non-specific hybridization. Diagnostics also utilized 60 perfect match/mismatch (PM/MM) oligonucleotide sets designed as part of the array elements (1, 2, 3, 5, 7 and 10 mismatched bases). A small number of negative controls showed consistently high signals suggesting they may not be suitable for use as negative controls. This work was supported in part by the USDA Pig Genome Coordination program. Michigan State University also used the Swine Protein-Annotated Long Oligonucleotide Microarray with pig longissimus dorsi (LD) samples for an expression QTL (eQTL) study. Microarrays have been completed for 176 LD samples, quality assessments of the arrays have been performed and data analysis is in progress. This work was supported by the USDA CSREES National Research Initiative.<br /> <br /> <br /> In collaboration with Dr. Chens Animal Genomics Laboratory at Nanjing Agricultural University, China, Washington State University has worked on porcine nuclear receptor coactivators 1 (NCOA1), 2 (NCOA2) and 3 (NCOA3) for their roles in adipogenesis. The group cloned these three porcine genes, identified their transcript variants and analyzed their expression level in relation to intramuscular fat (IMF) content in Longissimus Dorsi (LD) muscle. The station found that both NCOA1 transcript variant 2 (r=-0.554, p<0.01) and total NCOA1 (r=-0.516, p<0.01) expression levels were negatively correlated with IMF contents, while NCOA2 transcript variant 1 (r=0.605, p<0.01) and NCOA3 (r=0.435, p<0.05) were positively associated with IMF content in LD muscle. A similar study was also performed on porcine sterol regulatory element binding transcription factor 1 (SREBF1) for its role in intramuscular fat (IMF) deposition in pigs. <br /> <br /> <br /> Objective 2: Discover genetic mechanisms controlling animal health in pork production.<br /> <br /> <br /> Nomenclature and identification of new alleles for the SLA complex. USDA ARS BARC has focused their major efforts on updating the nomenclature for the SLA complex in collaboration with Michigan State University and other members of the ISAG SLA Nomenclature Committee. New SLA allele sequences and haplotypes have been designated: 74 new SLA alleles, including 18 SLA-1 alleles, 11 SLA-2 alleles, six SLA-3 alleles, two SLA-6 alleles, one SLA-DRA allele, 20 SLA-DRB1 alleles, three SLA-DQA alleles and 13 SLA-DQB1 alleles; in addition, 12 new SLA class I and 4 new class II haplotypes. These updates are now posted on the Immuno Polymorphism Database-Major Histocompatibility Complex (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla) which serves as the repository for maintaining a list of all recognized SLA genes and their allelic sequences.<br /> <br /> <br /> BARC, Japanese, and French scientists have worked on developing new methods for optimizing SLA allele genotyping. The analyses covered genetic polymorphisms in 23 SLA homozygous/heterozygous samples, proved that haplotype-specific patterns and variations of MS existed, and refined recombination points for several SLA haplotypes. These studies affirmed the existence of strong linkage disequilibrium (LD) in the entire SLA region; large haplotype blocks extended across >2-Mb segments. These MS markers constitute an alternative method to characterize the SLA haplotypes. <br /> <br /> <br /> BARC has also developed a simple and rapid method using the polymerase chain reaction (PCR)-sequence-specific primer (PCR-SSP) strategy for direct determination of SLA alleles, specifically, to type alleles at the multiple SLA class I genes and alleles at each of the three classical SLA class I loci (designated SLA-1, SLA-3 and SLA-2). The PCR-SSP typing system was designed with 47 discriminatory PCR primer pairs to amplify the current SLA class I alleles based on groups that have similar sequence motifs. Overall 24 class I allele groups corresponding to 56 class I genotypes were detected; additionally 23 low-resolution SLA class I haplotypes were identified in the 202 pig DNAs tested. This provides a reliable and unambiguous method for detecting SLA class I alleles. The MS and PCR-SSP typing methods provide important alternates to direct determination of the SLA alleles based on sequencing or SNP typing.<br /> <br /> <br /> Identification and mapping of genes responding to PRRS infection. BARC in collaboration with Kansas State and Iowa State has been coordinating the PRRS Host Genomic Consortium. This is a national effort to collect phenotype and genotype of 1000s of commercial pigs for their response to PRRSV infection. The PHGC database is being developed by Iowa State, Kansas State and BARC scientists to house the large amounts of phenotypic and genotypic data that will be collected across several research labs for the PHGC and stored for continued use by the PRRS research community. The schema for the database was originally designed based on data sets generated from the PRRS virus Big Pig project. This included data on pig, sex, birth date, infection details, weights, PRRS viral and serum antibody and cytokine levels. A new PRRS CAP2 grant will support BARC in collaboration with NC229 and PRRS CAP scientists to start SNP genotyping and whole genome association studies with this data. These analyses should reveal associations of PRRS disease resistance and growth traits with SNP alleles.<br /> <br /> <br /> BARC has used the new Pigoligoarray to identify immune regulatory and protective pathways in samples from swine infected with virulent PRRS virus with comparison to samples from vaccinated pigs. In their initial PRRS experiment animals were divided into three groups: (1) pigs infected with a virulent PRRSV isolate MNW2B; (2) pigs vaccinated using a contemporary PRRS ATP vaccine (Ingelvac®); and (3) control pigs. Different tissues were collected between days 3-6 post infection/vaccination. Results obtained for cranial lung tissues affirmed 923, 619 and 747 putatively differentially expressed genes for vaccinated versus control, vaccinated versus infected, and control versus infected, respectively. As expected, pathways involving interferons and other cytokines, as well as chemokines, have been identified as critical for differentiating infected from vaccinated pigs. Final statistical and pathway analyzes are underway to identify the biological functions and regulatory pathways that are most significant.<br /> <br /> <br /> At the University of Nebraska, two replications of a PRRSV challenge experiment with a total of 400 pigs have been conducted. Replication 1 occurred during summer 2002, and Replication 2 in winter of 2003. In each replicate a total of 100 PRRSV-negative, SEW pigs of the NE Index line (Line 2) and 100 pigs of a commercial Duroc-Hampshire (DH) line were used. Line 2, described above, is an inbred Large White-Landrace population that, at the time of the experiment, had been selected for 24 generations for increased litter size. It was expected to have low resistance to disease because of its relatively high inbreeding (~25%). Line DH is a non-inbred, terminal sire line that excels in growth and leanness and was expected to have greater disease resistance than Line 2. Two pigs from each of 200 litters by 163 dams and 83 sires were sampled to ensure genetic diversity within lines to maximize the chance that genes for both resistance and susceptibility to PRRSV existed in the sample. RNA was extracted from lung and lymph tissue of these same pigs and differences in gene expression between resistant and susceptible pigs was determined using microarray gene expression analyses.<br /> <br /> <br /> Identification and mapping of genes responding to Salmonella infection. Iowa State University reported their first study on Affymetrix-based transcriptional profiling in mesenteric lymph node for response to Salmonella infection, as well as a second paper on comparing the expression of genes responding to S. enterica serovar Cholerasuis (SC) versus S. enterica serovar Typhimurium (ST). The group has completed an Affymetrix-based transcriptional profiling study comparing the host response to infection by ST, and planned to submit a manuscript for publication in January 2008. They have identified genes that specifically respond to only one of these two infections, and they have evidence that many genes that respond to SC do not respond to ST infection. The Station has confirmed the microarray data for >20 genes tested by Q-PCR for both SC and ST infections, and has identified many regulatory pathways affected by Salmonella that have been shown to be involved in pathogen response in other species, as well as novel genes that indicates our understanding of pathogen response pathways needs to be expanded significantly.<br /> <br /> <br /> Characterization of the porcine circovirus associated disease complex caused by porcine circovirus type 2. The condition exists at the University of Nebraskas research farm. During the last three generations, the Station has scored all pigs of different lines from weaning through approximately 180 d of age for symptoms of PCVAD. Samples of pigs showing symptoms were submitted for necropsy to confirm typical symptoms in lymph and other tissues. PCR was conducted to confirm presence of circovirus. Pigs of Lines 1 and 2 from Generations 25-27 and from Lines 6 and 45, also from Generations 25-27, were scored for PCVAD at weaning (18 d), and at 60, 90, and 130 d of age. At each age, pigs were weighed and blood samples were collected. Serum collected at each age from all pigs scored positive for PCVAD and from a littermate or penmate without symptoms of PCVAD was submitted to the Iowa State University Veterinary Diagnostic Laboratory where PCV2 ELISA (antibody) and PCR (viremia) diagnostics were conducted. Analyses are complete for 3-4 samples from approximately 1000 pigs. Association of diagnostic data with PCVAD scores and pig weights will be used to determine degree of genetic influence in response to virus. <br />

