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利用 Illumina Ovine SNP50 BeadChip 研究吉尔吉斯绵羊的群体结构和选择特征。

Population structure and selective signature of Kirghiz sheep by Illumina Ovine SNP50 BeadChip.

机构信息

College of Life Science and Technology, Tarim University, Alar, Xinjiang, China.

College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China.

出版信息

PeerJ. 2024 Sep 19;12:e17980. doi: 10.7717/peerj.17980. eCollection 2024.

DOI:10.7717/peerj.17980
PMID:39308831
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11416764/
Abstract

OBJECTIVE

By assessing the genetic diversity and associated selective traits of Kirghiz sheep (KIR), we aim to uncover the mechanisms that contribute to sheep's adaptability to the Pamir Plateau environment.

METHODS

This study utilized Illumina Ovine SNP50 BeadChip data from KIR residing in the Pamir Plateau, Qira Black sheep (QBS) inhabiting the Taklamakan Desert, and commonly introduced breeds including Dorper sheep (DOR), Suffolk sheep (SUF), and Hu sheep (HU). The data was analyzed using principal component analysis, phylogenetic analysis, population admixture analysis, kinship matrix analysis, linkage disequilibrium analysis, and selective signature analysis. We employed four methods for selective signature analysis: fixation index (Fst), cross-population extended homozygosity (XP-EHH), integrated haplotype score (iHS), and nucleotide diversity (Pi). These methods aim to uncover the genetic mechanisms underlying the germplasm resources of Kirghiz sheep, enhance their production traits, and explore their adaptation to challenging environmental conditions.

RESULTS

The test results unveiled potential selective signals associated with adaptive traits and growth characteristics in sheep under harsh environmental conditions, and annotated the corresponding genes accordingly. These genes encompass various functionalities such as adaptations associated with plateau, cold, and arid environment (ETAA1, UBE3D, TLE4, NXPH1, MAT2B, PPARGC1A, VEGFA, TBX15 and PLXNA4), wool traits (LMO3, TRPS1, EPHA5), body size traits (PLXNA2, EFNA5), reproductive traits (PPP3CA, PDHA2, NTRK2), and immunity (GATA3).

CONCLUSION

Our study identified candidate genes associated with the production traits and adaptation to the harsh environment of the Pamir Plateau in Kirghiz sheep. These findings provide valuable resources for local sheep breeding programs. The objective of this study is to offer valuable insights for the sustainable development of the Kirghiz sheep industry.

摘要

目的

通过评估吉尔吉斯羊（KIR）的遗传多样性和相关的选择特征，我们旨在揭示有助于羊适应帕米尔高原环境的机制。

方法

本研究利用来自居住在帕米尔高原的 KIR、生活在塔克拉玛干沙漠的奇拉黑羊（QBS）以及引入的常见品种，如多赛特羊（DOR）、萨福克羊（SUF）和湖羊（HU）的 Illumina 羊 SNP50 BeadChip 数据。使用主成分分析、系统发育分析、群体混合分析、亲缘关系矩阵分析、连锁不平衡分析和选择特征分析对数据进行分析。我们采用了四种选择特征分析方法：固定指数（Fst）、跨群体扩展纯合度（XP-EHH）、综合单倍型评分（iHS）和核苷酸多样性（Pi）。这些方法旨在揭示吉尔吉斯羊种质资源的遗传机制，提高其生产性状，并探索其对挑战性环境条件的适应。

结果

测试结果揭示了与恶劣环境条件下绵羊适应性和生长特征相关的潜在选择信号，并相应注释了相应的基因。这些基因涵盖了各种功能，如与高原、寒冷和干旱环境相关的适应（ETAA1、UBE3D、TLE4、NXPH1、MAT2B、PPARGC1A、VEGFA、TBX15 和 PLXNA4）、羊毛性状（LMO3、TRPS1、EPHA5）、体型性状（PLXNA2、EFNA5）、繁殖性状（PPP3CA、PDHA2、NTRK2）和免疫（GATA3）。

结论

本研究鉴定了与吉尔吉斯羊生产性状和适应帕米尔高原恶劣环境相关的候选基因。这些发现为当地绵羊育种计划提供了有价值的资源。本研究的目的是为吉尔吉斯羊产业的可持续发展提供有价值的见解。

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