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

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.

Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side

“…This association was also found by Ding et al [6] and Duijvesteijn et al [13]. While these two groups speculated that teat number and vertebra number are controlled by a similar set of genes, none of the regions reported in Table 3 for TTN were found to be associated with vertebra number in this population [23]. However, two regions for individual side counts did overlap with QTL for vertebra number, i.e.…”

“…In spite of these two co-localizations of vertebra number and teat count in the proximity of VRTN and NR6A1 as well as the speculation mentioned in Duijvesteijn et al [13], none of the regions which exceeded 1% of the genomic variation for TTN (Fig. 1) were associated with vertebra number in this population [23]. The only region in the validation phase associated with vertebra number [23] was SSC12:26 Mb, which it had an extremely low additive effect (0.038).…”

“…The concept that additional mammary glands arise from somite division in the developing embryo is supported by the effects of the VRTN gene that were observed on vertebra number and teat count [6, 12, 16, 17, 23] and of the NR6A1 gene on SSC1 [6]. However, since genetic variation within NR6A1 is only observed in crosses between Asian and European breeds, we were not able to evaluate this result.…”

“…A total of 41,000 iterations were performed with the first 1000 discarded for posterior summaries. A 1-Mb window approach was conducted as described by Rohrer et al [23]. Therefore, SNPs were required to have a unique position in the current swine genome (Build 10.2; [24]) resulting in 41,148 SNPs included in the final analyses.…”

“…Genotypes for SNP NV090 were predicted as previously described [16]. SNP NV090 was selected because it is located 6 kb upstream of the transcriptional start site for VRTN (based on GenBank Accession AB554652), gave very reliable genotypes in our lab and was found to be in complete linkage disequilibrium with the 291-bp insertion into the intron of VRTN (NV123) [23], which may actually be the causative mutation. Windows that explained more than 1% of the genomic variation are presented.…”