Publications

Cardoso, F.F., J.P. Steibel, G.J.M. Rosa, C.W. Ernst, R.O. Bates and R.J. Tempelman. 2007. Assessment of different selective phenotyping strategies for genetical genomic studies with outbred F2 populations. J. Anim. Sci. 85(Suppl. 1):373.<br /> <br /> Choi, I.S., R.O. Bates, V.D. Rilington, D.B. Edwards, N.E. Raney, M.E. Doumit and C.W. Ernst. 2007. Association between corticotropin-releasing hormone receptor 2 genotypes and meat quality traits in pigs. J. Anim. Sci. 85(Suppl. 2):65.<br /> <br /> Edwards, D.B., C.W. Ernst, R.J. Tempelman, G.J.M. Rosa, N.E. Raney, M.D. Hoge and R.O. Bates. 2008. Quantitative trait loci mapping in an F2 Duroc x Pietrain resource population: I. Growth traits. J. Anim. Sci. 86:241-253.<br /> <br /> Edwards, D.B., C.W. Ernst, N.E. Raney, M.E. Doumit, M.D. Hoge and R.O. Bates. 2008. Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Meat quality traits. J. Anim. Sci. 86:254-266.<br /> <br /> Ernst, C.W. and M.F. Rothschild. 2008. Porcine microarrays, QTL and bioinformatic resources. Invited presentation at the Swine in Biomedical Research Conference, San Diego, CA, April 2-3, 2008, http://nsrrc.missouri.edu/Meetings.asp. <br /> <br /> Ernst, C.W., J.P. Steibel, A.M. Ramos, J.K. Lunney, M. Wysocki, D. Petry, R.K. Johnson, S.C. Fahrenkrug, R.J. Tempelman, M.F. Rothschild, B.S. Juneja, J. Garbe, C.G. Elsik, R.O. Bates, E.E. Helman, B.L. Varnes and M.E. Doumit. 2008. Assessment of the Swine Protein-Annotated Oligonucleotide Microarray and utility of the arrays for eQTL and transcriptional profiling studies. Plant and Animal Genome XVI Conference. San Diego, CA http://www.intlpag.org/16/abstracts/PAG16_W72_494.html. <br /> <br /> Steibel, J.P., A.M. Ramos, R.J. Tempelman, R.O. Bates, M. Wysocki, J.K. Lunney, D. Petry, R.K. Johnson, S.C. Fahrenkrug, B.S. Juneja, J. Garbe, M.F. Rothschild, C.G. Elsik and C.W. Ernst. 2008. Assessment of the Swine Protein-Annotated Oligonucleotide Microarray by utilizing designed control features included on the array. Plant and Animal Genome XVI Conference. San Diego, CA. http://www.intlpag.org/16/abstracts/PAG16_P07a_732.html.<br /> <br /> Alexander, L., Cutler, S., Rothschild, M. and Stahl, C. 2007. Dietary phosphorus and genetic background interact to affect growth performance and bone integrity in pigs. Proc. Midwest Animal Science Meeting, Des Moines IA.<br /> Baas, T., and Schwab, C. 2007. Selection for Intramuscular Fat in Duroc Swine. Journal of Animal Science, 85: 77.<br /> <br /> Baas, T.J., and Schwab C.R. 2007. ISU IMF Selection Project. Proc. 31st National Swine Improvement Federation Conference and Annual Meeting, Kansas City MO.<br /> <br /> Bearson, S., Uthe, J., Wang, Y., Qu, L., Dekkers, J., Nettleton, D., and Tuggle, C. 2007. Associations of the porcine immune response and genetic polymorphisms with the shedding of Salmonella enterica serovar Typhimurium. Proc. Safepork, 7th International Symposium Epidemiology Control Foodborne Pathogens, Pork, Verona Italy.<br /> <br /> Bunter, K., Cai, W., and Dekkers, J. 2007. Relationship of juvenile IGF-I with performance traits in lines selected for residual feed intake. Midwest Animal Science Meeting, Des Moines IA.<br /> <br /> Burkett, J., Baas, T., Beitz, D., Schwab, Berry, N., and Zhang, S. 2007. Correlated Response in Fatty Acid Composition from Five Generations of Selection for Intramuscular Fat in Duroc Pigs. Journal of Animal Science, 85: 627.<br /> <br /> Bushman, A., Baas, T., Schwab, C., and Stalder, K. 2007. Correlated Response in Litter Traits to Selection for Intramuscular Fat in Duroc Swine. Journal of Animal Science, 85: 61.<br /> <br /> Cai, W., Casey, D., and Dekkers, J. 2007. Selection Response and Genetic Parameters for Residual Feed Intake in Yorkshire Swine. Journal of Animal Science, 86: 287-298.<br /> <br /> Dekkers, J. 2007. Marker-Assisted Selection for Commercial Crossbred Performance. Journal of Animal Science, 85: 2104-2114.<br /> <br /> Dekkers, J. 2007. Prediction of Response to Marker-Assisted and Genomic Selection Using Selection Index Theory. Journal of Animal Breeding and Genetics, 124: 331-341.<br /> <br /> Dekkers, J., and Rothschild, M. 2007. New tools to make genetic improvement. London Swine Conference, London, ON, Canada. http://www.londonswineconference.ca/proceedings.htm<br /> <br /> Fitzgerald, R., Jones, G., and Stalder, K. 2007. A comparison of intrauterine and cervical artificial insemination catheters on farrowing rate and litter size in artificially mated sows. Iowa State University Animal Industry Report.<br /> <br /> Glenn, K., Ramos, A., and Rothschild, M. 2007. Analysis of FMO Genes and Off Flavor in Pork. Journal of Animal Breeding and Genetics, 124: 35-38. <br /> <br /> Guimaraes, S., Rothschild, M., Stahl, C., and Lonergan, S. 2007. SNP Discovery, Expression and Association Analysis for the SDHD Gene in Pigs. Journal of Animal Breeding and Genetics, 124: 246-253.<br /> <br /> Guimaraes, S., Stahl, C., Lonergan, S., Geiger, B., and Rothschild, M. 2007. Myostatin Promoter Analysis and Expression Pattern in Pigs. Livestock Production of Science, 112: 143-150.<br /> <br /> Ha, Y., Do, K., Glenn, K., Rothschild, M., and Kim, K. 2007. Investigation of adiponectin gene in Korean native pigs. Proc. 2006 Fifteenth Korea Genome Organization Conference, Seoul Korea.<br /> <br /> Habier, D., Fernando, R., and Dekkers, J. 2007. The Impact of Relationship Information Genome-Assisted Breeding Values. Genetics, 177: 2389-2397.<br /> <br /> Hart, E., Caccamo, M., Harrow, J., Humphray, S., Gilbert, J., Trevanion, S., Hubbard, T., Rogers, J., and Rothschild, M. 2007. Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 MB region of pig chromosome 17. Genome Biology 8: R168.<br /> <br /> Jiang, Z., and Rothschild, M. 2007. Swine Genome Science Comes of Age. International Journal of Biology Science, 3: 129-131.<br /> <br /> Jiang, Z., Pappu, S., and Rothschild, M. 2007. Hitting the Jackpot Twice: Identifying and Patenting Gene Tests Related to Muscle Lipid Accumulation for Meat Quality in Animals and Type 2 Diabetes/Obesity in Humans. Recent patents on DNA & Gene Sequences, 1: 100-111.<br /> <br /> Knauer, M., Karriker, L., Baas, T., Johnson, C., and Stalder, K. 2007. An Evaluation of the Precision of Farm Reported Data Used to Make Health Decisions About Sows. Journal of American Veterinary Medicine Association, 231: 433-436.<br /> <br /> Knauer, M., Stalder, K., Karriker, L., Baas, T., Johnson, C., Serenius, T., Layman, L., and McKean, J. 2007. A Descriptive Survey of Lesions from Cull Sows Harvested at Two Midwestern U.S. Facilities. Preventative Veterinary Medicine, 82: 198-212.<br /> <br /> Knauer, M., Stalder, K., Karriker, L., McKean, J., Serenius, T., Baas, T., Johnson, C., and Layman, L. 2007. Characterization of U.S. cull sows. Iowa State University Animal Industry Report.<br /> <br /> Knauer, M., Stalder, K., Serenius, T., Baas, T., Berger, P., Goodwin, R., and Mabry, J. 2007. Factors associated with sow stayability. Iowa State University Animal Industry Report.<br /> <br /> Lkhagvadorj, S., Qu, L., Cai, W., Couture, O., Wang, Y., Anderson, L., Dekkers, J., Nettleton, D., and Tuggle, C. 2007. Use of transcriptional profiling and assessment of blood parameters to understand biological mechanisms controlling feed intake and efficiency in pigs. Iowa State University Animal Industry Report. A.S. leaflet R2233.<br /> <br /> Lonergan, S., Stalder, K., Huff-Lonergan, E., Knight, T., Goodwin, R., Prusa, K., and Beitz, D. 2007. Influence of Lipid Content on Pork Sensory Quality within pH Classification. Journal of Animal Science, 85: 1074-1079.<br /> <br /> Lunney, J., Bearson, S., Wang, Y., Uthe, J., Qu, L., Couture, O., Zhao, S., Kuhar, D., Nettleton, D., Dekkers, J., and Tuggle, C. 2007. Comparing the porcine response to infection with Salmonella enterica serovars of food safety (Typhimurium) and animal health (Choleraesuis) importance. Proc. International Symposium on Animal Genomics for Animal Health, Paris France.<br /> <br /> Mote, B., Stalder, K., and Rothschild, M. 2007. Candidate genes for sow reproduction and productive life. Proc. Plant and Animal Genome XIV Meeting, San Diego CA.<br /> <br /> Onteru, S., Fan, B., Mote, B., Serenius, T., Nikkilae, M., Stalder, K., and Rothschild, M. 2007. SNP discovery in genes affecting leg health traits in pigs. Proc. International Symposium on Animal Genomics for Animal Health, Paris France.<br /> <br /> Pyiasatian, N., Fernando, R., and Dekkers, J. 2007. Genomic Selection for Marker-Assisted Improvement in Line Crosses. Theoretical Applied Genetics, 115: 665-674.<br /> <br /> Qu, A., Rothschild, M., and Stahl, C. 2007. Effect of Dietary Phosphporus and Its Interaction with Genetic Background on Global Gene Expression in Porcine Muscle. Journal of Animal Breeding and Genetics, 124: 214-224.<br /> <br /> Qu, L., Nettleton, D., and Dekkers, J. 2007. An A-optimal statistical design for post-hybridization washing procedures in Affymetrix microarray experiments. In Proc. Midwest Animal Science Meeting, Des Moines IA.<br /> Ramos, A., Serenius, T., Stalder, K., and Rothschild, M. 2007. Phenotypic Correlations Among Processing Quality Traits of Fresh and Dry-Cured Hams. Meat Science, 77: 182-189.<br /> <br /> Rothschild, M., Hu, Z., and Jiang, Z. 2007. Advances in QTL Mapping in Pigs. International Journal of Biol. Science, 3: 192-197.<br /> Rothschild, M.F. 2007. An update on sequencing the swine genome: Opportunities and Challenges. Proc. of the National Swine Improvement Federation Annual Meeting, Nashville, TN.<br /> <br /> Saxton, A., Stalder, K., and Simpson, R. 2007. Angus cow longevity estimates and relationship to production traits. University of Tennessee Animal Science Report.<br /> <br /> Schinckel, A., Bates, R., See, T., Pfortmiller, R., and Stalder, K. 2007. Capturing genetic gains in productivity with heterosis. Page 14 in the Gene Link. National Swine Registry, West Lafayette IN.<br /> <br /> Schinckel, A., Bates, R., See, T., Pfortmiller, R., and Stalder, K. 2007. Capturing genetic gains in productivity with heterosis. Page 179 in Proc. American Association of Swine Vet. Meeting, Orlando FL.<br /> <br /> Schwab, C., Baas, T., Stalder, K., and Mabry, J. 2007. Deposition Rates and Accretion Patterns of Intramuscular Fat, Loin Muscle Area, and Backfat of Duroc Pigs Sired by Boars from Two Time Periods. Journal of Animal Science, 85: 1540.<br /> <br /> Schwab, C., Mote, B., Rothschild, M., and Baas, T. 2007. Evaluation of Molecular Marker Information to Improve Efficacy of Selection for Iintramuscular Fat via Ultrasound in Duroc Swine. Journal of Animal Science, 85: 64.<br /> <br /> Schwab, C., Mote, B., Rothschild, M., and Baas, T. 2007. Evaluation of molecular marker information on the efficacy of Duroc swine selected for intramuscular fat via ultrasound. Proc. Midwest Animal Science Meeting, Des Moines IA. <br /> <br /> Schwab, C., Tait, R., Jr., and Baas, T. 2007. Genetic Parameter Estimates for Growth, Carcass Composition, and Meat Quality Traits in Duroc swine. Journal of Animal Science, 85: 625.<br /> <br /> Serenius, T., and Stalder, K. 2007. Longevity is Impacted by Farm Management, Leg Conformation, Sows Own Prolificacy, and Sows Origin Parity and Genetics. Animal, 1: 745.<br /> <br /> Serenius, T., Muhonen, P., and Stalder, K. 2007. Economic Values of Pork Production Related Traits in Finland. Agricultural Food Science, 16: 79-88.<br /> <br /> Smith, A., Stalder, K., Serenius, T., Baas, T., and Mabry, J. 2007. Effect of Piglet Birth Weight and Weaning Weight on Weight 42 Days Post-Weaning. Journal of Swine Health Production, 15: 213.<br /> <br /> Stalder, K. 2007. Benchmarking Series - Piglet Survival - A performance indicator. National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. 52(no.5): 40-42.<br /> <br /> Stalder, K. 2007. Breeding herd mortality - have we become complacent? PORK. Vance Publishing Corp., Lenexa, KS 66214 February Issue pp. 20-21.<br /> <br /> Stalder, K. 2007. Parity distribution will affect your bottom line? National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. 52(no.8): 32-33.<br /> <br /> Stalder, K. 2007. The sow stall debate continues. National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. 52(no.11):24-27.<br /> <br /> Stalder, K. J. 2007. Benchmarking Series - How does your farm stack up? National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. 52(no. 2):8-9.<br /> <br /> Stalder, K., Fitzgerald, R., Johnson, A., Karriker, L., and Meisinger, D. 2007. A summary of the 13th Discover Conference on sow productive lifetime. Proc. in 32nd National Swine Improvement Federal Conference Annual Meeting, Kansas City MO.<br /> <br /> Stalder, K., Huff-Lonergan, E., Knight, T., Goodwin, R., Prusa, K., and Beitz, D. 2007. Contributions of pH and intramuscular lipid to sensory quality of fresh pork loin. Iowa State University Animal Industry Report.<br /> <br /> Stalder, K., Karriker, L., Serenius, T., and Knauer, M. 2007. Factors influencing sow longevity. Page 115 in Proc. Iowa Veterinary Medical Association Winter Conference, Ames IA.<br /> <br /> Stalder, K., Karriker, L., Serenius, T., and Knauer, M. 2007. Influencing length of productive life of the sow herd. Reproduction: Optimizing genetics, health and production supplement. Page 13 in Proc. 2007 American Association of Swine Veterinary Annual Conference, Orlando FL.<br /> <br /> Stalder, K., Knauer, M., and Karriker, L. 2007. Are sows being culled for the right reasons? National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. 52(no.4): 26-30.<br /> <br /> Suwansopee, T., Koonawootrittriron, S., Mabry, J., Sopanarat, P., Markvichit, K., and Tumwasorn, S. 2007. Heterosis effect for weaning to estrus interval in a commercial swine population in Thailand. Proc. 45th Kasetsart University Animal Genetics Conference, Thailand.<br /> <br /> Tuggle C., Wang, Y., and Couture, O. 2007. Advances in swine transcriptomics. International Journal of Biological Sciences, 3: 132-152.<br /> <br /> Tuggle, C., Wang, O. P. Couture, L. Qu, J. J. Uthe, D. Kuhar, J. K. Lunney, D. Nettleton, J. C. Dekkers, S. M. D. Bearson. 2007. Bioinformatic integration of structural and functional genomics data across species to develop porcine inflammatory gene regulatory pathway information. 5-7 October 2007. Evanston, IL.<br /> <br /> Tuggle, C., Wang, Y., and Couture, O. (2007). Advances in Swine Transcriptomics. Plant & Animal Genome XV meeting proceedings (abstract W425) (P95). San Diego, CA.<br /> <br /> Tuggle, C., Wang, Y., Couture, O., Qu, L., Uthe, J., Kuhar, D., Lunney, J., Nettleton, D., Dekkers, J., and Bearson, S. 2007. Computational integration of structural and functional genomics data across species to develop porcine inflammatory gene regulatory pathway information. Proc. in Animal Genomics for Animal Health Meeting, Paris France.<br /> <br /> Tuggle, C., Wang, Y., Couture, O., Qu, L., Uthe, J., Kuhar, D., Lunney, J., Nettleton, D., Dekkers, J., and Bearson, S. 2007. Characterizing the porcine transcriptional regulatory response to infection by Salmonella: identifying putative new NFkB direct targets through comparative bioinformatics. Proc. In Genomics for Animal Health: E coli and Salmonella Workshop, Utrecht, The Netherlands.<br /> <br /> Uthe, J., Royaee, A., Lunney, J., Stabel, T., Zhao, S., Tuggle, C., and Bearson, S. 2007. Porcine Differential Gene Expression in Response to Salmonella Enterica Serovars Choleraesuis and Typhimurium. Molecular Immunology, 44: 2900.<br /> <br /> Wang, J., Koehler, K., and Dekkers, J. 2007. Interval Mapping of Quantitative Trait Loci with Selective DNA Pooling Data. Genetics Selection Evolution, 39: 685-709.<br /> <br /> Wang, Y., Qu, L., Uthe, J., Bearson, S., Kuhar, D., Lunney, J., Couture, O., Nettleton, D., Dekkers, J., and Tuggle, C. 2007. Global Transcriptional Response of Porcine Mesenteric Lymph Nodes to Salmonella Enterica Serovar Typhimurium. Genomics, 90: 72-84.<br /> <br /> Wang, Y., Qu, L., Uthe, J., Bearson, S., Kuhar, D., Lunney, J., Couture, O., Nettleton, D., Dekkers, J., and Tuggle, C. 2007. Global Transcriptional Response of Porcine Mesenteric Lymph Nodes to Salmonella enterica serovar Typhimurium. Genomics 90:72-84.<br /> <br /> Yu M., Geiger B., Dee, N., Rothschild, M. 2007. Investigation of TXNIP (Thioredoxin-Interacting Protein) and TRX (Thioredoxin) genes for growth-related traits in pigs. (abstract). Plant and Animal Genome XV Conference, San Diego, CA<br /> <br /> Yu M., Geiger B., Dee, N., Rothschild, M. 2007. Investigation of TXNIP (Thioredoxin-Interacting Protein) and TRX (Thioredoxin) Genes for Growth-Related Traits in Pigs. Mammal Genome, 18: 197.<br /> <br /> Zhang, S., Knight T. J., Stalder K. J., Goodwin R. N., Lonergan S. M., and Beitz D. C., 2007. Effects of breed, gender, and halothane genotype on fatty acid composition and healthfulness of pork longissimus dorsi muscle. J. Anim. Sci. 85:583-591.<br /> <br /> Zhang, W., Carriquiry A., Nettleton D., and Dekkers J.C.M., 2007. Pooling mRNA in microarray experiments and its effect on power. Bioinformatics 23: 1217-1224.<br /> <br /> Zhao, H., Nettleton, D., Dekkers, J.C.M., 2007. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms. Genetical Research. 89 1-6.<br /> <br /> Zhao, H.H., Fernando R.L., and Dekkers J.C.M., 2007. Effects of population structure on power and precision of regression-based linkage disequilibrium mapping of QTL. Midwest Animal Science Meeting, Des Moines.<br /> <br /> Zhao, H.H., Fernando R.L., and Dekkers J.C.M., 2007. Power and precision of alternate methods for linkage disequilibrium mapping of QTL. Genetics: 175: 1975-1986.<br /> <br /> Cassady, JP, JL Cagle, BJ Skelly, KM Youngs, CS Whisnant. 2008. Endocrine response to acute stress in pigs with differing backtest scores. J. Anim. Sci. Suppl. 2.<br /> <br /> J. S. Bates, A. R. Doster, and R. K. Johnson. 2007. Genetic analysis of incidence of porcine circovirus associated disease (PCVAD) in a composite swine population. Abstracts. 2007 ASAS Midwest Meeting, p 14.<br /> <br /> J. S. Bates, A. R. Doster, and R. K. Johnson. 2007. Genetic analysis of incidence of porcine circovirus associated disease (PCVAD) in a composite swine population. Abstracts. 2007 ASAS Midwest Meeting, p 14.<br /> <br /> J. S. Bates, D. B. Petry, J. Eudy , L. Bough , and R. K. Johnson.2008. Differential expression in lung and bronchial lymph node of pigs with high and low responses to infection with Porcine Reproductive and Respiratory Syndrome Virus. J. Anim.Sci. (Submitted)<br /> <br /> J. S. Bates, A. R. Doster, and R. K. Johnson. 2007. Analysis of incidence of Porcine Circovirus Associated Disease (PCVAD) in a landrace/large white composite population. J. Anim. Sci. Vol. 85, Suppl. 1: 627.<br /> <br /> C. Y. Chen, R. K. Johnson, S. D. Kachman, and L. D. Van Vleck. 2007. Effects of competition on expected response to selection for ADG. J. Anim. Sci. Vol. 85, Suppl. 1. : 134.<br /> <br /> Chen, C. Y., R. K. Johnson, S. Newman, and L. D. Van Vleck. 2007. A general review of genetic competition effects with an emphasis on swine breeding. Genetics and Molecular Research 6(3): 594-606.<br /> <br /> D. B. Petry, J. Lunney, P. Boyd, D. Kuhar, E. Blankenship, and R. K. Johnson. 2007. Differential immunity in pigs with high and low responses to porcine reproductive and respiratory syndrome virus (PRRSV) infection. J Anim Sci 2007: jas.2006-721v1.<br /> <br /> T. Serenius, K. J. Stalder, T. J. Baas, J. W. Mabry, R. N. Goodwin, R. K. Johnson, O. W. Robison, M. Tokach, and R. K. Miller . 2007. National Pork Producers Council Maternal Line National Genetic Evaluation Program: A comparison of sow longevity and trait associations with sow longevity. J Anim Sci 2006 84: 2590-2595.<br /> <br /> Lepper, A. N., Zerby, H. N., Moeller, S. J., Brueggemeier, K. M., and Naber, A. C. 2007. Efficacy of blood hemoglobin as an indicator of pork quality. J. Anim. Sci. Vol. 85, Suppl 1. p 491.<br /> <br /> Naber, A. C., Brueggemeier, K. M., Moeller, S. J., Zerby, H. N., and Irvin, K. M. 2007. Response to genetic selection for longissimus color in Landrace swine: Status following two generations of selection. J. Anim. Sci. Vol. 85, Suppl 1. p 478. <br /> <br /> Brueggemeier, K. M., Naber, A. C., Moeller, S. J., and Zerby, H. N. 2007. Comparison of pure Berkshire, Landrace, and the reciprocal crosses at two market endpoints. J. Anim. Sci. Vol. 85, Suppl 1. p 626.<br /> <br /> Wang XX, Chen J, Liu HL, Xu YX, Wang XN, Xue CY, Yu DB, Jiang Z. 2008. The pig p160 co-activator family: full length cDNA cloning, expression and effects on intramuscular fat content in Longissimus Dorsi muscle. Domestic Animal Endocrinology 35: 208  216.<br /> <br /> Chen J, Yang XJ, Xia D, Chen J, Wegner J, Jiang Z, Zhao RQ. 2008. Sterol regulatory element binding transcription factor 1 expression and genetic polymorphism significantly affect intramuscular fat deposition in the longissimus muscle of Erhualian and Sutai pigs. Journal of Animal Science 86:57-63. <br /> <br /> Ando A, Uenishi H, Kawata H, Tanaka M, Shigenari A, Flori L, Chardon P, Lunney JK, Kulski JK, Inoko H. 2008. Microsatellite diversity and crossover regions within homozygous and heterozygous SLA haplotypes of different pig breeds. Immunogenetics. 60: 399-407.<br /> <br /> Butler JE, Lager KM, Spichal I, Francis D, Kacskovics I, Sinkora M, Wertz N, Sun J, Zhao Y, Brown WR, DeWald R, Dierks SE, Muyldermans S, Lunney JK, McCray P, Christenson R, Rogers C, Welsch M, Navarro P, Klobasa F, Ramsoondar J. 2008. The Piglet as a Model for B cell and Immune System Development. Vet. Immunol. Immunopathol. 128: 147-70.<br /> <br /> Ho C-S, Lunney JK, Ando A, Rogel-Gaillard C, Lee J-H, Schook LB, Smith DM. 2008. Nomenclature for factors of the SLA system, update 2008. Tissue Antigens. 73: 307-315.<br /> <br /> Ho C-S, Lunney JK, Franzo-Romain MH, Martens GW, Lee Y-J, Lee J-H, Wysocki M, Rowland RRR, Smith DM. 2009. Molecular characterization of swine leukocyte antigen (SLA) class I genes in outbred pig populations. Animal Genetics. Submitted.<br /> <br /> Lunney JK. 2008. Genetics of Infectious Disease Resistance in Animals. Proceedings American College of Veterinary Pathologists Meeting 2008. p.240-242.<br /> <br /> Steibel JP, Wysocki M, Lunney JK, Ramos AM, Hu Z-L, Rothschild MF, Ernst CW. 2009. Validation of the Swine Protein-Annotated Oligonucleotide Microarray. Animal Genetics. Submitted.<br /> <br /> Wang YF, Couture OP, Qu L, Uthe JJ, Bearson SMD, Kuhar D, Lunney JK, Nettleton D, Dekkers JCM, Tuggle CK. 2008. Analysis of Porcine Transcriptional Response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkB are activated in the Mesenteric Lymph Node. BMC Genomics. 9: 437.<br /> <br /> Wang, Y., Qu, L., Uthe, J., Bearson, S., Kuhar, D., Lunney, J., Couture, O., Nettleton, D., Dekkers, J., and Tuggle, C. 2007. Global Transcriptional Response of Porcine Mesenteric Lymph Nodes to Salmonella enterica serovar Typhimurium. Genomics 90:72-84.<br /> <br /> Tuggle CK, Wang YF, Couture OP, Qu L, Uthe JJ, Kuhar D, Lunney JK, D. Nettleton D, J.C. Dekkers JC, Bearson SMD. 2008. Computational Integration of Structural and Functional Genomics Data across Species to Develop Information on Porcine Inflammatory Gene Regulatory Pathway. Dev Biol (Basel). 132: 105-13. <br /> <br /> Abstracts<br /> Ernst CW, Steibel JP, Ramos AM, Lunney JK, Wysocki M, Petry D, Johnson RK, Fahrenkrug SC, Tempelman RJ, Rothschild MF, Juneja BS, Garbe J, Elsik CG, Bates RO,Helman EE, Blaire L. Varnes BL, Matthew E. Doumit ME. 2008. Assessment of the Swine Protein-Annotated Oligonucleotide Microarray and Utility of the Arrays for eQTL and Transcriptional Profiling Studies. PAG-XVI (W494).<br /> Fritz E, Hu Z, Lunney J, Reecy J. 2008. The PHGC Database: management of large data sets. Intnl PRRS Symp. #324.<br /> Lunney JK. 2008. Genetics of Infectious Disease Resistance in Animals: Pig and PRRS. Proc. Am Coll Vet Pathol. Meeting.<br /> Lunney, J., Bearson, S., Wang, Y., Uthe, J., Qu, L., Couture, O., Zhao, S., Kuhar, D., Nettleton, D., Dekkers, J., and Tuggle, C. 2007. Comparing the porcine response to infection with Salmonella enterica serovars of food safety (Typhimurium) and animal health (Choleraesuis) importance. Proc. International Symposium on Animal Genomics for Animal Health, Paris France.<br /> Lunney JK, Ho C-S, Wysocki M, Smith DM. 2008. Update on SLA genes and their impact on immune and disease interactions. Intnl Society for Animal Genetics (ISAG 2008).<br /> Lunney JK, Wysocki M, Kuhar D, Steibel JP, Ernst CW, McCaw M, Rowland RRR. 2008. Genetic control of swine responses to porcine reproductive and respiratory syndrome virus infection. Intnl Society for Animal Genetics (ISAG 2008).<br /> Lunney JK, Wysocki M, Kuhar D, Steibel JP, Ernst CW, McCaw M, Rowland RRR. 2008. Genetic control of swine responses to porcine reproductive and respiratory syndrome virus infection. EuroPRRSworkshop, Belgium.<br /> Steibel JP, Ramos AM, Tempelman RJ, Bates RO, Wysocki M, Lunney JK, Petry D, Johnson RK, Fahrenkrug SC, Juneja BS, Garbe J, Rothschild MF, Elsik CG, Ernst CW. 2008. Assessment of the Swine Protein-Annotated Oligonucleotide Microarray by Utilizing Designed Control Features Included on the Array. PAG-XVI P732.<br /> Tuggle, C., Wang, O. P. Couture, L. Qu, J. J. Uthe, D. Kuhar, J. K. Lunney, D. Nettleton, J. C. Dekkers, S. M. D. Bearson. 2007. Bioinformatic integration of structural and functional genomics data across species to develop porcine inflammatory gene regulatory pathway information. 5-7 October 2007. Evanston, IL.<br /> Tuggle, C., Wang, Y., Couture, O., Qu, L., Uthe, J., Kuhar, D., Lunney, J., Nettleton, D., Dekkers, J., and Bearson, S. 2007. Computational integration of structural and functional genomics data across species to develop porcine inflammatory gene regulatory pathway information. Proc. in Animal Genomics for Animal Health Meeting, Paris France.<br /> Tuggle, C., Wang, Y., Couture, O., Qu, L., Uthe, J., Kuhar, D., Lunney, J., Nettleton, D., Dekkers, J., and Bearson, S. 2007. Characterizing the porcine transcriptional regulatory response to infection by Salmonella: identifying putative new NFkB direct targets through comparative bioinformatics. Proc. In Genomics for Animal Health: E coli and Salmonella Workshop, Utrecht, The Netherlands.<br /> Tuggle CK, Wang YF, Couture OP, Christian C, Qu L, Uthe JJ, Kuhar D, Lunney J, Nettleton D, Dekkers JCM, Bearson SMD. 2008. Comparative bioinformatic analysis of the transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkB are activated in the porcine mesenteric lymph node. Intnl Symp Animal Functional Genomics, UK.<br /> Tuggle CK, Zhao SH, Qu L, Wang Y, Couture OP, Kuhar D, Lunney JK, Ross JW, Lucy M, Nettleton D, Dekkers JCM, Geisert RD. 2008. Differential Endometrial Transcript Expression Between Yorkshire and the Prolific Meishan Breed of Pigs during the Critical Stage of Conceptus Elongation and Early Attachment. PAG-XVI P730.<br /> Wysocki M, Steibel JP, McCaw M, Kuhar D, Ernst CW, Lunney JK. 2008. Uncovering genetic components involved in early regulatory immune response during PRRSV infection. Intnl PRRS Symp. #285 and CRWAD #125.<br /> <br />

