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

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 selectionwere 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 nS L 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.

Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep

“…HS3ST5, an HS3ST2 paralog, was associated with reproductive seasonality traits in sheep [27]. Given the association of seasonality-associated DIO3 and LS in pigs and goats, and the empirical concurrence of higher LS and year-round estrus in goats [2,28], these results indicate that HS3ST2 may be involved in female reproductive health, and seasonal breeding in goats. Eight overlapping PSGs were revealed on the basis of Fst(YSD) and nSL of HG in goats: CHST11, SDCCAG8, ATF6, FAM13A, HSP90B1, IBSP, IFNLR1, and STAB2 (Figure 2).…”

“…This study included two Yunshang black goat populations (Yunshang black goats used for DNA sequencing (YSD), n = 40; Yunshang black goats used ovarian mRNA sequencing (YSR), n = 20) and three sheep populations (Finnsheep, FIN, n = 19; Romanov, ROM, n = 19; and Small Tailed Han sheep, STH, n = 12); the YSD, FIN and ROM data were obtained from previous studies [1,2]. All animals were as unrelated as possible as determined by pedigree or farmers' knowledge.…”

“…To reveal the potential genetic convergence in goat and sheep prolificacy, we focused on (1) PSGs, (2) DEGs, and ( 3) biological pathways at the level of gene set. Given the availability of PSGs in HG using the number of segregating sites by length (nSL), a haplotype-based statistic with test power to both soft and hard sweeps [2,22], convergent PSGs were identified as the intersection of ovine candidates identified by Fst_RMS and hircine candidates shared by Fst(YSD) and nSL (≥6) of HG. Convergent DEGs at LP and FP were defined as these genes that were shared by goats and sheep, but excluded their expression trend.…”

“…Litter size (LS), the lambing number per parturition per ewe or the kidding number per parturition per doe, is an important component of goat and sheep productivity. Importantly and interestingly, variation in individual LS is common within breeds, such as 1-4 in Yunshang black goats, 1-5 Romanov sheep, and 1-6 in Finnsheep [1,2]. Breeds with exceptional prolificacy can provide genetic material to develop new lines/populations with ideal performance.…”

Genomic characterization of world’s longest selection experiment in mouse reveals the complexity of polygenic traits

“…Other genes encode for proteins involved in the ovarian development and maintenance of the primordial follicle reserve ( Tsc1 75 , Trp63 76 ), in the vascularization of the placenta ( Atoh8 77 ) and facilitate maternal supplied lipids and dietary fat digestion in neonatal mice ( Cel 78,79 ). Furthermore, DUK shares a fecundity associated region ( Sftpb , Usp39 , Tmem150 , Rnf181 , Vamp5 , Vamp8 , Cgcx , Mat2a ) with Qsi5 mice 80 , an inbred mouse line known for its increased litter size, and candidate genes associated with birth rate and male fertility in humans ( Ntm 81 ) and litter size in cattle, goats and pigs ( Dio3 82–84 ). Interestingly, analysis of private SVs detected a 317bp deletion affecting Olfr279 (Supplementary Data 8).…”