Abstract
BackgroundFormation 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.ResultsA total of 1883 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-three 1 Mb windows each explained at least 1.0 % of the genomic variation for vertebrae counts while 16 regions were significant for kyphosis. Vertnin genotype significantly affected vertebral counts as well. The region with the largest effect for number of lumbar vertebrae and thoracolumbar vertebrae were located over the Hox B gene cluster and the largest association for thoracic vertebrae number was over the Hox A gene cluster. Genetic markers in significant regions accounted for approximately 50 % of the genomic variation. Less genomic variation for kyphosis was described by QTL regions and no region was associated with kyphosis and vertebra counts.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0286-9) contains supplementary material, which is available to authorized users.
Highlights
Formation of the vertebral column is a critical developmental stage in mammals
Number of ribs was considered the number of thoracic vertebrae and number of lumbar vertebrae (LVN) was computed by subtracting the number of ribs from the number of thoracolumbar vertebrae (LVN = Thoracolumbar vertebrae (TLV) – RIB)
The range observed for RIB was 14 to 17, LVN was 4 to 8 and TLV was 19 to 23
Summary
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. Variation in the number of thoracic and lumbar vertebrae across species does exist, but Narita and Kuratani [2]. Variation within species in thoracic, lumbar and thoracolumbar numbers has been observed in a limited number of mammalian species. While it is often speculated that variation in pigs exists due to selection for Rohrer et al BMC Genetics (2015) 16:129 increased body size, similar or greater changes in body size has occurred due to selection in other domesticated species (for example: cattle, sheep and dog) and yet variation within these species has not been widely reported
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