Impact Statements

1. We have identified QTL and candidate genes in different pig resource populations, which will facilitate fine mapping to identify quantitative trait nucleotides controlling growth, carcass composition, meat quality, residual feed intake, reproduction and longevity. Such new information of important genetic variation will be useful in marker-assisted selection for genetic improvement of U.S. swine herds.
2. Long-term selection experiments performed by the research group can lead to substantial advances in production efficiency and product quality, including increased litter size, improved growth rate and feed efficiency, improved product quality, and improved resistance to disease. These will result in the availability of high quality pork at the lowest possible price to the U.S. consumer and for international trade.
3. The working group has assessed and validated the new swine Protein-Annotated Oligonucleotide Microarray, which demonstrates its utility for a variety of porcine tissue types and is useful for other researchers who plan to use the array for their experiments. Such studies will allow other researchers and industry to capitalize on developed information, methods and databases.
4. Utilization of pigs as a model organism might provide new opportunities for alternate uses of swine through a greater understanding of the biological aspects of swine. These opportunities could create new businesses within the U.S. pork sector and increase profit potential for those participating in this unique industry.
5. Understanding the genetic complexity of resistance to disease would provide opportunities to reduce the use of antibiotics or allow for more effective use of antibiotics in swine production. This would likely lead to greater consumer acceptance of pork and improve U.S. pork profit potential by increasing the demand for pork and decreasing expenses associated with unhealthy pigs.

