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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE EFFICIENCY OF SWINE PRODUCTION AND PRODUCT QUALITY
2011 Annual Report


1a.Objectives (from AD-416)
Objective 1: Develop genetic tests which can be used as tools to improve selection in commercial swine populations for important production traits.

Objective 2: Determine interactions among traits, parental origin of alleles, loci and/or environment to better understand the basis of genetic correlations, inheritance of complex traits and to more accurately formulate selection plans in swine.

Objective 3: Utilize the knowledge gained from objective 2 and from USMARC collaborators in conjunction with the swine genome sequence to identify the causative genes underlying QTL.


1b.Approach (from AD-416)
The goal of this research is to ensure US swine producers are a competitive source of pork products by providing the genetic information necessary to maintain superior production levels. The approach will use genetic markers and genomic technologies to understand how the genome regulates animal performance and determine the molecular basis behind non-additive genetic effects. Availability of the draft swine genome sequence will allow continuation of research on genomic regions affecting components of reproductive performance, growth, and carcass quality to move faster and more efficiently. Future studies will include a broader list of phenotypes including metabolic parameters to understand nutrient utilization, animal disposition and incidence of disease during natural outbreaks in the population.

This project will use genomic approaches in combination with extensively phenotyped swine populations to identify genetic markers associated with production traits and understand these complex biological processes. Our approach will be to conduct genome-wide QTL scans and then fine map these QTL and develop SNP markers in tight linkage with the causative polymorphisms. QTL scans will be conducted in subsets of the USMARC BX swine population that have been extensively phenotyped for a wide variety of traits. This will permit a more complete biological understanding of each QTL region. Follow-up studies on QTL will be conducted in the BX population on larger groups of animals that may be phenotyped for a specific set of traits.

Standard QTL analyses will first be conducted followed by statistical models to identify components to nonadditive genetic variation affecting performance such as intra-locus (dominance and imprinting) and inter-locus (epistatic) interactions. These analyses will also yield valuable information about pleiotropic effects to understand the molecular bases of genetic correlations. A high density SNP map (5-20 SNP/cM) will be developed for the studied regions and genotyped across additional generations of BX animals to fine map QTL. Significant SNP markers developed from these approaches will be evaluated in additional commercially relevant lines of pig to ensure their applicability in commercial pigs. Markers that exhibit useful predictive genetic information will be disseminated to the swine industry.

Finally with all of the genetic and phenotypic knowledge in hand, we should be well-equipped to determine the causative gene for some QTL and greatly improve our understanding of the physiological effects of these QTL. A precise location of the causative gene as predicted from fine mapping studies, knowledge about different biological pathways affected from the extensively phenotyped population and knowledge about the genes located in the region from the swine genome sequence should allow selection of positional candidate gene to study for causative variation. These studies will be supplemented with functional genomic and marker-assisted animal experimentation.


3.Progress Report
Due to a critical vacancy in FY2009, we are a year behind in completing our milestones for Objective 2. Our milestone for FY2010 was to initiate scans for intra- and inter-locus interactions in QTL scans. This milestone has now been met. Two separate methods have been used to address intra- and inter-locus interactions. For qualitative traits, PLINK analyses have been conducted for cryptorchidism using the epistatic model option to evaluate all possible two-way locus interactions. For quantitative traits, dominance (intra-locus interactions) was directly evaluated for QTL by fitting genotypic information as a categorical fixed effect using MTDFREML. In addition, by using GenSel software for genome-wide scans of quantitative traits, both intra-locus and inter-locus genetic variation can be detected. We have not initiated matings to specifically test epistasis or dominance as we do not have specific regions to test at this time. In addition, the new structure of the USMARC swine population is not conducive to this type of study without considerable planning.

We have made significant progress in all of our research objectives. We completed analyses of genotypic data from the Illumina Porcine 60K BeadChip for many traits. Genome-wide association analyses have been conducted for measures of female reproduction, skeletal measures, and four categorical traits (cryptorchidism, response to PCV2 infection, kyphosis, and stress syndrome). These results are being prepared for publication. Our milestone for objective 1 was actually reported in FY2010’s annual report when we genotyped 700 boars used in commercial populations and conducted association analyses for first parity reproductive traits using daughter deviations as phenotypes for each boar.

The results from the association analyses of stress syndrome indicated the causative genetic variation was near the gene dystrophin. Samples were collected and lab analyses showed that affected pigs had significantly less dystrophin in cardiac and skeletal muscle tissues. In addition, affected animals had elevated plasma CPK values and abnormal ECGs (two peculiarities also noted in humans with mutations in dystrophin). Test matings continue to be conducted to enable future studies underlying the physiological effects of mutations in the dystrophin gene.

Significant progress was made in the sibling research project 31000-083-04S. The University of Illinois scientists identified novel genetic markers that may be associated with innate immunity while ARS completed heritability analyses on measures of passive immunity. This two-pronged approach will enable a more comprehensive analysis on genetic resistance to swine diseases.


4.Accomplishments
1. A defective gene causes a novel stress syndrome in pigs. A defect within a gene, mutated in human muscular dystrophies, causes a novel stress syndrome in pigs. The stress syndrome can result in death of affected pigs after handling or transportation. ARS researchers at Clay Center, NE, using sophisticated genetic and physiological techniques, determined that a defective gene called dystrophin leads to elevated blood enzymes, heart arrhythmias and dramatically reduced levels of the protein in heart and skeletal muscles. The researchers' findings are consistent with observations of genetic mutations in humans with milder forms of muscular dystrophy associated with muscle weakness and heart failure. This research will assist pork producers to eliminate this defect from their herds improving production efficiency, net return to farmers, and lower prices for consumers as well as provide a valuable biomedical model for muscular dystrophy research.

2. Genetic markers associated with pork tenderness made available to producers. Markers developed at USMARC residing in the calpastatin gene have been shown to be predictive of aged pork tenderness in multiple commercial populations of pigs. Based on the results of several validation studies completed at USMARC, the best performing markers were transferred to a commercial genotyping company to add to the list of markers producers may have genotyped in their populations. The utilization of these markers will result in improved and more consistent pork products.


Review Publications
Cepica, S., Bartenschlager, H., Ovilo, C., Zrustova, J., Masopust, M., Fernandez, A., Lopez, A., Knoll, A., Rohrer, G.A., Snelling, W.M., Geldermann, H. 2010. Porcine NAMPT gene: search for polymorphism, mapping and association studies. Animal Genetics. 41:646-651.

Casas, E., Ford, J.J., Rohrer, G.A. 2010. Quantitative Genomics of Male Reproduction. In: Jiang, Z., and Ott, T. L., Editors. Reproductive Genomics in Domestic Animals. Ames, IA:Wiley-Blackwell. p. 53-66.

Lindholm-Perry, A.K., Rohrer, G.A., Kuehn, L.A., Keele, J.W., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Nonneman, D.J. 2010. Genomic regions associated with kyphosis in swine. BMC Genetics. 11:112.

Masopust, M., Vykoukalova, Z., Knoll, A., Bartenschlager, H., Mileham, A., Deeb, N., Rohrer, G.A., Cepica, S. 2011. Porcine insulin receptor substrate 4 (IRS4) gene: cloning, polymorphism and association study. Molecular Biology Reports. 38:2611-2617.

Last Modified: 12/20/2014
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