Abstract
Litter size (LS), an important economic trait in livestock, is so complicate that involves many aspects of reproduction, the underlying mechanism of which particularly in goat has always been scanty. To uncover the genetic basis of LS, the genomic sequence of Jining Gray goat groups (one famous breed for high prolificacy in China) with LS 1, 2, and 3 for firstborn was analyzed, obtaining 563.67 Gb sequence data and a total of 31,864,651 high-quality single nucleotide polymorphisms loci were identified. Particularly, the increased heterozygosity in higher LS groups, and large continuous homozygous segments associated with lower LS group had been uncovered. Through an integrated analysis of three popular methods for detecting selective sweeps (Fst, nucleotide diversity, and Tajima’s D statistic), 111 selected regions and 42 genes associated with LS were scanned genome wide. The candidate genes with highest selective signatures included KIT, KCNH7, and KMT2E in LS2 and PAK1, PRKAA1, and SMAD9 in LS3 group, respectively. Meanwhile, functional terms of programmed cell death involved in cell development and regulation of insulin receptor signaling pathway were mostly enriched with 42 candidate genes, which also included reproduction related terms of steroid metabolic process and cellular response to hormone stimulus. In conclusion, our study identified novel candidate genes involving in regulation of LS in goat, which expand our understanding of genetic fundament of reproductive ability, and the novel insights regarding to LS would be potentially applied to improve reproductive performance.
Highlights
Goat (Capra hircus), one of the most important livestock animals, has been domesticated from wild goat near Fertile Crescent in Middle East around 10,000 years ago (Naderi et al, 2008; Daly et al, 2018)
We provided the comprehensive evidence of genetic background of high fecundity in goat
The whole-genomic sequence was performed with groups of Jining Gray goat with Litter size (LS) 1, 2, and 3 for first-born and we got a plenty of genome-wide variants
Summary
Goat (Capra hircus), one of the most important livestock animals, has been domesticated from wild goat near Fertile Crescent in Middle East around 10,000 years ago (Naderi et al, 2008; Daly et al, 2018). More attentions have been attracted in reproductive trait study of sheep, four major prolificacy (that is LS) genes have been identified, that are bone morphogenetic protein receptor 1B (BMPR1B, FecB), bone morphogenetic protein 15 (BMP15, FecX), growth differentiation factor 9 (GDF9, FecG), and beta-1,4-N-acetyl-galactosaminyl transferase 2 (B4GALNT2, FecL) (Polley et al, 2010; Drouilhet et al, 2013; Våge et al, 2013; Abdoli et al, 2016) It has been proved an extra ovulation increased per estrus for one copy of BMP15 (0.4) and BMPR-1B (1.5) mutation (Davis, 2005; Abdoli et al, 2016; Talebi et al, 2018). One research of genome-wide association studies (GWAS) in sheep had focused on LS trait, the highand low-prolificacy sheep breeds were applied to explore the significant variants associated with LS, it revealed amount of candidate single nucleotide polymorphisms (SNPs), including BMPR1B, FBN1, and MMP2 in Wadi sheep, SMAD1 and CTNNB1 in Hu sheep, NCOA1 in Icelandic sheep, FLT1, NF1, PTGS2, and PLCB3 in Finn sheep, ESR2 in Romanov sheep, and ESR1, ETS1, FLI1, SPP1, and MMP15 in Texel sheep (Xu et al, 2018)
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