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Report Information

Participants

NC-1037 Members and Associates;
Cathy Ernst MSU;
Chris Tuggle Iowa State University;
Juan P. Steibel MSU;
Joan Lunney USDA-ARS-BARC;
Hongbo Chen USDA-ARS-BARC;
Daniel Ciobanu UNL;
Zhihua Jiang WSU;
Gary Rohrer USMARC;
Bert Stromberg Minnesota;
Jon Beever Illinois;
Max Rothschild Iowa State University;
Jim Reecy Iowa State University;
Jack Dekkers Iowa State University;
Wangshen Liu PSU;
Hongbo Chen USDA-ARS-BARC;
Bin Fan Iowa State University;
Zhiliang Hu Iowa State University;
Dan Nonneman USMARC;
Zengxiang Pan WSU;
Jeff Vallet USMARC;
Melissa Ashwell NC State University;
O Suneel Kumar Iowa State University;
x;
Non-NC-1037 Members;
Elisabetta Giuffra PTP-Lab 1 (Italy);
Armaud Sanchez UAB-Barcelona (Spain);
Xuemei Deng China Agricultural University;
Stephen Tsai University of Alberta;
Gijs van Rooijen Genome Alberta;
Merete Fredholm University of Copenhagen;
Benny Mote Fast Genetics;
Li Zhu Sichuan Agricultural University;
Jun Heon Lee Chungnam National University;
Chankyu Park Konkuk University;
Kyung-Tai Lee National Institute of Animal Science;
Ho Jun choi Konkuk University;
C. Looft University of Bonn;
Bethany Bauer University of Missouri;
Kristin Whitworth University of Missouri;
Ben Cocks Department of Primary Industries, Victoria, Aust.;
Harvey Blackburn NAG-ARS-USDA;
Brian Dalrymple CSIRO Livestock Industries;
Randy Prather University of Missouri;
Bruno Stefanon University Udine, Italy;
Brinda Dass FDA-CVM;
Hirohide Uenishi NIAS (Japan);
Karine Hugot INRA;
A. Mirchef USC Keck Som;
L. Rudenko FDALCRAU;
Shuhong Zhao China;
Christy Gladney PIC;
Claire Rogel-Gaillard INRA-France;
Archie Clutter Newsham Choice Genetics;
Alan Mileham Genus;
Bin Crosby UNW.Windsor;
Benedicte Renaville University of Udine;
Michael Gonda South Dakota State University;
John Williams PTP;
Alan Emsley Gates Foundation;
John Bastiaansen Wageningen, UR;
Hendrik-Jan Megens Wageningen University;
Honghao Li University of Alberta;
Elisa Marques Beefbooster Inc.;

Brief Summary of Minutes

January 9, 2010

8:00 am - 12:00 pm
The morning of January 9 was a joint symposium with NRSP8 cattle/swine Subcommittees. Both Penny Riggs (Texas A&M University) and Cathy Ernst (Michigan State University) presided over the morning session. Four speakers were invited to speak and their topics are listed below.

8:00-8:15 am Penny Riggs (Texas A&M University, riggs@tamu.edu) and Cathy Ernst (Michigan State University, ernstc@msu.edu)
"Introduction"
8:15-9:00 am Erdogan Memili, Mississippi State University (em149@ads.msstate.edu)
"Molecular determinants of fertility in bovine gametes & embryos and regulation of developmental competency"
9:00-9:45 am Martien Groenen, Wageningen University (martien.groenen@wur.nl)
"The Porcine Hapmap Project: Genome-wide assessment of nucleotide diversity, haplotype diversity and footprints of selection in the pig"
9:45-10:15 am "Break"
10:15-11:00 am Chris Tuggle, Iowa State University (cktuggle@iastate.edu)
"Developing predictive models for identifying pigs with superior immune response and improved food safety"
11:00 am - 11:45 pm David Threadgill, NC State (threadgill@ncsu.edu)
"Moving from QTL to systems: the role of genetic interactions in driving phenotypes"

1:30 pm - 6:30 pm
The afternoon of January 9 was a joint workshop with NRSP8 swine Subcommittee. Dr. Cathy Ernst (Michigan State University) presided over the afternoon session. Three people were invited to speak, covering pig models for human disease, eQTL for identification of candidate genes and application of porcine 50KSNP chips. Elisabetta Guiffra, a visiting scientist from Italy also discussed and updated her PRRSv QTL study. The topics are listed below.

1:30-2:00 Melissa Ashwell, North Carolina State University (melissa_ashwell@ncsu.edu)
Chondrocyte gene and protein expression in a porcine osteoarthritis model  Early detection of tissue degenerative factors
2:00-2:30 Juan Steibel, Michigan State University (steibelj@msu.edu)
Genome-wide linkage analysis of gene expression of loin muscle tissue identifies candidate genes in pigs
2:30-3:00 Max Rothschild, Iowa State University (mfrothsc@iastate.edu)
Applications of new porcine genomic tools to trait discovery and understanding genomic architecture
3:00-3:10 Elisabetta Giuffra, Italy
Update on GWAS for PRRS viremia in Italian commercial pigs

3:10-3:45 NC-1037 Planning and Organizing Session
After the talks, there was a break and the meeting then reconvened as the NRSP8/NC-1037 membership group. Initially, there was informal discussion on the level of participation of members of both NRSP8 Swine subcommittee and NC-1037, and what could be done to encourage greater participation from absent members, especially NC-1037 members. There are two general groups of individuals who are members of NC-1037; quantitative geneticists/breeders and genome mappers/molecular geneticists. Attendance at PAG meetings is less attractive to the former group members, who also have a Quantitative Genetics Multi-state project meeting available to them. It was decided that as Georgia had agreed to host the next meeting they would be consulted for methods to improve attendance; one possibility was to have the meeting in conjunction with the National Swine Improvement Federation meeting in December, which usually is held in Tennessee.

3:45-3:55 NRSP-8 Swine Coordination Report
Max Rothschild as NRSP8 Swine Genome Coordinator presented his report and indicated he was asking for community ideas on how to spend support funds for advancing the community, indicating that recently a large amount of such funds had gone to purchase of SNPchips for the PHGC project; Joan Lunney indicated that support was invaluable in developing this important Multi-State project. Max indicated that two projects requesting funds for SNPchips had been brought to his attention, a meat quality project from S. Lonergan at Iowa State and a PCV2 project from Daniel Ciobanu at University of Nebraska-Lincoln. Daniel also introduced himself to the group as a new member and described the project as a collaboration with several faculty members at UNL including Rodger Johnson, as well as Max R. at ISU and Montse Torremorell at University of Minnesota. Subsequent to this discussion, Jack Dekkers indicated he would request funds for maintaining his residual feed intake lines so that members of NRSP8 would have access to these resources, and several members indicated they would request support for pig genome annotation efforts. Please send additional ideas to Max.

3:55-4:05 NRSP-8 Bioinformatics Coordination Report
Jim Reecy provided a report on Bioinformatics coordination team efforts, including several tools of value to the NRSP8/NC-1037 subcommittees, including Animal Trait Ontology, animal QTLdb, genome annotation efforts, and the PHGC database development.

4:05-4:15 NRSP-8/NC-1037 Administrative Reports
Peter Burfening provided information in place of Muquarrab Quereshi (NRSP8 Administrator), indicating that 2009 was a year of significant advancement but also of change much of which was not beneficial as of yet to animals genome research support.

Bert Stromberg (NC-1037 Administrator) indicated that a new project will be due to NIMS in December 2011 to start in October 2012, and that the NC-1037 group should be considering how to both provide evidence of collaboration across stations and what the direction of any renewal should be. He indicated there was concern expressed within Experiment station administration because NC-1037 did not physically meet during the previous year. Joan Lunney asked whether the numerous conference calls to develop and implement the PHGC should be documented as evidence of significant inter-station collaboration. Bert indicated he would check into that. At any rate, the next meeting, to be held after October 1, 2010, should have a major focus on the future and a possible re-write.

4:15-4:25 Harvey Blackburn, National Animal Germplasm Program, DNA Repository Discussion
Harvey Blackburn of the National Animal Germplasm Program provided details on his group and invited scientists to explore storage of genetic material and germplasm there. Such services are free to both send and receive samples.

4:25-4:30 NC-1037 Officer Elections
NC-1037 members unanimously agreed to the following changes in our rotating leadership schedule:
Chair V Chair Sec
2010 R. Rekaya GA Jon Beever IL NC rep
2011 Jon Beever IL NC rep MI rep
2012 NC rep MI rep IA rep

4:30-5:30 NRSP-8 Swine Committee/NC-1037 Station Reports
Additional members then presented updates on their research, including Jack Dekkers at ISU, who discussed his RFI selection lines, Chris Tuggle who discussed the functional genomics and endocrinological analysis of these lines, Jiang Zhihua who discussed two mapping projects on genetic networks for economically important trait and HAAPY mapping with new generation sequencing. Written station reports were received from BARC, Georgia, Iowa, Michigan, Nebraska, Penn State and Washington.

5:30-6:30 Joan Lunney, USDA-BARC, Update on PRRS Host Consortium
Joan Lunney introduced members and updated everyone on currently funded projects (PAG PHGC slide 18) and their current progress in terms of PHGC phenotyping and genotyping. The group further discussed traits that are important to use for GWAS and results of Steibels statistical analyses to identify pigs in high/low (H/L) virus/weight groups. Gene expression plans were also reviewed at the meeting. Several industry representatives were in attendance, including Archie Clutter (Newsham) and Alan Mileham (Genus).

Thanks to Dr. Tuggle for providing materials for preparation of the minutes.

