Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing

Abstract

Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient F_ROH, calculated based on ROH, was 0.018 ± 0.016, and the F_PED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.

Keywords: candidate gene; inbreeding coefficient; local breed; runs of homozygosity; whole genome resequencing.

Figure 1

ROH number statistics of Baoshan pigs. (A) Distribution of ROH numbers on chromosomes; (B) distribution of ROH numbers on individual BS pigs.

Figure 2

Statistics of ROH length and distribution in BS pigs. (A) Distribution of different lengths of ROH on chromosomes; (B) position of different lengths of ROH on chromosomes; (C) distribution of different lengths of ROH on individual BS pigs; and (D) number and proportion of long, medium, and short ROHs.

Figure 3

Identification and statistics of ROH islands in BS pigs. (A) Identification of ROH islands in BS pigs; the red dashed line in the figure indicates the threshold line and the colored dots overlapping with or above the threshold line indicate the detected ROH islands. (B–E) Statistics of the distribution of ROH islands on chromosomes in terms of the number of ROH islands in BS pigs, their lengths, the number of SNPs, and the number of genes.

Figure 4

GO and KEGG enrichment and gene interactions in ROH islands. (A,C) GO/KEGG enrichment of genes in ROH islands. Horizontal coordinates indicate the first level of classification, vertical coor-dinates indicate the third level of classification, the size of the dots indicates the enrichment factor (the ratio of the number of genes enriched to the island to the total number of all the genes in the entry), the bigger the dots, the more genes enriched, and the color of the dots indicates the signifi-cance, the darker the color, the more significant the relationship. (B,D) Network diagram of gene interactions in the GO entry/KEGG pathway. A dot indicates a gene, the size and color of the dot indicates interactions, the larger the dot and the darker the color, the more interactions of the gene, the gene at the center is the one with the most interactions.