Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology.

Haiyu Ma,Wujun Liu,Jueken Aniwashi,Chao Fang,Yiming Sulaiman,Lingling Liu,Kezierkailedi Abudilaheman,Qiong Wang

doi:10.7717/peerj.8079

Abstract

BackgroundThere are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep.MethodsIndigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis.ResultsWe identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (GenBank ID: 443299, g. 75320741G>A site), GUCY1A1 (GenBank ID: 101110000, g. 43266624C>T site), and COIL (GenBank ID: 101123134, g. 7321466C>G site) were found to be significantly or extremely significantly associated with litter size. These three loci are expected to be used as molecular markers to determine differences in litter size in sheep.

Highlights

Fertility is one of the most important economic traits in sheep
We identified 685,300 single nucleotide polymorphisms (SNPs) using the SLAF-seq technique for subsequent genome-wide analysis
30 loci of seven genes and candidate genes (CXCL12, Follicular stimulating hormone receptor (FSHR), SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis

Summary

Introduction

Fertility is one of the most important economic traits in sheep. Sheep populations with high reproductive performance show two to three times higher production efficiency and economic benefit from lambs than those with low reproductive performance do. A few major genes affecting high fecundity have been found in Cambridge and Belclare (Hanrahan et al, 2004), Icelandic (Eiriksson & Sigurdsson, 2017), Romanov (Deniskova et al, 2017), Finnish (Mullen & Hanrahan, 2014), and other high fecundity sheep breeds abroad, whereas domestic studies have mainly focused on Hu (Yue, 1996) and Small Tail Han sheep (He et al, 2012). The major genes identified in small-tailed Han sheep have been selected as markers for domestic mutation detection for sheep litter size, which has led to pseudoscience in this field. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. We used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep

Methods

Results

Conclusion