Accomplishments

Objective 1. Further understand the dynamic genetic mechanisms that influence production efficiency and quality of pork.<br /> <br /> Georgia Station worked on identification of genes and pathways that respond to intracerebroventricular injection of melanocortin-4 receptor (MC4R) agonist, NDP-MSH, in pigs homozygous for MC4R, D298 allele (n= 12), N298 allele (n = 12) or heterozygous (n = 12). Although a small number of animals were used in each combination of experimental factors (genotype and treatment), every effort was made to balance the design by assigning animals with similar weight and gender distribution to each group in order to avoid potential confounding with genotype by treatment interaction. A total of 1724, 40 and 2 genotype x treatment interactions were detected for adipose tissue, liver and hypothalamus, respectively. As Nesfatin-1 is a secreted factor and expressed in adipose tissue, the station hypothesized that it plays an important role in regulating feed intake of the pig. To test this hypothesis, the group fitted prepubertal gilts with intracerebroventricular (i.c.v.) cannulas. Cumulative feed intake for each pig was monitored for 48 h following i.c.v. injection of 100 g of either recombinant human leptin or nesfatin-1 in 150 _l of phosphate buffered saline (n = 5 per treatment). Control animals received i.c.v. injection of 150 _l of phosphate buffered saline alone (n = 5). The station found that Nesfatin-1 suppressed (P < 0.01) feed intake for 48 h after i.c.v. injection in an almost identical fashion as leptin. The availability of reliable and inexpensive genotyping platforms for single nucleotide polymorphism (SNP) markers has made the possibility for genomic breeding value estimation in several livestock species a reality. Unfortunately, at around two hundred dollars per animal this technology is still too expensive for its massive use at the commercial level. Currently, this technology is mainly used for genotyping top animals and then used in a two-step procedure for estimating genomic breeding values. For its use at the population level, the SNPs genotypes of non-typed animals have to be inferred somehow from the already genotyped animals and their relationships. Therefore, the station proposed combining genotyping information from high and low density SNP panels with the latter being used for large scale genotyping. This low density and low cost chip will provide an additional source of information, linkage disequilibrium, in inferring genotypes of non-typed animals. The group found that their proposed method is able to increase the accuracy of the estimated breeding values by 6 to 13% depending on the number of SNPs in the low-density panel and the number of genotyped animals.<br /> <br /> A group of researchers at Iowa Station performed a variety of projects in order to improve intramuscular fat, sow longevity, feet and leg soundness, and residual feed intake in pigs. The Station developed methods, models, and software to predict intramuscular fat (IMF) on the live pig using real-time ultrasound, which increased IMF by 2.1% after six generations of experimental selection, with slightly more backfat and slower growth, but little or no effect on other meat quality traits. A new selection line based on an index of composition and meat quality, including IMF, has been initiated. The station continued their research in the sow longevity utilizing a commercial sow population and identified early predictors of longevity (leg score and early reproduction) using commercially available lines. The group reported low heritability estimates for the majority of the feet and leg soundness traits and for other visually evaluated body conformation traits. Using information from the new DNA sequence that is now available, the porcine single nucleotide polymorphism (SNP) 60K chip is being used to examine associations with reproduction, feet and leg soundness and growth and performance traits. These efforts have resulted in several genetic markers that may be useful in the industry in the near future. The station completed a sixth generation selection experiment for residual feed intake and evaluated pigs from the efficient and control lines to get insight into the biological basis of the line differences. Selection for efficiency has resulted in a strong correlated response in serum IGF-1 concentration measured at an early age. The group used the 60k high density array to genotype 750 pigs from these lines and identified several regions with effects on feed intake, growth, backfat, and efficiency. Microarray gene expression profiling in these lines identified several transcription factors that regulate gene expression in back fat and liver tissues, in response to fasting. Genes that are differentially expressed during trophoblastic elongation in porcine embryos were identified. To facilitate integrated analysis of gene expression data, a pig gene expression database (www.anexdb.org) has been developed for the Affymetrix platform and all 1.6 million porcine ESTs were used to create improved annotation of the Affymetrix porcine Genechip.<br /> <br /> Michigan Station focused on four research areas: 1) Assessment of the swine protein-annotated oligonucleotide microarray; 2) Genome-wide expression QTL (eQTL) analysis of loin muscle tissue for identification of candidate genes in pigs, 3) Transcriptional profiling during fetal skeletal muscle development of Piau and commercial pigs, and 4) Factors affecting measures of longevity and stayability in Yorkshire sows. The station evaluated the specificity and utility of the Swine Protein-Annotated Oligonucleotide Microarray, or Pigoligoarray (www.pigoligoarray.org) by profiling the expression of transcripts from four porcine tissues. Of the total 20,400 oligonucleotides on the Pigoligoarray, the group found 12,429 transcripts that were putatively differentially expressed (DE). Analyses for tissue-specific expression [over-expressed in one tissue with respect to all the remaining three tissues (q<0.01)] identified 958 DE transcripts in liver, 726 in muscle, 286 in uterine endothelium and 1027 in brain stem. These hybridization results were confirmed by quantitative PCR (QPCR) expression patterns for a subset of genes after affirming that cDNA and amplified antisense RNA (aRNA) exhibited similar QPCR results. The station performed a first comprehensive genome-wide eQTL scan on loin muscle tissue from 176 F2 Duroc X Pietrain pigs. Based on 124 microsatellite markers and measured transcript abundance of 20,400 oligonucleotides, the group detected 62 unique eQTL, with 40 oligonucleotides physically aligned to the pig genome including 24 that mapped to the chromosome where their linkage peak occurs. In order to identify differentially expressed genes in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation, the group isolated total RNA from fetuses obtained from gilts at each gestational age (n=3 commercial gilts; n=4 Piau gilts) for transcriptional profiling using the Pigoligoarray (www.pigoligoarray.org). Interestingly, the station found that only 226 (24%) of these genes were common to the two breed types, whereas 422 (45%) were preferential to the Piau breed and 270 (29%) were preferential to the commercial pigs. In order to assess the relationship of developmental performance factors with longevity and to determine the genetic variation within six different descriptions of longevity, the Michigan Station collected 14,262 records from Yorkshire females with at least one farrowing record, from both nucleus and multiplication herds across 21 farms. The group found that 1) within a contemporary group, fatter, slower growing gilts had a decreased risk of being culled; 2) sows that had more pigs born alive, fewer stillborn, and heavier litters at weaning in their first litter had a decreased risk of being culled; and 3) sows from nucleus herds experienced a greater risk of being culled. These results indicated that there are early indicators that can be monitored to provide insight to the future productivity or length of productive life of Yorkshire females. Additionally, sufficient genetic variation exists, regardless of definition, to improve sow longevity.<br /> <br /> Nebraska Station also reported their work on sow longevity, but focused on examination whether restricting energy intake during gilts developmental period would increase their longevity and lifetime productivity. Two lines, L45X, a cross of the NE litter selection Line 45, and an industry Large White Landrace cross (LWxLR) were used. Project gilts of both lines were sired by boars of an industry maternal line and thus were half sibs. The lines differed in fertility, litter size, and rate of lean growth and were managed with ad libitum access to feed to breeding age or with 25% restriction of energy from 123 d of age to breeding. The group found that both line and treatment significantly affect the probability that gilts expressed pubertal estrus by 230 d of age; 95% of L45X gilts reached puberty compared with 88% of LW x LR gilts (P = 0.01), and 96% of gilts developed with ad libitum intake reached puberty compared with 86% of gilts developed with energy restriction (P = 0.0001). Overall, energy restriction decreased the proportion of gilts that expressed estrus by 230 d of age and increased the age at puberty. Thereafter, females developed with both regimens had similar reproductive performance at each parity and similar lifetime production. DNA was extracted from tissue of each pig and SNP genotypes using the 60K SNP chip were determined and will be used to identify regions of the genome associated with sow longevity and reproduction traits. <br /> <br /> Penn Station reported development of over 10,000 markers on the pig IMNpRH212,000rad panel to obtain 10,030 mapping vectors, including 2635 MSs, 2530 ESTs, 2759 genes, 2043 BESs and 63 SNPs. The station merged these with ~50% of those markers typed on the IMpRH-7000rad panel to construct parallel framework maps at LOD >=10, thus integrating the porcine genetic-RH-FPC sequence maps and improving the pig-human comparative map. The group observed a ~3.0-fold increase in map resolution in the IMNpRH212,000rad panel over the IMpRH7000rad panel. In addition, Penn Station also built an initial high-resolution comprehensive radiation hybrid (RH) map of the pig chromosome (SSC) 4 that integrates the corresponding RH12,000rad, RH7000rad, genetic, BAC finger-printed contig (FPC) maps, pig RNA-seq data, and a comparative map to human chromosome (HSA) 1 and 8. The map contains 573 markers, including 71 microsatellites (MS), 168 genes and ESTs, and 89 BESs, within three linkage groups. Two linkage groups (62 and 39 markers) cover the entire SSC4p with an accumulated map distance of 1999.7 cR7000 and 3790.8 cR12,000. The other group (227 markers) covers the whole SSC4q with a map distance of 3508.1.8 cR7000 and 7416.5 cR12,000. The group also used transcriptomic data developed from RNA-seq, the NCBI Ssc UniGene (Build 37), and the Sanger gene annotation (September, 2009) within Build 9 of the Sus scrofa genome to identify conserved regions in the human and swine genomes. Approximately 42 million Illumina RNA-Seq reads were aligned to Build 9 of the Sus scrofa genome using GSNAP. RNA-seq contigs were assembled de novo using a hybrid protocol incorporating ABySS-P and PCAP, and previously-unpublished EST data was assembled into contigs using CAP3. The contigs were aligned to the swine and human genomes, integrated into the Alpheus database, and compared in a series of permutations designed to identify regions that were 1) expressed in swine, 2) not present in the porcine UniGene assembly, 3) identified in the human genome, and 4) not currently represented in the annotation of swine genome. <br /> <br /> The major activities at the Washington Station included molecular characterization of adipocytes, association analysis of functional genes and in silico construction of QTLs/candidate gene maps for pork quality. In molecular characterization of adipocytes, the station obtained mature (lipid-filled) pig-derived adipocytes from the perirenal adipose depot after routine slaughter at the Washington State University meats laboratory. The isolated mature adipocytes were purified by using serial differential plating methods to prevent any contamination of mature adipocyte cultures by fibroblast-like cells. At the end of the procedure, clonal mature adipocytes were marked using a fine-tip pen on the bottom of the flask, and photomicrographs of cell transitions were then captured for these marked adipocytes during dedifferentiation. The group observed that clonal cultures of pig-derived mature adipocytes are capable of dedifferentiating and forming proliferative-competent progeny cells in vitro. Mature pig adipocytes extrude lipid before proliferation, whereas beef-derived adipocytes divide without expelling lipid. In collaboration with Dr. Chen at Nanjing Agricultural University and Dr. Liu at Huazhong Agricultural University, China, the group also reported candidate genes for pork quality, such as splicing factor serine-arginine rich protein (SFRS18) for intramuscular fat content and cardiomyopathy associated 1 (CMYA1) for backfat in pigs. Furthermore, the Washington Station pursued an in silico construction of a pork quality QTL/candidate gene map based on the current PigQTLdb. The database contains a total of 1831 QTLs from 113 publications representing 316 different pig traits. Among them, at least 520 significant or suggestive QTLs were identified for 86 traits related to fat deposition and fatty acid composition in pigs, such as abdominal fat, backfat (average) thickness, backfat at shoulder, backfat at first rib, backfat between 3rd and 4th rib, backfat at tenth rib, backfat at last rib, backfat at last lumbar, backfat weight, fat percentage in carcass, intermuscular fat percentage, marbling, fat androstenedione level and fatty acid composition. The group found that these QTLs for fat deposition and composition are not evenly distributed in the porcine genome, ranging from 2 on SSC16 to 68 on SSC7. Among these 14 clusters of traits, 8 are related to backfat measurements. Of them, most QTL data refers to average backfat. Although both marbling and intramuscular fat content measure fat stored in muscle and they are well correlated, their genetic backgrounds are quite different. So far, at least 30 candidate genes have been identified that affect fat deposition in pigs.<br /> <br /> <br /> Objective 2: Discover genetic mechanisms controlling animal health in pork production.<br /> <br /> In collaboration with Kansas Station and Iowa Station, BARC reported progress on the PRRS Host Genomic Consortium (PHGC) to use a nursery pig infection model to determine the role of host genetics in resistance to PRRS and in effects on pig health and related growth effects. Crossbred pigs from high health farms were donated by 4 different commercial sources (PIC/Genus, Newsham, Fast Genetics, Genetiporc). To date 6 trials of 200 have been completed or started. The project uses a Nursery Pig Model to assess pig resistance/ susceptibility to primary PRRSV infection. After acclimation, the pigs were infected with PRRSV and followed for 42 days post infection (dpi). Blood samples were collected at 0,4,7,10,14,21,28,35 and 42 dpi and weekly weights recorded. Results from the first 5 trials of 200 pigs each have affirmed that all pigs become PRRSV infected; some pigs clear virus from serum quicker and weight effects are variable. Multivariate analyses of viral load and weight data have identified PHGC pigs in different virus/weight categories, so that ongoing serum cytokine and gene expression studies can compare data from PRRS resistant/maximal growth pigs to PRRS susceptible/reduced growth pigs. Genomic DNA from PHGC pigs has been prepared. The first 850 samples have been genotyped with the PorcineSNP60 Genotyping BeadChip (containing over 60K single nucleotide polymorphisms or SNPs). The next 450 DNAs will be genotyped in the spring 2010. <br /> <br /> Scientists at Michigan Station and BARC performed analyses to validate the utility of the new Swine Protein-Annotated Oligonucleotide Microarray (www.pigoligoarray.org), a second generation porcine 70-mer oligonucleotide-microarray comprised of 20,400 oligos. BARC and NCSU scientists then used the Pigoligoarray to probe immune regulatory and protective pathways in samples from swine infected with virulent PRRS virus and compare them to samples from vaccinated pigs as part of the national PRRS CAP grant. Animals were divided into groups: pigs infected with 2 different virulent PRRSV isolates, NC Powell and MNW2B and compared to control pigs and pigs vaccinated using a contemporary PRRS ATP vaccine. Tissues [cranial lung, distal lung, tracheobronchial lymph nodes (TBLN) and tonsils] were collected between days 3-6 post infection/vaccination. Total RNA was isolated and labeled using Alexa Fluor® 555 and Alexa Fluor® 647 dyes (Invitrogen). A microarray loop design was applied to compare gene expression between individuals from all three groups and additionally to investigate differences due to day post infection within the PRRSV infected group. Analyzes were carried out using R and SAS software. Results obtained for cranial lung tissues affirmed 923, 619 and 747 putatively differentially expressed genes for vaccinated versus control, vaccinated versus infected, and control versus infected, respectively. As expected, pathways involving interferons and other cytokines, as well as chemokines, have been identified as critical for differentiating infected from vaccinated pigs. More detailed statistical and Ingenuity pathway analyses are underway to identify the biological functions and regulatory pathways that are most significant.<br /> <br /> BARC, ISU and NADC scientists also used real-time expression studies to affirm results using the NRSP8-Qiagen long oligo arrays to determine gene expression in tissues collected from Salmonella enterica serovar Choleraesuis infected porcine lung and lymph nodes. These results demonstrated key genes regulating responses from control, 24 hour (hr), and 48 hr Salmonella enterica serovar Choleraesuis infected porcine lung tissue and implicated NFkB regulated immune pathways. Separate studies are underway with reproductive endothelium tissues from early pregnant and cycling Yorkshire and Meishan gilts using the Affymetrix porcine GeneChipÔ. <br /> <br /> BARC developed a new bead based assay and optimized it with South Dakota Station using the BioRad Bio-Plex (Luminex) platform. This multiplex assay will detect innate inflammatory [interleukin-1beta (IL-1 ²), IL-6, IL-8, interferon-alpha (IFN ±), TNF ±]; regulatory (IL-10), Th1 (IL-12, IFN ³) and Th2 (IL-4) cytokines. A 9-plex cytokine assay has been developed and its use verified comparing cytokine levels in sera from PRRSV vaccinated and challenged pigs. Further evaluation and collaborative utilization of swine cytokine multiplex assays are being targeted including assays for oral fluids and detection of different infectious agents. <br /> <br /> The PRRS Host Genomic Consortium (PHGC) Database was developed by Iowa Station, Kansas Station and BARC scientists to house large amounts of phenotypic and genotypic data that will be collected across several research labs for the PRRS research community. The schema for the database was originally designed based on data sets generated from the PRRS virus Big Pig project. This included data on pig, sex, birth date and infection details, PRRS viral levels in serum over time and tissue levels at kill, anti-PRRSV antibody (ELISA and neutralizing antibody) responses, serum cytokine levels and tissue gene expression results, and SLA alleles. This internet accessible relational database was designed to allow for the addition of new data types as they are generated over the course of the project. This flexibility will allow real-time data updates and sharing among users from geographically different locations. Access to the PHGC database is controlled through a Cooperative Research and Development Agreement (CRADA) Material Transfer Agreement (MTA); the core data is restricted to PHGC members prior to publication.<br /> <br /> Nebraska Station conducted two replications (211 and 220 pigs) of a PRRSV infection experiment. At 34 ± 5 days of age (8.2 ± 1.8 kg body weight), weaned pigs free of PRRSV were transported from their farm of origin to the wean-to-finish barn at the Haskell Agricultural Laboratory and allotted to one of 16 pens. After a 7-day (Rep1) or 19-day (Rep2) adjustment period, pigs were weighed, blood samples were collected, and they were inoculated with PRRSV FL12 (104.8 TCID50/2 mL). Blood was drawn at 4, 7, and 14 d post-inoculation, weight was recorded at 4, 7, 14, and 35 d post-inoculation and every 2-wk after d 35. Blood samples were analyzed for viremia and interleukin 8 (IL8). An index of serum viremia and body weight changes were used to describe response. Levels of IL8 were related to viremia and body weight. The station found that mean viremia for Rep 1 and 2 was similar at 4 d (5.76 and 5.59 viremia, log10) and 7 d (6.15 and 5.67) post-infection, dropped sharply at 14 d in Rep 2 (3.82), but not in Rep 1. Correlations among weights at 0, 4, 7, 14 and 35 d after inoculation with PRRSV, viremia at 4, 7 and 14 d after inoculation, and pre-inoculation levels of IL8 were low. Weight gain from 0 to 4, 4 to 7, 7 to 14, and 14 to 35 d after inoculation, viremia at 4, 7, and 14 d after inoculation, and pre-inoculation levels of IL8 were negatively correlated. Tissue, blood samples, and data from these pigs and from 400 pigs infected in previous experiments will be used for SNP associations studies to identify markers associated with resistance.<br /> <br /> Nebraska Station also examined genetic and environmental variance/co-variances for incidence of Porcine Circovirus Associated Disease (PCVAD) and immune responses to the PCV2 virus. Incidence of PCVAD was recorded in 3,440 pigs, 14.4% showed definitive symptoms, and blood samples at several ages were drawn. Based on these data, additional experiments in which pigs are infected with PCV2 virus were planned. In the first replication of that experiment, 229 weaning age pigs were transported to the wean-to-finish barn at the Haskell Agricultural Laboratory. Serial weights and blood samples were collected through 90 d of age. Pigs were not vaccinated for PRCV2 and came from a herd positive for this virus. Pigs showed symptoms of natural infection at approximately 90 d of age. They were euthanized at approximately 110 d of age and blood, lung, spleen, and lymph tissue was collected. The station found that heritable variation existed for incidence of PCVAD, body weights, PCV2 viremia and PCV2 antibody titers. Incidence of PCVAD was negatively correlated genetically with post-weaning weights and antibody titers, and positively correlated with viremia levels. Post-weaning weight was negatively correlated with viremia and positively correlated with antibody titers, and viremia and antibody titers were negatively correlated. Males had a greater incidence of PCVAD than females (P < 0.001). Additional replications of this experiment are planned for 2010. When sufficient replication occurs, gene expression and SNP association analyses will be performed.

