Analysis of whole genome sequence and genome-wide SNPs in highly inbred pigs

Abstract

Not only fulfilling a large portion of the worldwide meat consumption, pigs also serve as a model organism in biomedical studies due to the shared similarity with humans at both physiological and genetic levels. However, as a diploid organism, a normal pig holds two versions of genetic code simultaneously, creating an obstacle for many studies in the related field. For the first time in history, we have been able to successfully inbred pigs for more than three decades. In this paper, we sequenced and analyzed the genome of a highly inbred miniature Chinese pig strain, Banna Mini-pig Inbred Line (BMI). This specific strain of pigs has been inbred for 24 generations, the longest inbreeding history ever published. In contrast to the high level of heterozygosis in Chinese pigs, the BMI pigs show high level of homozygosis and a clear pattern on the distribution of heterozygosis along the genome. Less than 0.5% of all the short variants identified are located in coding regions, suggesting high homozygosis at the transcriptome level. We also conducted genome-wide SNP genotyping in 48 inbred pigs that are in different generations of inbreeding. Results show that overall the homozygosity of the pigs increases with the higher generation of inbreeding and comparison of the SNPs among the inbred lines shows clear trend reflecting the inbreeding history of the pigs. Thus both the whole genome sequence and SNP genotyping demonstrate that the prolonged inbreeding has led to the inbred lines to have nearly identical homologous chromosomes, and thus can provide homozygotic genes and clear genetic background. Our result could reduce the gap of linking phenotypes with genotypes, facilitate the building of pharmaceutical pig models, and shed light on the effect of extensive inbreeding.