Genetic and Functional Genomic Approaches to Improve Production and Quality of Pork

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3510	1080	25%
303	3520	1080	25%
304	3510	1080	25%
304	3520	1080	25%

Progress 10/01/07 to 09/30/12

Outputs
OUTPUTS: The MSU pig resource population, established from 4 F0 Duroc sires and 15 F0 Pietrain dams, was initially genome scanned with 124 microsatellite markers and 510 F2 pigs. Based on this scan, 20 additional markers on 9 chromosomes were genotyped for all 954 F2 pigs and 20 markers used in the first scan were genotyped for 444 additional F2 animals to identify QTL influencing growth, carcass composition and meat quality. Three least-squares Mendelian models were applied to identify QTL segregating between and within parental breeds: a line-cross (LC) model, a half-sib (HS) model, and a combined line-cross and half-sib (CB) model. For growth traits, 26 QTL using the LC model, 12 QTL using the HS model and 3 additional QTL using the CB model were detected (false discovery rate, FDR<5%). For carcass and meat quality traits, 50 QTL using the LC model, 38 QTL using the HS model and 3 additional QTL using the CB model were detected (FDR<5%). Additional marker and animal genotypes increased the power for QTL detection, and applying different analysis models allowed confirmation of QTL and detection of new QTL. Putative QTL regions on 5 chromosomes (SSC3, 6, 12, 15, and 18) were selected for further evaluation in a commercial Duroc population (n = 331). A total of 81 gene-specific single nucleotide polymorphism (SNP) markers were genotyped and 33 were segregating. The MDH1 SNP on SSC3 was associated with 45-min and ultimate pH (pHu), and pH decline. PRKAG3 on SSC15 was associated with pHu. The HSPG2 SNP on SSC6 was associated with marbling score and days to 113 kg. Results in the commercial Duroc population showed a general consistency with genome scan results. An expression QTL (eQTL) study was performed using a whole genome microarray (Pigoligoarray) and the MSU resource population to conduct a global eQTL analysis for loin muscle tissue. Sixty-two unique eQTL (FDR<0.10) were found and 3 gene networks were identified enriched with genes involved in lipid metabolism, DNA replication and cell cycle regulation. Strong evidence of cis regulation was observed and these eQTL were compared to pQTL to help identify potential candidate genes. Thirteen genomic regions had overlapping eQTL and pQTL involving 14 cis-acting eQTL. Results of this analysis provide novel candidate genes for important complex pig phenotypes. The Pigoligoarray was used to examine longissimus dorsi (LD) muscle transcriptional profiles in Piau and Yorkshire-Landrace (YL) crossbred pigs at 40 and 70 d of gestation. A total of 486 oligos were differentially expressed (FC≥1.5; FDR≤0.05) between 40 and 70 d in either YL or Piau pigs, and a total of 1,300 oligos were differentially expressed (FC≥1.5; FDR≤0.05) between YL and Piau pigs at either age. This study revealed both developmental and breed type-specific patterns of gene expression in fetal pig LD muscle. Direct sequencing (RNAseq) was used for transcriptional profiling of pig LD muscle in a cross-platform comparison with the Pigoligoarray. Microarray oligonucleotides were matched to RNAseq tags based on HGNC annotation resulting in 1,410 matching pairs and correlation of log-FC between the technologies was 0.72. PARTICIPANTS: Catherine W. Ernst, Project participant; coordinate project activities and reporting, molecular genetics activities. Ronald O. Bates, Co-project participant; quantitative genetics activities. Juan P. Steibel, Collaborator; statistical genetics. Robert J. Tempelman, Collaborator; statistical genetics. Joan K. Lunney, Collaborator; immunogenetics. Guilherme J.M. Rosa, Collaborator; statistical genetics. Ig Seo Choi, Ph.D. student (completed); QTL mapping. Bruna Sollero, Ph.D. student (completed); muscle transcriptional profiling. Nancy E. Raney, Technician; lab management. Valencia D. Rilington, Technician (completed); transcriptional profiling. Ashok Ragavendran, Ph.D. student (completed); eQTL database development. A. Marcos Ramos, Post-doc (completed); molecular genetics. David B. Edwards, Ph.D. student (completed); QTL mapping. TARGET AUDIENCES: Animal geneticists; Swine producers; Pork consumers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project identified new QTL regions and refined the positions of QTL by using more animal and marker genotypes to increase the power of QTL detection. In addition, this project represents the first comprehensive genome-wide expression quantitative trait loci (eQTL) study reported for a livestock species in the US. This work integrated gene expression profiles with genetic marker and phenotypic data to identify genes controlling economically important traits in pigs. Experimentally identified genomic regions were also evaluated in a commercial population in order to determine if variation in these regions is segregating in an industry population and to facilitate their incorporation into swine genetic improvement programs. In addition, comparison analysis between RNAseq and microarray data using the same biological samples demonstrated good agreement between the technologies supporting both techniques as reliable, and that RNAseq may complement and extend microarray studies.