Publications

Georgia Station<br /> <br /> Lkhagvadory, S., Qu, L., Cai, W., Couture, L., Barb, C.R., Hausman, G.J., Rekaya, R., Nettleton, D., Anderson, L., Dekkers, J., Tuggle, C. 2009. Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant. Physiological Genomics. 38(1)98. <br /> Wang Y., R. Rekaya. 2009. A comprehensive analysis of gene expression evolution between humans and mice. Evolutionary bioinformatics online. 5:81-90. <br /> Lkhagvadorj, S., Qu, L., Cai, W., Couture, Barb, C.R., Hausman, G.J., Nettleton, D., Anderson, L., Deckers, J., Tuggle, C. 2009. Leptin mediates discriminate response to feed restriction in feed efficient pigs. Meeting Abstract. <br /> Barb, C.R., Hausman, G.J. 2009. Insulin-like growth factor-I feedback regulation of growth hormone and luteinizing hormone secretion in the pig: Evidence for a pituitary site of action. Animal. v.3 (6) p. 844-849. <br /> Wang, H, R. Rekaya. 2009. Low density SNP chip for non-genotyped animals. J. Anim. Sci. Vol. 87, E-Suppl. 2 p. 125.<br /> <br /> Iowa Station<br /> Alexander, L.S., A. Qu, S.A. Cutler, A. Mahajan, M.F. Rothschild, W. Cai, J.C. Dekkers, and C.H. Stahl. 2009. A calcitonin receptor (CALCR) single nucleotide polymorphism is associated with growth performance and bone integrity in response to dietary phosphorus deficiency. J. Anim. Sci. 2009 Nov 20. [Epub ahead of print].<br /> Boddicker, N., D. Nettleton, N. Gabler, M. Spurlock, and J. C. M. Dekkers. 2009. Performance and carcass composition of pigs selected for residual feed intake on restricted and ad libitum diets. ADSA/ASAS annual meeting. Abstract # 410<br /> Boddicker, N., N. Gabler, M. Spurlock, and J. C. M. Dekkers. 2009. Growth and Efficiency of Pigs Selected for Residual Feed Intake on Restricted and Ad Libitum Diets. Midwest ADSA/ASAS Meeting, Des Moines.<br /> Boddicker, N., N. Gabler, M. Spurlock, D. Nettleton, and J.C.M. Dekkers. 2009. Growth and Efficiency of Pigs Selected for Residual Feed Intake on Restricted and Ad Libitum Diets. A.S. Leaflet R2453. Iowa State Animal Industry Report.<br /> Burkett, J. L., K. J. Stalder, W. J. Powers, J. L. Pierce, T. J. Baas, T. B. Bailey, B. L. Shafer, and K. Bregendahl. 2009. Effect of inorganic and organic trace mineral supplementation on the performance, carcass characteristics, and fecal mineral excretion of phase-fed, grow-finish swine. Aust. J. Anim. Sci.22:1279-1287.<br /> Cai W., H. Wu, and J. C. M. Dekkers. 2009. Longitudinal random regression analysis of growth and feed intake in selection lines for residual feed intake in Yorkshire swine. ADSA/ASAS annual meeting. Abstract # 412.<br /> Cai, C., H. Wu, J. Dekkers, professor of animal science. 2009. Longitudinal Analysis of Body Weight and Feed Intake in Selection Lines for Residual Feed Intake in Pigs. A.S. Leaflet R2394. Iowa State Animal Industry Report.<br /> Cai, W., H. Wu, J. C.M. Dekkers. 2009. Longitudinal Analysis of Body Weight and Feed Intake in Selection Lines for Residual Feed Intake in Pigs. Midwest ADSA/ASAS Meeting, Des Moines.<br /> Christian, C., O. Couture, C. Y. Demirkale, D. Nettleton, J.J. Uthe, S.M.D. Bearson, V. Honavar, C. K. Tuggle. Identification of Common Functions of Differentially Expressed Gene Sets in Porcine Whole Blood in Response to Infection with Salmonella enterica serovar Typhimurium Plant and Animal Genome meeting: January 10-14, 2009, San Diego; abstract #P641; page 120.<br /> Dekkers, J. C. M., H. H. Zhao, D. Habier, and R. L. Fernando. 2009. Opportunities for genomic delection with redesign of breeding programs. ADSA/ASAS annual meeting. Abstract # 275. <br /> Doeschl-Wilson, A.B., I. Kyriazakis, A. Vincent, M.F. Rothschild, E. Thacker, and L. Galina-Pantoja. 2009. Clinical and pathological responses of pigs from two genetically diverse commercial lines to porcine respiratory and reproductive syndrome virus infection. J. Anim. Sci. 87: 1638-1647.<br /> Du, Z.-Q., B. Fan, X. Zhao, R. Amoako, and M.F. Rothschild. 2009. Association analyses between type 2 Diabetes genes and obesity traits in pigs. Obesity 17: 323-329.<br /> Du, Z.-Q., D.M. Gorbach, Z.-L. Hu, and M.F. Rothschild. 2009. Fatness genes and segmental duplications in pigs. Pig Genome III Conference. November 2-4. Hinxton, UK. Abstract No. 8.<br /> Du, Z.-Q., X. Zhao, N. Vukasinovic, F. Rodriguez, A.C. Clutter, and M.F. Rothschild. 2009. Association and haplotype analyses of positional candidate genes in five genomic regions linked to scrotal hernia in commercial pig lines. PLoS one. 4: e4837.<br /> Eisenmann, J.C., M.A. Sarzynski, K. Glenn, M.F. Rothschild, and K.A. Heelan. 2009. ACE I/D genotype, adiposity, and blood pressure in children. Cardiovasc. Diabetol. 8: 14.<br /> Engblom, L., K. Stalder, and J. Mabry, 2009. Save money by keeping sows longer. Benchmark 2008 Summary of the PigCHAMP database. Farms.com Media & PigCHAMP, Ames, IA. 4:26-28.<br /> Fan, B., Onteru, S.K, Garrick, D., Stalder, K.J, and M.F. Rothschild. 2009. A genome-wide association study for pig production and feet and leg structure traits using the PorcineSNP60 BeadChip. Pig Genome III Conference, November 2-4, 2009, Hinxton, Cambridge, UK. Abstract No. 6.<br /> Fan, B., S. Lkhagvadorj, W. Cai, J. Young, R.M. Smith, J.C.M. Dekkers, E. Huff-Lonergan, S.M. Lonergan, and M.F. Rothschild. 2009. Identification of genetic markers associated with residual feed intake and meat quality traits in the pig. Meat Science. (doi:10.1016/j.meatsci.2009.10.025).<br /> Fan, B., S.K. Onteru, B. Mote, T. Serenius, K.J. Stalder, and M.F. Rothschild. 2009. Large-scale association study for structural soundness and leg locomotion traits in the pig. Genet. Sel. Evol. 41: 14.<br /> Fan, B., S.K. Onteru, G.S. Pastow, and M.F. Rothschild. 2009. Detailed characterization of the porcine MC4R gene in relation to fatness and growth. Anim. Genet. 40: 401-409.<br /> Fan, B., S.K. Onteru, K.J. Stalder, and M.F. Rothschild. 2009. Identification of genetic markers associated with fatness and leg weakness traits in the pig. Anim. Genet. 40: 967-970.<br /> Fan, B., S.K. Onteru, M. Nikkilä, K.J. Stalder, and M.F. Rothschild. 2009. Identification of genetic markers associated with sow reproductive traits. Iowa State University Animal Industry Report 2009.<br /> Fan, B., S.K. Onteru, M.T. Nikkilä, K.J. Stalder, and M.F. Rothschild. 2009. Large-scale association studies for reproductive traits in pigs. The International Plant & Animal Genome XVII Conference. January 10-14, 2009. San Diego, California. P535.<br /> Fan, B., S.K. Onteru, M.T. Nikkilä, K.J. Stalder, and M.F. Rothschild. 2009. Identification of genetic markers associated with fatness and leg weakness traits in the pig. Midwestern Section ASAS and Midwest Branch ADSA. March 16-18, Des Moines, Iowa. Abstract No. 32.<br /> Fan, B., S.K. Onteru, M.T. Nikkilä, K.J. Stalder, and M.F. Rothschild. 2009. The COL9A1 gene is associated with longissmus dorsi muscle area in the pig. Anim. Genet. 40: 788.<br /> Fan, B., S.K. Onteru., and M.F. Rothschild 2009. The GGT1 and IGFBP5 genes are associated with fat deposition traits in the pig. Archiv Tierzucht. 52: 337-339.<br /> Fan, B., Z.-Q. Du, and M.F. Rothschild. 2009. The Fat mass and Obesity-Associated (FTO) gene is associated with intramuscular fat content and growth rate in the pig. Anim. Biotechnol. 20: 58-70.<br /> Fitzgerald, R. and K. Stalder. 2009. Reducing transport losses. National Hog Farmer Penton Media, Inc. Minneapolis, MN 55425. 54(no.6):28-30.<br /> Fitzgerald, R. F., K. J. Stalder, J. O. Matthews, C. M. Schultz - Kaster, and A. K. Johnson. 2009. Factors associated with fatigued, injured and dead pig frequency during transport and lairage at a commercial abattoir. J. Anim. Sci. 87:1156-1166.<br /> Fitzgerald, R. F., K. J. Stalder, P. M. Dixon, A. K. Johnson, L. Karriker, and G. F. Jones. 2009. The accuracy and repeatability of sow body condition scoring. Prof. Anim. Sci. 25:415-425.<br /> Garvey, J., A. K. Johnson, L. J. Sadler, K. J. Stalder, and J. McGlone. 2009. Piglet Mortality in an Outdoor Farrowing Hut: What Contributes to their Demise Over the First 72-h After Parturition? Animal Industry Report. Iowa State University, Ames, IA 50011.<br /> Gorbach, D.M., W. Cai, J.C.M. Dekkers, J.M. Young, D.J. Garrick, R.L. Fernando, and M.F. Rothschild. 2009. Whole-genome analyses for genes associated with residual feed intake and related traits utilizing the PorcineSNP60 BeadChip. Pig Genome III Conference. November 2-4. Hinxton, UK. Abstract No. 11.<br /> Gorbach, D.M., W. Cai, J.C.M. Dekkers, J.M. Young, D.J. Garrick, R.L. Fernando, and M.F. Rothschild. 2009. Whole-genome analyses for genes associated with residual feed intake and related traits utilizing the PorcineSNP60 BeadChip. Pig Genome III Conference, United Kingdom.<br /> Guo,Y.M., H.S. Ai, J. Ren, G.J. Wang, Y. Wen, H.R. Mao, L.T. Lan, J.W. Ma, B. Brenig, M.F. Rothschild, C.S. Haley, and L.S. Huang. 2009. A whole genome scan for quantitative trait loci for leg weakness and its related traits in a large F2 intercross population between White Duroc and Erhualian. J. Anim. Sci. 87: 1569-1575.<br /> Ibanez-Escriche, N., R.L. Fernando, A. Toosi, and J.C.M. Dekkers. 2009. Genomic selection of purebreds for crossbred performance. Genet. Select. Evol. 41:12.<br /> Isaacson, B., T. J. Baas, C. R. Schwab, and K. Schulte. 2009. Effect of Extracted Corn Meal from a Fractionation Process on Pig Growth Performance and Carcass Characteristics. Midwest ASAS Meeting, Des Moines, IA.<br /> Jackson, C. J., A. K. Johnson, L. J. Sadler, K. J. Stalder, L. A. Karriker, R. E. Edler, and J. Tyler Holck, 2009. Drinker to Nursery Pig Ratio: Preference for a Drinker Location within a Pen and its Effects on Aggression. Animal Industry Report. Iowa State University, Ames, IA 50011.<br /> Jackson, C. J., L. A. Karriker, K. J. Stalder, and A. K. Johnson. 2009. Number of visits and length of each visit to a nipple cup drinker by 7-week-old pigs after a water deprivation period or ad libitum access to water. J. Swine Health Prod. 17:76-80.<br /> Johnson, A. K., J. McGlone, L. J. Sadler, A. M. Meisberg, and K. J. Stalder. 2009. Risky behaviors performed by the piglet 72 hours after parturition that can contribute to pre-weaning mortality when housed in farrowing huts. Acta Agric. Scand. A Animal Sci. 59:53-58.<br /> Johnson, A. K., L. J. Sadler, K. J. Stalder, and W. Powers. Corn Co-products; How Do They Affect the Behavior of Grow-Finish Swine? Animal Industry Report. Iowa State University, Ames, IA 50011.<br /> Johnson, A. L. Sadler, J. Kline, R. Witte, W. Holt, K. Stalder, L. Layman, L. Karriker, and B. de Rodas. 2009. The Effect of Supplementing Dry Feed with a Nutritional Gel Product at the Time of Vaccination on Nursery Pig Maintenance Behaviors and Postures. Animal Industry Report. Iowa State University, Ames, IA 50011.<br /> Lkhagvadorj, S., L. Qu, W. Cai, O.P. Couture, C.R. Barb, G.J. Hausman, D. Nettleton, L.L. Anderson, J.C.M. Dekkers, C.K. Tuggle. 2009. Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant. Physiological Genomics 38:98-111.<br /> Lkhagvadorj, S., L. Qu, W. Cai, O.P. Couture, C.R. Barb, G.J. Hausman, D. Nettleton, L.L. Anderson, J.C.M. Dekkers, C.K. Tuggle. 2009 Leptin mediates discriminate response to feed restriction in feed efficient pigs. Experimental Biology Meeting.<br /> Mabry, J., K. Stalder, and L. Engblom. 2009. Genetic improvement of farrowing rate in pigs. Benchmark 2008 Summary of the PigCHAMP database. Farms.com Media & PigCHAMP, Ames, IA. 4:34.<br /> Makgahlela, M.L., B. Fan, Z.-Q. Du, and M.F. Rothschild. 2009. Investigation of effects of three candidate genes on leg action and fat deposition traits in pigs. S. Afr. J. Anim. Sci. 39: 127-130.<br /> Mote, B.E., J.W. Mabry, K.J. Stalder, and M.F. Rothschild. 2009. Evaluation of current reasons for removal of sows from commercial farms. The Professional Animal Scientist 25: 1-7.<br /> Mote, B.E., K.J. Koehler, J.W. Mabry, K.J. Stalder, and M.F. Rothschild. 2009. Identification of genetic markers for productive life in commercial sows. J. Anim. Sci. 87: 2187-2195.<br /> Nikkilä, M., K. Stalder, B. Mote, J. Lampe, B. Thorn, M. Rothschild, A. Johnson, L. Karriker, and T. Serenius. 2009. Associations between body and leg structure traits in gilts. Animal Industry Report. Iowa State University, Ames, IA 50011.<br /> Nikkilä, M., K. Stalder, B. Mote, J. Lampe, B. Thorn, M. Rothschild, A. Johnson, L. Karriker, and T. Serenius. 2009. Impact of Gilts Body Composition and Body Structure on Reproductive Performance. Animal Industry Report. Iowa State University, Ames, IA 50011.<br /> Nikkilä, M., K. Stalder, B. Mote, J. Lampe, B. Thorn, M.F. Rothschild, A. Johnson, L. Karriker, and T. Serenius. 2009. Impact of gilts body composition and body structure on reproductive performance. Midwestern Section ASAS and Midwest Branch ADSA. March 16-18, Des Moines, Iowa. Abstract No. 27.<br /> Nikkilä, M., K.J. Stalder, B. Mote., J. Lampe, B. Thorn, M.F. Rothschild and A. Johnson. 2009. Associations between body and leg structure traits in gilts. Iowa State University Animal Industry Report 2009.<br /> Nikkilä, M., K.J. Stalder, B. Mote., J. Lampe, B. Thorn, M.F. Rothschild and A. Johnson. 2009. Impact of gilts body composition and body structure on reproductive performance. Iowa State University Animal Industry Report 2009.<br /> Nikkilae, M., K. Stalder, B. Mote, M. Rothschild, A. Johnson, L. Karriker, T. Serenius, J. Lampe, B. Thorn. 2009. Structural soundness in commercial gilts studied. National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. available at: http://nationalhogfarmer.com/geneticsreproduction/evaluation-selection/structural-soundness-commercial-gilts/?cid=research accessed:March 3, 2009.<br /> Nikkilae, M., K. Stalder, T. Serenius, B. Mote, M. Rothschild, A. Johnson, L. Karriker, and B. Thorn. 2009. Trait interactions offer clues to sow lifetime performance. National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. 54(1):36-38.<br /> Onteru, S.K., B. Fan, and M.F. Rothschild. 