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

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

doi:10.7717/peerj.8079

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

PeerJ. 2019 Nov 26:7:e8079. doi: 10.7717/peerj.8079. eCollection 2019.

Authors

Haiyu Ma¹, Chao Fang², Lingling Liu¹, Qiong Wang¹, Jueken Aniwashi¹, Yiming Sulaiman¹, Kezierkailedi Abudilaheman³, Wujun Liu¹

Affiliations

¹ College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang, China.
² Department of Veterinary Managment of Animal Resources, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
³ People's Congress of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China.

Abstract

Background: There 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.

Methods: Indigenous 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.

Results: We 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.

Keywords: GWAS; KASP; Litter size; SLAF-seq.

Grants and funding

This work was supported by the National Natural Science Foundation of China (No. U1603232), the National Key R&D Program of China (No. 2018YFD0502100), the Autonomous Region Key Research and Development Project (No. 2017B01005-2-1), and the Xinjiang Agricultural University Graduate Research and Innovation Project (No. XJAUGRI2017033). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.