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. 2020 Dec;51(6):924-934.
doi: 10.1111/age.12999. Epub 2020 Sep 28.

Combined approaches to reveal genes associated with litter size in Yunshang black goats

L Tao  1 , X Y He  1 , Y T Jiang  2 , R Lan  2 , M Li  3 , Z M Li  3 , W F Yang  3 , Q H Hong  2 , M X Chu  1
Affiliations

Combined approaches to reveal genes associated with litter size in Yunshang black goats

L Tao et al. Anim Genet. 2020 Dec.

Abstract

Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches - GWAS, ROH analysis and detection of signatures of selection - were employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nSL statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.

Keywords: extended haplotype homozygosity; genome-wide association study; goat; kidding number; runs of homozygosity; signatures of selection.

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