2009. The MMP2 gene may be associated with longissimus dorsi muscle area in the pig (Sus scrofa). J. Appl. Genet. 50: 251-252.<br /> Onteru, S.K., B. Fan, D. Garrick, K.J. Stalder, and M.F. Rothschild. 2009. Whole genome analyses for pig reproductive traits using the PorcineSNP60 BeadChip. Pig Genome III Conference. November 2-4, 2009, Hinxton, Cambridge, UK. Abstract No. 5.<br /> Onteru, S.K., J.W. Ross, and M.F. Rothschild. 2009. The role of gene discovery, QTL analyses and gene expression in reproductive traits in the pig. Soc. Reprod. Fertil. Suppl. 66: 87-102.<br /> Opriessnig, T., A.R. Patterson, D.M. Madson, N. Pal, M.F. Rothschild, D. Kuhar, J. Lunney, N.M. Juhan, X.J. Meng, and P.G. Halbur. 2009. Difference in severity of porcine circo virus type 2 induced pathological lesions between Landrace and Pietrain pigs J. Anim. Sci. 87: 1582-1590.<br /> Pyiasatian, N., R.L. Fernando, and J.C.M. Dekkers. 2009. Models for marker-assisted genetic evaluation with multiple QTL in a crossbred population. Livestock Sci. 125: 141-148.<br /> Qiu, H., X. Xu, B. Fan, M.F. Rothschild, Y. Martin, and B. Liu. 2009. Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2. Mol. Biol. Rep. 2009 Oct 16. [Epub ahead of print].<br /> Ramos, A.M., R.H. Pita, M. Malek, P.S. Lopes, S.E.F. Guimarães, and M.F. Rothschild. 2009. Analysis of the mouse high-growth region in pigs. J. Anim. Breed. Genet. 126: 404-412.<br /> Ramos, A.M., R.P. Crooijimans, N.A. Affara, A.J. Amaral, A.L. Archibald, J.E. Beever, C. Bendixen, C. Churcher, R. Clark, P. Dehais, M.S. Hansen, J. Hedegaard, Z.L. Hu, H.H. Kerstens, A.S. Law, H.J. Megens, D. Milan, D.J. Nonneman, G.A. Rohrer, M.F. Rothschild, T.P. Smith, R.D. Schnabel, C.P. Van Tassell, J.F. Taylor, R.T. Wiedmann, L.B. Shook, and M.A. Groenen. 2009. Design of high density SNP genotyping assay in the using SNPs identified and characterized by next generation sequencing technology. PLoS One: e6524.<br /> Ramos, M., J.B. Bastiaansen, and M.F. Rothschild. 2009. Genes located on a SSC17 meat quality QTL region are associated with growth in outbred pig populations. Anim. Genet. 40: 774-778.<br /> Renaville, B., E. Piasentier, M. Vitale, M.F. Rothschild, and A Prandi. 2009. SCD polymorphism affect oleic to stearic acid ratio in San Daniele Ham. The International Plant & Animal Genome XVII Conference. January 10-14, 2009. San Diego, California. P532.<br /> Ross, J.A., M. D. Ashworth, D.R. Stein, O. Couture, C.K. Tuggle, and R. Geisert. 2009. Identification of Differential Gene Expression during Porcine Conceptus Rapid Trophoblastic Elongation and Attachment to the Uterine Luminal Epithelium. Physiological Genomics 36: 140-148.<br /> Rothschild, M.F., D.M. Gorbach, B. Fan, S.K. Onteru, Z.-Q. Du, J.C.M. Dekkers, K. Stalder, D. Garrick, and R. Fernando. 2009. Improving swine genetics using new genotyping technology. National Hog Farmer, December Research Issue.<br /> Sadler, L. J., A. K. Johnson, J. Newton, K. J. Stalder, and J. C. M. Dekkers. 2009. Grow-finish Pigs Activity Levels when Fed Using a Feed Intake Recording Equipment (F.I.R.E.) Feeder. Animal Industry Report. Iowa State University, Ames, IA 50011.<br /> Schwab, C. R., B. E. Mote, Z. Du, R. Amoako, M. F. Rothschild, and T. J. Baas. 2009. An evaluation of four candidate genes for use in selection programs aimed at increased intramuscular fat in Duroc swine. J. Anim. Breed. Genet. 126:228-236.<br /> Schwab, C. R., T. J. Baas, K. J. Stalder, and D. Nettleton. 2009. Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. I. Direct and correlated phenotypic responses to selection. J. Anim. Sci. 87: 2774-2780.<br /> Schwab, C.R., B.E. Mote, Z.-Q. Du, R. Amoako, T.J. Baas, and M.F. Rothschild. 2009. An evaluation of four candidate genes for use in selection programmes aimed at increased intramuscular fat in Duroc swine. J. Anim. Breed. Genet. 126: 228-236.<br /> Sironen, A.I., P. Uimari, T. Serenius, B. Mote, M. Rothschild, and J. Vilkki. 2009. Effect of polymorphisms in candidate genes on reproduction traits in Finnish pig populations. J. Anim. Sci. 2009 Nov 20. [Epub ahead of print].<br /> Smith, R.M., J.M. Young, M.J. Anderson, R.C. Johnson, E. Huff-Lonergan, J. Dekkers, S.M. Lonergan. 2009 Influence of selection for reduced residual feed intake on pork quality. Midwest ADSA/ASAS Meeting, Des Moines.<br /> Smith, R.M., J.M. Young, M.J. Anderson, R.C. Johnson, E. Huff-Lonergan, J. Dekkers, S.M. Lonergan. 2009 Influence of selection for reduced residual feed intake on pork quality. A.S. Leaflet R2447. Iowa State Animal Industry Report.<br /> Stalder, K. J. 2009. Calculating payback parity for replacement gilts. National Hog Farmer. Penton Media, Inc. Minneapolis, MN 55425. 54:18-24.<br /> Stalder, K. J., L. Engblom, and C. Johnson. 2009. Understanding sow lameness. Western Hog Journal. Alberta Pork, Edmonton, Alberta, Canada, 30:38-41<br /> Stalder, K., L. Engblom, and J. Mabry. 2009. Benchmarking sow lifetime productivity. Benchmark 2008 Summary of the PigCHAMP database. Farms.com Media & PigCHAMP, Ames, IA. 4:10-12.<br /> Stalder, K., L. Karriker, A. Johnson, and M. Nikkilä. 2009. Sire impacts on sow longevity in commercial breeding herds. In: Pre-Conference Seminar #10: Boar Studs: Disease updates and tools to reduce cost. Proc. Amer. Assoc. Swine Vet. pp. 9-18.<br /> Steibel, J.P., M. Wysockic, J.K. Lunneyc, A.M. Ramosa, Z.L. Hu, M.F. Rothschild, and C.W. Ernst. 2009. Assessment of the swine protein-annotated oligonucleotide microarray. Anim. Genet. 40: 883-893.<br /> Uthe, J.J., S.M.D. Bearson, J.C. Dekkers, A.M. OConnor, J.D. McKean, K.M. Steffensmeier, and C.K. Tuggle. 2009. Identifying Genetic Polymorphisms Associated with Salmonella Shedding for Improved Food Safety and Porcine Disease Resistance. Plant and Animal Genome, San Diego, January, 2009.<br /> Uthe, J.J., S. M.D.Bearson, J. Dekkers, A. OConnor, J. McKean, K. M. Steffensmeier, C. K. Tuggle. Identifying genetic polymorphisms associated with Salmonella shedding for improved food safety and porcine disease resistance. Plant and Animal Genome meeting: January 10-14, 2009, San Diego; abstract #P168; page 69.<br /> Uthe, J.J., Y. Wang, L. Qu, D. Nettleton, C.K. Tuggle and S.M.D. Bearson 2009. Correlating blood immune parameters and a CCT7 genetic variant with the shedding of Salmonella enterica serovar Typhimurium in swine. Veterinary Microbiology 135:384-388.<br /> Xu, X.L., X.W. Xu, P.W. Pan, K.Li, Z.H. Jiang, M.Yu, M.F. Rothschild, and B. Liu. 2009. Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits. Anim. Genet. 40: 255-261.<br /> Xu, X.W., H.F. Qiu, Z.Q. Du, B. Fan, F. Yuan, M.F. Rothschild, and B. Liu. 2009. Porcine CSRP3: polymorphism and association analyses with meat quality traits and comparative analyses with CSRP1 and CSRP2. Mol. Biol. Rep. (doi 10.1007/s11033-009-9632-1).<br /> Young J. M., W. Cai, and J. C. M. Dekkers. 2009. Effect of selection for residual feed intake on feeding behavior and daily feeding patterns in pigs. ADSA/ASAS annual meeting. Abstract # 411.<br /> Young, J., J. Dekkers, D. Nettleton, and W. Cai.. 2009. Feeding behavior traits in Yorkshires selected for residual feed intake. A.S. Leaflet R2454. Iowa State Animal Industry Report.<br /> Young, J.M., W. Cai, and J.C.M. Dekkers. 2009. Effect of selection for residual feed intake on feeding behavior in pigs. Midwest ADSA/ASAS Meeting, Des Moines.<br /> Zhang, S., T. J. Knight, K. J. Stalder, R. N. Goodwin, S. M. Lonergan, and D. C. Beitz. 2009. Effect of breed, sex, and halothane genotype on fatty acid composition of triacylglycerols and phospholipids in pork longissimus muscle. J. Anim. Breed. Genet. 126:259-268.<br /> Zhao, X., Z.-Q. Du, N. Vukasinovic, F. Rodriguez, A.C. Clutter, and M.F. Rothschild. 2009. Biological candidate gene analyses identify that HOXA10 and MMP2 are associated with scrotal hernias in pigs. Am. J. Vet Res. 70: 1006-1012.<br /> <br /> Michigan Station<br /> Bates, R.O. 2009. Genetic considerations for different sow housing options. J. Anim. Sci. 87: (E-Suppl. 3):63.<br /> Ernst, C.W., J.P. Steibel, G.J.M. Rosa, R.J. Tempelman, R.O. Bates, V.D. Rilington, A. Ragavendran, N.E. Raney, A.M. Ramos, F.F. Cardoso and D.B. Edwards. 2009. Genome-wide expression QTL (eQTL) analysis of loin muscle tissue to identify candidate genes in pigs. J. Anim. Sci. 87(E-Suppl. 2):ii <br /> Schinckel, A., R. Bates, T. See and C. Schwab. 2009. Impact of increased feed costs on the STAGES indexes and selection for terminal sire and maternal lines. Proc. 40th Ann. Mtg. AASV. Dallas, TX.<br /> Sollero, B.P., V.D. Rilington, R.J. Tempelman, S.E.F. Guimaraes, J.D. Guimaraes, M.S. Lopes, N.E. Raney, J.P. Steibel and C.W. Ernst. 2009. Transcriptional profiling during fetal skeletal muscle development of Piau and commercial pigs. J. Anim. Sci. 87(E-Suppl. 2):125-6.<br /> Steibel, J.P., G.J.M. Rosa, R.J. Tempelman, R.O. Bates, V.D. Rilington, A. Ragavendran, N.E. Raney, A.M. Ramos, F.F. Cardoso, D.B. Edwards and C.W. Ernst. 2009. Integration of genomic sequence information, DNA markers and transcript abundance data reveals cis and trans acting eQTL in pigs. Proceedings of the Pig Genome III Conference, Hinxton, UK.<br /> Steibel, J.P., M. Wysocki, J.K. Lunney, A.M. Ramos, Z.-L. Hu, M.F. Rothschild and C.W. Ernst. 2009. Assessment of the swine protein-annotated oligonucleotide microarray. Animal Genetics. 40:883-893.<br /> Straw, B., R. Bates and G. May. 2009. Anatomical abnormalities in a group of finishing pigs: prevalence and pig performance. Swine Health and Prod. 17:28-31.<br /> <br /> Nebraska Station<br /> W. L. Hsu, R. K. Johnson, and L. D. Van Vleck. Effect of Pen mates on Growth, Backfat Depth and Longissimus Muscle Area of Swine. J Anim Sci 2009: jas.2009-1879v1-20091879.<br /> C. Y. Chen, R. K. Johnson, S. Newman, S. D. Kachman, and L. D. Van Vleck. Effects of social interactions on empirical responses to selection for average daily gain of boars. J Anim Sci 2009 87: 844-849.<br /> J. S. Bates, D. B. Petry, J. Eudy, L. Bough, and R. K. Johnson . Differential expression in lung and bronchial lymph node of pigs with high and low responses to infection with porcine reproductive and respiratory syndrome virus. J Anim Sci 2008 86: 3279-3289.<br /> C. Y. Chen, S. D. Kachman, R. K. Johnson, S. Newman, and L. D. Van Vleck. Estimation of genetic parameters for average daily gain using models with competition effects. J Anim Sci 2008 86: 2525-2530.<br /> J. S. Bates, A. R. Doster, R. Moreno, and R. K. Johnson. Genetics and environment affect host immune response in pigs to Porcine Circovirus 2. Submitted to J. Anim. Breed. And Genet.<br /> P. Miller, R. K. Johnson, R. Moreno, M. Anderson, J. Perkins, D. McClure, T. McGargill,. 2009. Effects of nutrition during gilt development on lifetime productivity of sows of two prolific maternal lines: Summary of growth characteristics and sow productivity. NE Swine report EC 219: 18-20.<br /> R. K. Johnson, P. Miller, M. Anderson, J. Perkins, K. Rhynalds, T. Glidden, D. McClure, T. McGargill, D. Barnhill, and R. Moreno. 2009. Effects of nutrition during gilt development and genetic line on farrowing rates through Parity 3, causes of culling, sow weights and backfats through Parity 4, and factors affecting farrowing rates. NE Swine report EC 219: 21-26.<br /> T. Burkey, P. Miller, R. Johnson, d. Reese, and r. Moreno. 2009. Does dam parity affect progeny health status. NE Swine report EC 219: 33-36.<br /> <br /> Penn Station<br /> Ma, J.-G., H. Yasue, K. Eyer, H. Hiraiwa, T. Shimogiri, S.N. Meyers, J.E. Beever, L.B. Schook, C.W. Beattie, and W.-S. Liu. 2009. An integrated RH map of porcine chromosome 10 (SSC10). BMC Genomics 10, 211 doi:10.1186/1471-2164-10-211.<br /> Ma, J.-G., H. Yasue, K. Eyer, H. Hiraiwa, T. Shimogiri, S.N. Meyers, J.E. Beever, L.B. Schook, C.W. Beattie, and W.-S. Liu. 2009. An integrated RH map of porcine chromosome 10 (SSC10). PAG-XVII, San Diego, CA. January 10-14, 2009. p. 538.<br /> Farmer, A.D. Crow, J.A., Retzel, E.F., Liu, W.-S., and Beattie, C. 2009. Can Comparative Genomics Assist in the Improvement of the Swine Genome Map? Proceedings of the Pig Genome III Conference, Hinxton, UK.<br /> W.-S. Liu, H. Yasue, Farmer, A.D. Crow, J.A., Ma, J.-G., K. Eyer, J.E. Beever, L.B. Schook, Retzel, E.F., and C.W. Beattie, 2009. A High Resolution Porcine RH Map with 10,000 Markers. Proceedings of the Pig Genome III Conference, Hinxton, UK.<br /> <br /> Washington Station<br /> Chen J, Guridi M, Fernyhough ME, Jiang Z, Guan LL, Hausman GJ, Dodson MV. 2009. Initial differences in lipid processing leading to pig- and beef-derived mature adipocyte dedifferentiation. Basic and Applied Myology 19:243-246. <br /> Chen J, Guridi M, Fernyhough ME, Jiang Z, Guan LL, Hausman GJ, Dodson MV. 2009. Clonal mature adipocyte production of proliferative-competent daughter cells requires lipid export prior to cell division. International Journal of Stem Cells 2:76-79. <br /> Xu XL, Xu XW, Pan PW, Li K, Jiang Z, Yu M, Rothschild MF, Liu B. 2009. Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits. Animal Genetics 40: 255 - 261.<br /> Wang XX, Xue CY, Wang XN, Liu HL, Xu YX, Zhao RQ, Jiang Z, Dodson MV, Chen J. 2009. Differential display of expressed genes reveals a novel function of SFRS18 in regulation of intramuscular fat deposition. International Journal of Biological Sciences 5: 28 - 33.<br /> Hausman GJ, Dodson MV, Ajuwon K, Azain M, Barnes KM, Guan LL, Jiang Z, Poulos SP, Sainz RD, Smith S, Spurlock M, Novakofski J, Fernyhough ME, Mersmann H. 2009. Board Sponsored Invited Review: Domestic animal carcass composition: The biology and regulation of preadipocytes and adipocytes. Journal of Animal Science 87:1218-1246.<br /> Kunej T, Wu X-L, Michal JJ, Milosevic-Berlic T, Jiang Z, Dovc P. 2009. The porcine mitochondrial transcription factor A gene: molecular characterization, radiation hybrid mapping and genetic diversity among 12 pig breeds. American Journal of Animal and Veterinary Sciences 4: 129-135.

