Possible introgression of the VRTN mutation increasing vertebral number, carcass length and teat number from Chinese pigs into European pigs

Abstract

Vertnin (VRTN) variants have been associated with the number of thoracic vertebrae in European pigs, but the association has not been evidenced in Chinese indigenous pigs. In this study, we first performed a genome-wide association study in Chinese Erhualian pigs using one VRTN candidate causative mutation and the Illumina Porcine 60K SNP Beadchips. The VRTN mutation is significantly associated with thoracic vertebral number in this population. We further show that the VRTN mutation has pleiotropic and desirable effects on teat number and carcass (body) length across four diverse populations, including Erhualian, White Duroc × Erhualian F2 population, Duroc and Landrace pigs. No association was observed between VRTN genotype and growth and fatness traits in these populations. Therefore, testing for the VRTN mutation in pig breeding schemes would not only increase the number of vertebrae and nipples, but also enlarge body size without undesirable effects on growth and fatness traits, consequently improving pork production. Further, by using whole-genome sequence data, we show that the VRTN mutation was possibly introgressed from Chinese pigs into European pigs. Our results provide another example showing that introgressed Chinese genes greatly contributed to the development and production of modern European pig breeds.

Figure 1. GWAS mapping for the number of thoracic vertebrae in the Erhualian population.

(a) Manhattan plots of the GWAS for the number of thoracic vertebrae in the Erhualian population. In the Manhattan plots, negative log₁₀ P values of the quantified SNPs were plotted against their genomic positions. Different colors indicate different chromosomes. The red dot represents the VRTN mutation, and the top GWAS SNP (DLAS0000795) on the Illumina Porcine 60K Beadchips is indicated. The solid and dashed lines indicate the 5% genome-wide and chromosome-wide Bonferroni-corrected thresholds, respectively. (b) When the VRTN mutation was include as a fixed effect in the GWAS model, no other SNP on SSC7 showed association signal.

Figure 2. Regional association plot for the number of teats in the Duroc population.

(a) Association of the VRTN mutation and 60K chip SNPs on SSC7 with the number of teats in the Duroc population. Negative log₁₀ P values of the quantified SNPs were plotted against their genomic positions. The red dot represents the VRTN mutation, and the top GWAS chip SNP (MARC0038565) is indicated. The solid and dashed lines indicate the 5% genome-wide and chromosome-wide Bonferroni-corrected thresholds, respectively. (b) When the VRTN mutation was include as a fixed effect in the GWAS model, no other SNP on SSC7 showed association signal.

Figure 3. Possible introgression of the VRTN haplotype from Chinese pigs into European pigs.

(a) Maximum likelihood (ML) phylogenic tree for the 9 kb region containing the VRTN gene. (b) ML phylogenic tree for the 200 kb region flanking (not including) the VRTN gene. Haplotypes of the two regions were first inferred, and then the two ML phylogenic trees were built for major haplotypes with frequencies of greater than 0.04 (see Methods). Q denotes the major haplotype harboring the Q allele (the mutant allele, ins), q denotes major haplotypes containing the q allele (the wild-type allele, del). EW, European wild boar; ED, European domestic pig; CW, Chinese wild boar; CD, Chinese domestic pig; anc, Beared pigs (Sus barbatus) as an outgroup to European and Chinese pigs. Scale bars represent the number of nucleotide substitutions per SNP site. Values in the tree indicate percentages (%) of observations in 1,000 bootstrap replicates.