A further look at porcine chromosome 7 reveals VRTN variants associated with vertebral number in Chinese and Western pigs

Abstract

The number of vertebrae is an economically important trait that affects carcass length and meat production in pigs. A major quantitative trait locus (QTL) for thoracic vertebral number has been repeatedly identified on pig chromosome (SSC) 7. To dissect the genetic basis of the major locus, we herein genotyped a large sample of animals from 3 experimental populations of Chinese and Western origins using 60K DNA chips. Genome-wide association studies consistently identified the locus across the 3 populations and mapped the locus to a 947-Kb region on SSC7. An identical-by-descent sharing assay refined the locus to a 100-Kb segment that harbors only two genes including VRTN and SYNDIG1L. Of them, VRNT has been proposed as a strong candidate of the major locus in Western modern breeds. Further, we resequenced the VRTN gene using DNA samples of 35 parental animals with known QTL genotypes by progeny testing. Concordance tests revealed 4 candidate causal variants as their genotypes showed the perfect segregation with QTL genotypes of the tested animals. An integrative analysis of evolutional constraints and functional elements supported two VRTN variants in a complete linkage disequilibrium phase as the most likely causal mutations. The promising variants significantly affect the number of thoracic vertebrae (one vertebra) in large scale outbred animals, and are segregating at rather high frequencies in Western pigs and at relatively low frequencies in a number of Chinese breeds. Altogether, we show that VRTN variants are significantly associated with the number of thoracic vertebrae in both Chinese and Western pigs. The finding advances our understanding of the genetic architecture of the vertebral number in pigs. Furthermore, our finding is of economical importance as it provides a robust breeding tool for the improvement of vertebral number and meat production in both Chinese indigenous pigs and Western present-day commercial pigs.

Figure 1. GWAS map the major QTL for the number of thoracic vertebrae to SSC7.

GWAS were performed on the White Duroc × Erhualian F₂ intercross (A), Sutai pigs (B), Erhualian × Tongcheng F₂ intercross (C) and meta-analysis (D). Negative log10 P-values of all SNPs are plotted against position on each pig chromosome in the y-axis. Chromosomes are shown in different colors for clarity in the x-axis. Log (1/P) values of more than 5 are genome-wide significant.

Figure 2. All Q-bearing chromosomes for increased vertebral number share a 100-Kb region harboring the VRTN gene.

The IBD critical regions defined by the 60 K SNP data (panel A) and the characterized SNPs (panel B) are indicated by shaded boxes. Two annotated genes, VRTN and SYNDIG1L, are located in the IBD region. SNP alleles are shown by 1 and 2 for the major and minor alleles, respectively. The characterized SNPs shown in panel B are numbered according to their locations in the current pig genome assembly (Sscrofa10.2). Identities of animals carrying the Q-chromosome are given in the left axis. Animals C14, C2027 and C2042 are from the Erhualian × Tongcheng F₂ intercross, and the others are from the White Duroc × Erhualian F₂ intercross.

Figure 3. Visualization of evolutionary constraints and functional significance of VRTN candidate causal variants.

Four variants showing 100% concordance with the QTL genotypes of parental pigs are shown in the genomic structure of the VRTN gene. Exons are indicated by boxes and non-coding regions by thin lines (medium panel). The sequences for the alignment were taken from the following accessions: NC_010449.4 (Sus scrofa), AC_000167.1 (Bos taurus), NC_006590.3 (Canis lupus familiaris), NC_000014.8 (Homo sapiens) and NC_000078.6 (Mus musculus). The positions of variants are indicated by shaded boxes and the missing sequences are marked by the dash (upper panel). An integrative genomic analysis was performed on a 4-kb region harboring the two most likely causal variants via the UCSC Genome Browser (lower panel). GERP, GERP scores for mammalian alignments; Digital DNaseI, digital DNaseI hypersensitivity clusters; H3K27AC, histone 3 lysine 27 acetylation; H3K4me3, histone 3 lysine 4 trimethylation; H1-hESC, chromatin segmentation by Hidden Markov Model predicted from the ENCODE consortium; TF, transcription binding sites.