Impact Statements

1. The PRRS Host Genomic Consortium coordinated by BARC is a multi-year project that is funded by a US consortium representing the US National Pork Board (NPB), USDA, universities and private companies; it represents the first-of-its-kind approach to food animal infectious disease research. Overall, the PHGC project will enable researchers to verify important genotypes and phenotypes that predict resistance/ susceptibility to PRRSV infection.
2. The finding on the large number of significant interactions between MSH treatment and MC4R genotype observed at Georgia Station for adipose tissue demonstrates its dynamic and complex role in the regulation of feed intake. Gene expression analysis supports the hypothesis that it is a signal to the central nervous system regarding metabolic state. Results from combining low and high density SNP panels suggest that for some livestock industries, the proposed procedure could offer a practical and cost effective tool for large scale use of genomic information in the genetic evaluation.
3. QTL mapping projects conducted at Iowa Station have led to a better understanding of the genetic basis of economic traits in the pig and in methods that can be used in genetic selection to improve the efficiency and quality of pork production. For example, by using three genetic markers, a farrow-to-finish producer can increase average parities/sow from e.g. 3.4 to 3.5, which increases profit $0.23 for every market hog sold. Likewise, a farrow-to-wean producer can realize a return of $0.13 for every pig sold for the same increase of 0.1 average parities.
4. Assessment and evaluation of the new Swine Protein-Annotated Oligonucleotide Microarray conducted at Michigan Station and BARC demonstrates its utility for a variety of porcine tissue types and is useful for other researchers who plan to use the array for their experiments. Genome-wide expression QTL (eQTL) analysis of loin muscle tissue for identification of candidate genes in pigs performed at Michigan Station represents the first comprehensive genome-wide expression quantitative trait loci (eQTL) study reported for a livestock species.
5. Experiments conducted at Nebraska Station improve our understanding of genetic basis for resistance to two important disease pathogens (PRRSV, and PCV2 virus) and to genetic variation in sow longevity. SNP association analyses applied to data collected in these experiments will identify procedures to enhance genetic selection response for these important economic traits.
6. The high-resolution integrated IMNpRH2-12,000rad and IMpRH-7000rad maps as well as the genetic and BAC FPC maps developed at Penn Station provide an inclusive comparative information/knowledge between pig and human genome (or other mammalian genomes). The maps should be useful for the swine genome sequencing, genome annotation and QTL fine mapping.
7. The cell culture system and results observed at Washington Station suggest that this in vitro system will aid in our understanding of lipid metabolism, regulation of single cells, processes involved in characteristics of putative stem cells residing in adipose tissue. Identification of QTL and QTN for economically important traits will faciliate marker-assisted selection to optimize production, quality, nutritional value and resistance to diseases in pigs.

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