Publications

Badke, Y.M., Bates, R.O., Ernst, C.W., Schwab, C. and Steibel, J.P. 2012. Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics. 13:24.
Badke, Y.M., Bates, R.O., Ernst, C.W. and Steibel, J.P. 2012. Comparison of three methods for tagSNP selection. J. Anim. Sci. 90(E-Suppl. 2):22.
Bates, R.O., Doumit, M.E., Raney, N.E., Helman, E.E. and Ernst, C.W. 2012. Association of halothane sensitivity with growth, carcass merit and meat quality. Animal. 6:1537-1542.
Choi, I., Bates, R.O., Raney, N.E., Steibel, J.P. and Ernst, C.W. 2012. Evaluation of QTL for carcass merit and meat quality traits in a US commercial Duroc population. Meat Sci. 92:132-138.
Choi, I., Steibel, J.P., Bates, R.O., Raney, N.E. and Ernst, C.W. 2012. Identification and evaluation of quantitative trait loci influencing carcass composition and meat quality traits in pigs. Plant and Animal Genome XX Conference. San Diego, CA. http://pag.confex.com/pag/xx/webprogram/Paper3042.html.
Choi, I., Steibel, J.P., Bates, R.O., Raney, N.E. and Ernst, C.W. 2012. Identification and evaluation of quantitative trait loci influencing growth, carcass composition, and meat quality traits in pigs. J. Anim. Sci. 90(E-Suppl. 2):22.
Gualdron Duarte, J.L., Bates, R.O., Ernst, C.W., Raney, N.E., Cantet, R.J.C. and Steibel, J.P. 2012. Genotype imputation accuracy in an F2 pig cross using high-density and low-density SNP panels. J. Anim. Sci. 90(E-Suppl. 3):527.

Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: The MSU pig resource population, established from 4 F0 Duroc sires and 15 F0 Pietrain dams, was initially genome scanned with 124 microsatellite markers and 510 F2 animals. Based on this scan, 20 additional markers on 9 chromosomes were genotyped for all 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals to identify QTL influencing carcass composition and meat quality. Three least-squares Mendelian models for QTL analysis were applied to identify QTL segregating between and within parental breeds: a line-cross (LC) model, a half-sib (HS) model, and a combined line-cross and half-sib (CB) model. Fifty QTL using the LC model, 38 QTL using the HS model and 3 additional QTL using the CB model were detected with a 5% false discovery rate (FDR). The LC and HS models revealed strong evidence for QTL regions on SSC6 for carcass traits (e.g. 10th-rib BF; FDR < 0.0001) and on SSC15 for meat quality traits (e.g. color, pH; FDR < 0.01), respectively. QTL for pH (SSC3), dressing percent (SSC7), marbling score and moisture percent (SSC12), CIE a* (SSC16) and carcass length (SSC18) were also significant (FDR < 0.01). Additional marker and animal genotypes increased the statistical power for QTL detection, and applying different analysis models allowed confirmation of QTL and detection of new QTL. Putative QTL regions on 5 chromosomes (SSC3, 6, 12, 15, and 18) were selected for further evaluation in a commercial Duroc population (n = 331). A total of 81 gene-specific single nucleotide polymorphism (SNP) markers were genotyped and 33 were segregating. The MDH1 SNP on SSC3 was associated with 45-min and ultimate pH (pHu), and pH decline. PRKAG3 on SSC15 was associated with pHu. The HSPG2 SNP on SSC6 was associated with marbling score and days to 113 kg. Markers for NUP88 and FKBP10 on SSC12 were associated with 45-min pH and L*, respectively. The SSC15 marker SF3B1 was associated with L* and LMA, and the SSC18 marker ARF5 was associated with pHu and color score. These results in a commercial Duroc population showed a general consistency with genome scan results. An expression QTL (eQTL) study was published in 2011 which utilized a whole genome microarray and the MSU resource population to conduct a global eQTL analysis for loin muscle tissue. Sixty-two unique eQTL (FDR<0.10) were found and 3 gene networks were identified enriched with genes subject to genetic control involved in lipid metabolism, DNA replication and cell cycle regulation. Strong evidence of cis regulation was observed (40 out of 59 eQTL with known genomic position) and these eQTL were compared to pQTL to help identify potential candidate genes. Thirteen genomic regions had overlapping eQTL and pQTL involving 14 cis-acting eQTL. Results of this analysis provide novel candidate genes for important complex pig phenotypes. Also in 2011, direct sequencing (RNAseq) was used for transcriptional profiling of pig skeletal muscle in a cross-platform comparison with the Pigoligoarray. Microarray oligonucleotides were matched to RNAseq tags based on HGNC annotation resulting in 1,410 matching pairs and correlation of log-FC between the technologies was 0.72. PARTICIPANTS: Catherine W. Ernst, Project participant; coordinate project activities and reporting, molecular genetics activities. Ronald O. Bates, Co-project participant; quantitative genetics activities. Juan P. Steibel, Collaborator; statistical genetics. Robert J. Tempelman, Collaborator; statistical genetics. Joan K. Lunney, Collaborator; immunogenetics. Guilherme J.M. Rosa, Collaborator; statistical genetics. Ig Seo Choi, Ph.D. student (completed); QTL mapping. Bruna Sollero, Ph.D. student (completed); muscle transcriptional profiling. Nancy E. Raney, Technician; lab management. Valencia D. Rilington, Technician (completed); transcriptional profiling. Ashok Ragavendran, Ph.D. student (completed); eQTL database development. A. Marcos Ramos, Post-doc (completed); molecular genetics. David B. Edwards, Ph.D. student (completed); QTL mapping. TARGET AUDIENCES: Animal geneticists; Swine producers; Pork consumers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project identifies new QTL regions and refines the positions of QTL by using more animal and marker genotypes to increase the power of QTL detection. In addition, this project represents the first comprehensive genome-wide expression quantitative trait loci (eQTL) study reported for a livestock species in the US. This work integrates gene expression profiles with genetic marker and phenotypic data to identify genes controlling economically important traits in pigs. Experimentally identified genomic regions were also evaluated in a commercial population in order to determine if variation in these regions is segregating in an industry population and to facilitate their incorporation into swine genetic improvement programs. In addition, comparison analysis between RNAseq and microarray data using the same biological samples demonstrated good agreement between the technologies supporting both techniques as reliable, and that RNAseq may complement and extend microarray studies.

