Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin

Jieru Wang; Jieru Wang; Jiajia Suo; Ruizhi Yang; Cheng-long Zhang; Cheng-long Zhang; Xiaopeng Li; Xiaopeng Li; Zhipeng Han; Zhipeng Han; Wen Zhou; Wen Zhou; Shudong Liu; Shudong Liu; Shudong Liu; Qinghua Gao; Qinghua Gao; Qinghua Gao

doi:10.3389/fgene.2023.1281601

Frontiers in Genetics (Nov 2023)

Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin

Jieru Wang,
Jieru Wang,
Jiajia Suo,
Ruizhi Yang,
Cheng-long Zhang,
Cheng-long Zhang,
Xiaopeng Li,
Xiaopeng Li,
Zhipeng Han,
Zhipeng Han,
Wen Zhou,
Wen Zhou,
Shudong Liu,
Shudong Liu,
Shudong Liu,
Qinghua Gao,
Qinghua Gao,
Qinghua Gao

Affiliations

Jieru Wang: College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
Jieru Wang: Key Laboratory of Utilization of Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, Xinjiang, China
Jiajia Suo: College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
Ruizhi Yang: College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
Cheng-long Zhang: College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
Cheng-long Zhang: Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
Xiaopeng Li: College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
Xiaopeng Li: Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
Zhipeng Han: College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
Zhipeng Han: Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
Wen Zhou: College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
Wen Zhou: Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
Shudong Liu: Key Laboratory of Utilization of Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, Xinjiang, China
Shudong Liu: College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
Shudong Liu: Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
Qinghua Gao: Key Laboratory of Utilization of Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, Xinjiang, China
Qinghua Gao: College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
Qinghua Gao: Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang, China

DOI: https://doi.org/10.3389/fgene.2023.1281601
Journal volume & issue: Vol. 14

Abstract

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Local sheep in the northeastern Tarim Basin can adapt to dry and low-rainfall regional environments. In this study, three local sheep breeds in the northeastern Tarim Basin, LOP (LOP) sheep, Bayinbuluke (BYK) sheep, and Kunlun (KUN, also known as the Qiemo sheep) sheep, and three introduced sheep breeds, Suffolk (SUF) sheep, Dorset (APD) sheep, and Texel (TEX) sheep, were analyzed for genetic diversity, population structure, and selective signature using the Illumina OvineSNP50K BeadChip. We found that LOP, BYK, and KUN had lower observed heterozygosity and expected heterozygosity than TEX, SUF, and ADP, which were differentiated based on geographic distribution. We performed fixation index (FST) analysis on three local sheep breeds in the northeastern Tarim Basin (LOP, BYK, and KUN) and introduced sheep breeds (TEX, SUF, and ADP) to measure genetic differentiation. Nucleotide diversity (PI) analysis was performed on single-nucleotide polymorphism (SNP) data of LOP, BYK, and KUN. A total of 493 candidate genes were obtained by taking the intersection at a threshold of 5%. Among them, SMAD2, ESR2, and HAS2 were related to reproductive traits. PCDH15, TLE4, and TFAP2B were related to growth traits. SOD1, TSHR, and DNAJB5 were related to desert environmental adaptation. Analyzing the genetic patterns of local sheep in the northeastern Tarim Basin can protect the germplasm resources of local sheep and promote the development and utilization of sheep genetic resources.

Published in Frontiers in Genetics

ISSN: 1664-8021 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Biology (General): Genetics
Website: http://journal.frontiersin.org/journal/genetics

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