Brief Summary of Minutes of Annual Meeting

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.

Objective 1. Further understand the dynamic genetic mechanisms that influence production efficiency and quality of pork. 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. 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. 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. 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. 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. 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. Objective 2: Discover genetic mechanisms controlling animal health in pork production. 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. 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. 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. 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. 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. 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. 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.

Georgia Station 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. Wang Y., R. Rekaya. 2009. A comprehensive analysis of gene expression evolution between humans and mice. Evolutionary bioinformatics online. 5:81-90. 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. 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. Wang, H, R. Rekaya. 2009. Low density SNP chip for non-genotyped animals. J. Anim. Sci. Vol. 87, E-Suppl. 2 p. 125. Iowa Station 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]. 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 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. Boddicker, N., N. Gabler, M. Spurlock, D. Nettleton, and J.C.M. Dekkers. 2009. 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