Publications

Bates, R.O., Edwards, D.B., Ernst, C.W., Doumit, M.E. and Hoge, M.D. 2011. Influence of finishing environment on pig growth performance and carcass merit. J. Swine Health Prod. 19:86-93.
Choi, I., Steibel, J.P., Bates, R.O., Raney, N.E., Rumph, J.M. and Ernst, C.W. 2011. Identification of carcass and meat quality QTL in an F2 Duroc x Pietrain pig resource population using different least-squares analysis models. Frontiers in Genetics (Livestock Genomics). 2:18.
Ernst, C.W., Steibel, J.P., Sollero, B.P., Strasburg, G.M., Guimaraes, S.E.F. and Raney, N.E. 2011. Transcriptional profiling during pig fetal skeletal muscle development using direct high-throughput sequencing and cross-platform comparison with gene expression microarrays. J. Anim. Sci. 89(E-Suppl. 1):ii.
Sollero, B.P., Guimaraes, S.E.F., Rilington, V.D., Tempelman, R.J., Raney, N.E., Steibel, J.P., Guimaraes, J.D., Lopes, P.S., Lopes, M.S. and Ernst, C.W. 2011. Transcriptional profiling during foetal skeletal muscle development of Piau and Yorkshire-Landrace crossbred pigs. Anim. Genet. 42:600-612.
Steibel, J.P., Bates, R.O., Rosa, G.J.M., Tempelman, R.J., Rilington, V.D., Ragavendran, A., Raney, N.E., Ramos, A.M., Cardoso, F.F., Edwards, D.B. and Ernst, C.W. 2011. Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PLoS ONE. 6:e16766.

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: The MSU pig resource population, established from 4 F0 Duroc sires and 15 F0 Pietrain dams, was initially genome scanned with 124 microsatellite markers and 510 F2 animals. Based on this scan, 20 additional markers on 9 chromosomes were genotyped for all 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals to identify QTL influencing growth, carcass composition and meat quality. Three least-squares Mendelian models for QTL analysis were applied to identify QTL segregating between and within parental breeds: a line-cross (LC) model, a half-sib (HS) model, and a combined line-cross and half-sib (CB) model. For growth traits, 26 QTL using the LC model, 12 QTL using the HS model and 3 additional QTL using the CB model were detected with a 5% false discovery rate (FDR). In the LC analysis, highly significant QTL for fat deposition were detected on SSC6. In the HS analysis, a QTL for loin muscle area at 19-wk of age was detected on SSC7 and QTL for 10th-rib backfat at 19- and 22-wk of age were detected on SSC15 (FDR<0.01). For carcass and meat quality traits, 51 QTL using the LC model, 38 QTL using the HS model and 3 additional QTL using the CB model were identified (FDR<0.05). In the LC analysis, highly significant QTL were revealed for backfat thickness traits on SSC6 including 10th rib backfat (FDR < 0.0001), and in the HS analysis QTL influencing carcass composition and meat quality were revealed on SSC15 including protein percentage (FDR < 0.0001). Additional markers and animals contributed to reduce the confidence intervals and increase the test statistics for QTL detection. Different models allowed detection of new QTL which indicated differing frequencies for alternative alleles in parental breeds. A whole genome microarray was used to examine longissimus dorsi (LD) muscle transcriptional profiles in Piau and Yorkshire-Landrace (YL) crossbred pigs at 40 and 70 d of gestation. A total of 486 oligonucleotides were differentially expressed (FC≥1.5; FDR≤0.05) between 40 and 70 d in either YL or Piau pigs, and a total of 1,300 oligonucleotides were differentially expressed (FC≥1.5; FDR≤0.05) between YL and Piau pigs at either age. This study revealed both developmental and breed type-specific patterns of gene expression in fetal pig skeletal muscle including genes not previously associated with myogenesis. Also in 2010, an expression QTL (eQTL) study was completed which utilized a whole genome microarray and the MSU resource population to conduct a global eQTL analysis for loin muscle tissue. Sixty-two unique eQTL (FDR<0.10) were found and 3 gene networks were identified enriched with genes subject to genetic control involved in lipid metabolism, DNA replication and cell cycle regulation. Strong evidence of cis regulation was observed (40 out of 59 eQTL with known genomic position) and these eQTL were compared to pQTL to help identify potential candidate genes. Thirteen genomic regions had overlapping eQTL and pQTL involving 14 cis-acting eQTL. Results of this analysis provide novel candidate genes for important complex pig phenotypes. PARTICIPANTS: Catherine W. Ernst, Project participant; coordinate project activities and reporting, molecular genetics activities. Ronald O. Bates, Co-project participant; quantitative genetics activities. Juan P. Steibel, Collaborator; statistical genetics. Robert J. Tempelman, Collaborator; statistical genetics. Joan K. Lunney, Collaborator; immunogenetics. Guilherme J.M. Rosa, Collaborator; statistical genetics. Ig Seo Choi, Ph.D. student; QTL mapping. Bruna Sollero, Ph.D. student (completed); muscle transcriptional profiling. Nancy E. Raney, Technician; lab management. Valencia D. Rilington, Technician (completed); transcriptional profiling. Ashok Ragavendran, Ph.D. student (completed); eQTL database development. A. Marcos Ramos, Post-doc (completed); molecular genetics. David B. Edwards, Ph.D. student (completed); QTL mapping. TARGET AUDIENCES: Animal geneticists; Swine producers; Pork consumers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project identifies new QTL regions and refines the positions of QTL by using more animal and marker genotypes to increase the power of QTL detection. In addition, this project represents the first comprehensive genome-wide expression quantitative trait loci (eQTL) study reported for a livestock species. This work integrates gene expression profiles with genetic marker and phenotypic data to identify genes controlling economically important traits in pigs. Experimentally derived genetic markers will be evaluated in commercial populations in order to facilitate their incorporation into swine genetic improvement programs. This project also provides fundamental knowledge regarding gene expression profiles associated with cellular events that are critical for myogenesis and muscle growth.

