Revealing Genomic Footprints of Selection for Fiber and Production Traits in Three Indian Sheep Breeds

ABSTRACT

The present broad range of sheep phenotypic variation is the consequence of selection for various production characteristics such as wool, milk, meat, and natural adaptability to diverse situations. In the current study, the genomic data of 79 animals from three Indian sheep breeds (Changthangi, Deccani, and Garole) were explored to decipher regions under positive selection for various productive traits using various statistical tools. We found 61, 102 regions using Tajima’s D, CLR and 58, 38, and 71 regions using F_ST, FLK, and hapFLK, respectively, under selective sweep. Significant candidate genes related to various important traits, such as KLHL for fibre diameter and the OMA1 gene for feed-induced thermogenesis in Changthangi, were identified. In addition, the SYCP2 and NAPAS3 genes were found to be associated with seasonal reproductivity, and BMPR1B for fertilization capacity in Garole. In a previous study, the HSPA6 gene (Garole) was found to be associated with thermo-tolerance in the Angus sheep breed. The outcomes discussed here provide a basis for detecting selective sweeps that underlie genetic variations of traits that have functional importance.

摘要

目前绵羊表型变异的范围很广, 这是对各种生产特性 (如羊毛, 牛奶, 肉) 进行选择的结果, 以及对不同情况的自然适应性. 在目前的研究中, 利用各种统计工具, 对来自三个印度绵羊品种 (昌塔吉, 德卡尼和加罗尔) 的79只动物的基因组数据进行了探索, 以破译各种生产性状的正选择区域. 我们在选择性扫描下分别发现了61, 102个使用Tajima’s D, CLR的区域和58, 38, 71个使用FST, FLK, hapFLK的区域. 与各种重要性状相关的重要候选基因已被确定, 例如用于纤维直径的KLHL和用于长滩鸡饲料诱导产热的OMA1基因. 此外, 还发现SYCP2和NAPAS3基因与季节性繁殖能力有关, 而BMPR1B则与Garole的受精能力有关. 在之前的一项研究中, 发现HSPA6基因 (Garole) 与安格斯羊品种的耐热性有关. 这里讨论的结果为检测具有功能重要性的性状遗传变异的选择性扫描提供了基础.

KEYWORDS:

• Composite likelihood ratio
• genomic footprints
• selective sweep
• sheep
• Tajima’s D

关键词:

• 综合似然比
• 基因组足迹
• 选择性扫描
• 羊

Acknowledgments

The authors wish to acknowledge and thank the International Sheep Genomics Consortium (https://www.sheephapmap.org/) to provide access to the OvineSNP50K datasets for eight sheep breeds used in this study. The respective citations for using these datasets are duly given in the manuscript. We thank the anonymous reviewers for their helpful comments on earlier drafts of the manuscript.

Data availability statement

Genotypic data taken for the analysis of the study can be found in the WIDDE database and at the Dryad repository (http://widde.toulouse.inra.fr/widde/widde/main.do?module=sheep).

Disclosure statement

No potential conflict of interest was reported by the author(s).