Abstract
A previous whole-genome association analysis identified lysine demethylase 6A (KDM6A), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats. KDM6A mRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis); the expression levels in testes at different developmental stages [1-week-old (wk), 2, 3 wk, 1-month-old (mo), 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying that KDM6A may have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P < 0.01), and the average first-born litter size of individuals with an insertion/insertion genotype higher than that of those with the deletion/deletion genotype (P < 0.05). There was also a significant difference in genotype distributions of the 16 bp indel between mothers of single-lamb and multi-lamb litters in the studied goat population (P = 0.001). Consistently, the 16 bp indel also had a significant effect on KDM6A gene expression. Additionally, there was no significant linkage disequilibrium (LD) between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel in KDM6A may be useful for marker-assisted selection (MAS) of goats.
Highlights
Improvements in female fertility are of critical importance for the goat industry
Whole-genome sequencing and genome-wide association studies (GWAS) are used to explore genetic variants strongly associated with production traits (Lai et al, 2016; Mota et al, 2017; Wu et al, 2018); numerous potential genes identified by GWAS have not been fully verified
Our results demonstrate that lysine-specific demethylase 6A (KDM6A) mRNA expression levels during the mitosis stage were lower than those in the meiosis stage (P < 0.05), suggesting KDM6A may be associated with the mitosis-to-meiosis transition in the Shaanbei white cashmere goat
Summary
Improvements in female fertility are of critical importance for the goat industry. As one of the most important factors restricting female fertility, increasing litter size has received much more consideration (Naicy et al, 2016; Yang et al, 2017). Whole-genome sequencing and genome-wide association studies (GWAS) are used to explore genetic variants strongly associated with production traits (Lai et al, 2016; Mota et al, 2017; Wu et al, 2018); numerous potential genes identified by GWAS have not been fully verified To address this problem, methods which combine GWAS analysis results and MAS to screen for critical genetic variations in large livestock populations have been developed. A genome scan in a French dairy goat population found that variants in diacylglycerol o-acyltransferase 1 (DGAT1) were associated with a notable decrease in milk fat content (Martin et al, 2017) These results demonstrate the feasibility of using combined methods to screen for important genetic variations
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