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Title: Genomic regions associated with kyphosis in swine

Author
item Lindholm-Perry, Amanda
item Rohrer, Gary
item Kuehn, Larry
item Keele, John
item HOLL, JUSTIN - Former ARS Employee
item Shackelford, Steven
item Wheeler, Tommy
item Nonneman, Danny - Dan

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2010
Publication Date: 12/21/2010
Citation: 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.

Interpretive Summary: A kyphosis type of back curvature defect in swine has been detected in two commercial-like populations of animals. The condition is similar to human spine defects. A previous study on this condition in pigs concluded that the condition is moderately heritable, thus the objective of this study was to identify candidate genes that may be playing a role in this disorder and to identify genetic markers in those genes that are associated with this trait. Chromosomal regions of association with the swine kyphosis condition were identified and candidate genes in these regions with known involvement in human skeletal defects were selected for further evaluation. Sixteen genes were partially sequenced to detect genetic variation among animals, these single nucleotide variants were used to genotype two populations of swine (n=1628). Genetic variants in the genes PLOD1, SOX9, RYR1, HOXC6 and HOXC8 were found to be significantly associated with the back defect; however, none of the markers were detected in both populations of animals. This suggests that the skeletal defect found in these swine herds is under the control of many genes and that the mechanisms and genes involved may be different in unrelated populations of animals.

Technical Abstract: Background: A back curvature defect similar to kyphosis in humans has been observed in swine herds. The defect ranges from mild to severe curvature of the thoracic vertebrate in split carcasses and has an estimated heritability of 0.3. The objective of this study was to identify genomic regions that affect this trait. Results: Single nucleotide polymorphism (SNP) associations performed with 198 SNPs and microsatellite markers in a Duroc-Landrace-Yorkshire resource population (U.S. Meat Animal Research Center, USMARC resource population) of swine provided regions of association with this trait on 15 chromosomes. Positional candidate genes, especially those involved in human skeletal development pathways, were selected for SNP identification. SNPs in 16 candidate genes were genotyped in an F2 population (n = 371) and the USMARC herd (n = 1,257) with back curvature scores. SNPs in KCNN2 on SSC2, RYR1 and PLOD1 on SSC6 and MYST4 on SSC14 were significantly associated with kyphosis in the resource population of swine (P = 0.05). SNPs in CER1 and CDH7 on SSC1, PSMA5 on SSC4, HOXC6 and HOXC8 on SSC5, ADAMTS18 on SSC6 and SOX9 on SSC12 were significantly associated with the back curvature trait in the F2 population of swine (P = 0.05). Conclusions: These data suggest that this back curvature trait may be affected by several loci and that these may differ by population. Carcass value, cutability and animal health and well-being could be improved by effectively removing this undesirable trait from pig populations.