Publications

Steibel, J.P., Rosa, G.J.M., Tempelman, R.J., Bates, R.O., Rilington, V.D., Ragavendran, A., Raney, N.E., Ramos, A.M., Cardoso, F.F., Edwards, D.B. and Ernst, C.W. 2010. Genome-wide linkage analysis of gene expression of loin muscle tissue identifies candidate genes in pigs. http://intl-pag.org/18/abstracts/W86_PAGXVIII_613.html.
Choi, I., Steibel, J.P., Bates, R.O., Raney, N.E., Rumph, J.M. and Ernst, C.W. 2010. Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population. BMC Genetics. 11:97.
Dawes, M.J., Bates, R.O., Raney, N.E., Steibel, J.P. and Ernst, C.W. 2010. Evaluation of single nucleotide polymorphism markers on pig chromosomes 3 and 6 for potential associations with meat quality traits. J. Anim. Sci. 88(E-Suppl. 3):143-4.
Ernst, C.W., Steibel, J.P., Rosa, G.J.M., Tempelman, R.J., Bates, R.O., Rilington, V.D., Ragavendran, A., Raney, N.E., Ramos, A.M., Cardoso, F.F. and Edwards, D.B. 2010. Genome-wide expression QTL (eQTL) analysis of loin muscle tissue identifies candidate genes in pigs. http://intl-pag.org/18/abstracts /P07b_PAGXVIII_788.html.

