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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Reproduction Research » Research » Publications at this Location » Publication #318839

Research Project: Genetic and Genomic Approaches to Improve Swine Reproductive Efficiency

Location: Reproduction Research

Title: A study of vertebra number in pigs confirms the association of vertnin and reveals additional QTL

Author
item Rohrer, Gary
item Nonneman, Danny - Dan
item Wiedmann, Ralph
item Schneider, James

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2015
Publication Date: 10/30/2015
Publication URL: http://handle.nal.usda.gov/10113/61641
Citation: Rohrer, G.A., Nonneman, D.J., Wiedmann, R.T., Schneider, J.F. 2015. A study of vertebra number in pigs confirms the association of vertnin and reveals additional QTL. BMC Genetics. 16(1):129.

Interpretive Summary: Formation of the vertebral column is critical to mammalian development. Most mammals have the same number of vertebrae within a species. The pig is quite unique as considerable variation exists in number of thoracic vertebrae as well as number of lumbar vertebrae. Previous studies have identified two genes that affect number of vertebrae in pigs yet considerable genetic variation still exists. Therefore, we conducted a study to identify additional genes that affect this trait. Thirty-one unique regions of the genome were associated with vertebra numbers along with one of the previously reported genes (vertnin). The two most important regions were located near a family of genes that regulate embryonic development (HOX genes) and are likely candidates for the observed associations. Further evaluation of these regions and characterization of genetic variants will aid our understanding of vertebral development using natural genetic variants segregating in commercial swine. In addition, genetic markers can be developed to modify the number of vertebrae in commercial swine populations if desired.

Technical Abstract: Background: Formation of the vertebral column is a critical developmental stage in mammals. The strict control of this process has resulted in little variation in number of vertebrae across mammalian species and no variation within most mammalian species. The pig is quite unique as considerable variation exists in number of thoracic vertebrae as well as number of lumbar vertebrae. At least two genes have been identified that affect number of vertebrae in pigs yet considerable genetic variation still exists. Therefore, a genome-wide association (GWA) analysis was conducted to identify additional genomic regions that affect this trait. Results: A total of 1,883 animals were phenotyped for the number of ribs and thoracolumbar vertebrae as well as successfully genotyped with the Illumina Porcine SNP60 BeadChip. After data editing, 41,148 SNP markers were included in the GWA analysis. These animals were also phenotyped for kyphosis. Fifty 1 Mb windows each explained at least 1.0 % of the genomic variation for vertebrae counts while 16 regions were significant for kyphosis. There was considerable overlap of regions associated with vertebrae counts as the 50 associations represented only 31 unique 1 Mb windows. Vertnin genotype significantly affected vertebral counts as well. The region with the largest effect for number of ribs and thoracolumbar vertebrae was located over the Hox B gene cluster and the largest association for lumbar vertebrae number was over the Hox A gene cluster. Genetic markers in significant regions accounted for approximately 50 % of the genomic variation. Genomic heritability for kyphosis was low and no region was associated with kyphosis and vertebra counts. Conclusions: The importance of the Hox gene families in vertebral development was highlighted as significant associations were detected over the A, B and C families. Further evaluation of these regions and characterization of variants within these genes will expand our knowledge on vertebral development using natural genetic variants segregating in commercial swine.