Screening of reproduction‐related single‐nucleotide variations from MeDIP‐seq data in sheep

Abstract

Extensive variation in reproduction has arisen in Chinese Mongolian sheep during recent domestication. Hu and Small-tailed Han sheep, for example, have become non-seasonal breeders and exhibit higher fecundity than Tan and Ujumqin breeds. We therefore scanned reproduction-related single-nucleotide variations from methylated DNA-immunoprecipitation sequencing data generated from each of those four breeds to uncover potential mechanisms underlying this breed variation. We generated a high-quality map of single nucleotide variations (SNVs) in DNA methylation enriched regions, and found that the majority of variants are located within non-coding regions. We identified 359 SNVs within the Sheep Quantitative Trait Locus (QTL) database. Nineteen of these SNVs associated with the Aseasonal Reproduction QTL, and 10 out of the 19 reside close to genes with known reproduction functions. We also identified the well-known FecB mutation in high-fecundity sheep (Hu and Small-tailed Han sheep). When we applied these FecB finding to our breeding system, we improved lambing rate by 175%. In summary, this study provided strong candidate SNVs associated with sheep fecundity that can serve as targets for functional testing and to enhance selective breeding strategies. Mol. Reprod. Dev. 83: 958-967, 2016 © 2016 Wiley Periodicals, Inc.

Genome-wide analysis of DNA Methylation profiles on sheep ovaries associated with prolificacy using whole-genome Bisulfite sequencing

“…Recently, studies have been conducted to identify the genome-wide methylation profiles of farm animals [ 15 – 18 ]. Previously, some studies have been conducted to describe DNA methylation for sheep ovary [ 19 – 22 ], but few reports from the ovarian genome-wide methylation pattern [ 23 ]. WGBS, which allows unbiased genome wide DNA methylation profiling, has allowed us to investigate prolificacy related DNA methylation in unprecedented detail [ 9 ].…”

Recent advances in understanding genetic variants associated with economically important traits in sheep (Ovis aries) revealed by high-throughput screening technologies

“…Methylated-DNA immunoprecipitation sequencing has also been employed to identify genes for phenotypic traits in domestic animals. To data, there has only been one study reported using this method [58] . In that study, 19 single nucleotide variations and nine candidate genes (ADIPOQ, ABCG1, BRWD1, GRIN2B, METTL6, SIAH2, SLCO2A1, TNIK and UMODL1) were identified as being related to sheep reproductive traits.…”

Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

“… Demars et al (2013) reported the mutations FecX Gr in Grivette sheep and FecX O in Olkuska sheep associated with the highly prolific phenotype by a genome-wide association analysis. Cao et al (2016) found that nine candidate genes including the well-known FecB mutation played important roles in the variable litter size in Hu and Small-tailed Han sheep through methylated DNA-immunoprecipitation sequencing data. Miao et al (2016) identified a set of differentially expressed genes (e.g., FecB) between low- and high-prolificacy breeds (Dorset vs. Small-tailed Han sheep) through implementing integrated analysis of miRNAs and lncRNAs.…”