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: Integration of transcriptional profiling with genome scans using DNA markers to identify chromosomal regions controlling variation in important phenotypes is referred to as expression quantitative trait loci (eQTL) analysis and enhances candidate gene discovery for complex traits. Our objective was to conduct an eQTL analysis of loin muscle tissue from F2 pigs in our Duroc X Pietrain resource population. Pigs from the F2 generation have previously been evaluated to discover QTL affecting growth, composition and meat quality traits. The Pigoligoarray (www.pigoligoarray.org) has been validated and used for transcriptional profiling of skeletal muscle samples for a subset of 176 F2 pigs. Subcutaneous fat tissue samples are also being evaluated in a similar analysis. The QTL models used for crosses between outbred populations included fixed effects of sex, dye and QTL, and random effects of array and litter. Nominal p-values were corrected for multiple tests using false discovery rate (FDR). To rapidly screen over 20,000 QTL profiles in the eQTL scan, peaks of LOD-score functions for each expression trait in each chromosome were selected using FDR < 0.1, leaving 975 tests of which 62 were unique peaks (highest peak in a LOD-score function for a transcript within a chromosome). Physical localization to the pig genome sequence assembly was determined for 40 oligos. Comparing the positions of putative eQTL with 173 putative growth and carcass trait QTL (tQTL) revealed 11 common linkage regions between tQTL and eQTL. Of these, 7 regions involved putative cis-acting eQTL for 8 oligos that provide strong positional candidates for tQTL. For example, a tQTL for LMA on SSC1 is located in the same marker interval as an eQTL for the gene dynein light chain. This study demonstrates the power of integrating genetic markers, phenotypes, transcript profiles, comparative human gene annotation and the pig genome sequence assembly for identifying candidate genes controlling economically important complex traits. We have also used the Pigoligoarray to identify differentially expressed genes in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. A total of 937 unique genes with Human Gene Nomenclature (HGNC) annotation were differentially expressed (FDR < 0.05) between 40 and 70 d gestation in either commercial or Piau pigs. Interestingly, 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. The remaining 19 genes (2%) had multiple oligos on the array for which different oligos were differentially expressed in each breed. This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types. PARTICIPANTS: Catherine W. Ernst, Project participant; coordinate project activities and reporting, molecular genetics activities. Ronald O. Bates, Co-project participant; quantitative genetics activities. Juan P. Steibel, Collaborator; statistical genetics. Robert J. Tempelman, Collaborator; statistical genetics. Joan K. Lunney, Collaborator; immunogenetics. Guilherme J.M. Rosa, Collaborator; statistical genetics. Ig Seo Choi, Ph.D. student; QTL mapping. Bruna Sollero, Ph.D. student; muscle transcriptional profiling. Nancy E. Raney, Technician; lab management. Valencia D. Rilington, Technician (completed); transcriptional profiling. Ashok Ragavendran, Ph.D. student (completed); eQTL database development. A. Marcos Ramos, Post-doc (completed); molecular genetics. David B. Edwards, Ph.D. student (completed); QTL mapping. TARGET AUDIENCES: Animal geneticists; Swine producers; Pork consumers PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
This project represents the first comprehensive genome-wide expression quantitative trait loci (eQTL) study reported for a livestock species. This project integrates gene expression profiles with genetic marker and phenotypic data to identify genes controlling economically important traits in pigs. Experimentally derived genetic markers will be evaluated in commercial populations in order to facilitate their incorporation into swine genetic improvement programs. This project also provides fundamental knowledge regarding gene expression profiles associated with cellular events that are critical for myogenesis and muscle growth.

Publications

Ernst, C.W., Steibel, J.P., Rosa, G.J.M., Tempelman, R.J., Bates, R.O., Rilington, V.D., Ragavendran, A., Raney, N.E., Ramos, A.M., Cardoso, F.F., and Edwards, D.B. 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
Sollero, B.P., Rilington, V.D., Tempelman, R.J., Guimaraes, S.E.F., Guimaraes, J.D., Lopes, M.S., Raney, N.E., Steibel, J.P., and Ernst, C.W. 2009. Transcriptional profiling during fetal skeletal muscle development of Piau and commercial pigs. J. Anim. Sci. 87(E-Suppl. 2):125-6.
Steibel, J.P., Rosa, G.J.M., Tempelman, R.J., Bates, R.O., Rilington, V.D., Ragavendran, A., Raney, N.E., Ramos, A.M., Cardoso, F.F., Edwards, D.B., and Ernst, C.W. 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.
Steibel, J.P., Wysocki, M., Lunney, J.K., Ramos, A.M., Hu, Z.-L., Rothschild, M.F., and Ernst, C.W. 2009. Assessment of the swine protein-annotated oligonucleotide microarray. Animal Genetics. 40:883-893.

Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: We have previously reported quantitative trait loci (QTL) affecting carcass composition and pork quality on pig chromosome 6 (SSC6) in the MSU Duroc x Pietrain F2 resource population. We aimed to confirm these QTL by incorporating marker genotype data for an additional 452 F2 pigs into the QTL analysis, thus improving the QTL detection power by nearly doubling the number of informative meioses. 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 1% chromosome-wise level were found for first rib, tenth rib, last rib and last lumbar vertebra backfat, and for hot carcass weight, carcass length, loin muscle area, ham weight, loin weight and belly weight. 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). In addition, F-ratios and LOD scores were increased for all traits except marbling score. However, three previously identified QTL failed to reach significance (subjective color score, CIE a* and spareribs weight). The incorporation of additional F2 animal genotypes into the QTL analysis helped to improve the power and precision of QTL detection and our results confirm QTL for carcass composition and pork quality on SSC6 in the MSU resource population. Also during 2008, the specificity and utility of the Swine Protein-Annotated Oligonucleotide Microarray, or Pigoligoarray (www.pigoligoarray.org), was evaluated by profiling the expression of transcripts from four porcine tissues. Tools for comparative analyses of expression on the Pigoligoarray were developed including HGNC identities and comparative mapping alignments with human orthologs. Hybridization results based on sets of control, perfect match (PM) and deliberate mismatch (MM) probes provide an important means for assessing non-specific hybridization. Samples of RNA from liver, brain stem, longissimus muscle and uterine endothelium from four pigs were prepared and hybridized to the arrays. Of the total 20,400 oligonucleotides on the Pigoligoarray 12,429 transcripts 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. Comparison to human ortholog expression confirmed the value of this array for experiments of both agricultural importance and for tests using pigs as a biomedical model for human disease. We are continuing to use the Pigoligoarray for transcript profiling of skeletal muscle in an expression QTL (eQTL) analysis of our Duroc x Pietrain resource population. PARTICIPANTS: Catherine W. Ernst, Project participant; coordinate project activities and reporting, molecular genetics activities. Ronald O. Bates, Co-project participant; quantitative genetics activities. Juan P. Steibel, Collaborator; statistical genetics. Joan K. Lunney, Collaborator; immunogenetics. Ig Seo Choi, Ph.D. student; QTL mapping. Nancy E. Raney, Technician; lab management. Valencia D. Rilington, Technician; transcriptional profiling. A. Marcos Ramos, Post-doc (completed); molecular genetics. David B. Edwards, Ph.D. student (completed); QTL mapping. TARGET AUDIENCES: Animal geneticists; Swine producers; Pork consumers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Evaluation and validation of the Swine Protein Annotated Oligonucleotide Microarray demonstrates the utility of the arrays for transcriptional profiling studies and the application of the designed control features on the arrays. Identification of QTL and evaluation of candidate genes in a unique pig resource population will facilitate identification of genes controlling growth, carcass composition and meat quality. These genes can then be incorporated into marker-assisted selection programs to accelerate genetic improvement in pig populations.

Publications

Choi, I.S., R.O. Bates, N.E. Raney, D.B. Edwards, M.E. Doumit and C.W. Ernst. 2008. Confirmation of quantitative trait loci for carcass and meat quality traits on pig chromosome 6 in a Duroc x Pietrain resource population. National ASAS/ADSA Annual Meeting, Indianapolis, IN, July 2008.
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.
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.
Ernst, C.W. and A.M. Ramos. 2008. Pig. In C. Kole and N.E. Cockett (eds), Genome Mapping and Genomics in Domestic Animals. Springer-Verlag, Berlin, Heidelberg, New York.
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.
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. Invited.
Martinez-Montemayor, M.M., G.M. Hill, N.E. Raney, V.D. Rilington, R.J. Tempelman, J.E. Link, C.P. Wilkinson and C.W. Ernst. 2008. Gene expression profiling in hepatic tissue of newly weaned pigs fed pharmacological zinc and phytase supplemented diets. BMC Genomics. 9:421.
Prasongsook, S., R.O. Bates, I.S. Choi, V.D. Rilington, N.E. Raney, C.C. Beattie, M.E. Doumit and C.W. Ernst. 2008. Association of insulin-like growth factor binding protein 2 genotypes with growth, carcass and meat quality traits in pigs. J. Anim. Sci. 86(ESuppl. 3):Sec. 2 p. 51.
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.
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