Genome wide copy number diversity in Indian goat breeds scaled to world-wide breeds

IF 1.6 3区农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Small Ruminant Research Pub Date : 2025-05-08 DOI:10.1016/j.smallrumres.2025.107525

Nidhi Sukhija , Indrajit Ganguly , K.K. Kanaka , S.P. Dixit , Sanjeev Singh , Avnish Bhatia , Rangasai Chandra Goli , Pallavi Rathi

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引用次数: 0

Abstract

Copy number variations (CNVs), heritable chromosomal structural changes characterized by deletions or insertions exceeding 50 base pairs, is an emerging area in genetic diversity research due to their significant roles in morphological, metabolic, and adaptive traits. Despite the global exploration of CNVs across various species, limited attention has been given to goats, particularly Indian breeds. This study utilized whole-genome resequencing (WGRS) data from Indian goat breeds in comparison to transboundary and global breeds/populations, including wild relatives, to investigate copy number variation regions (CNVRs) as markers of genetic diversity and population structure. A total of 103 sequences from indigenous breeds and nine publicly available trans-boundary sequences representing Black Bengal and Beetal goats were analyzed as Dataset-I, while Dataset-II comprised 262 whole genome sequences from global breeds and wild relatives. CNVRs were identified using CNVcaller, leveraging normalized read depth across sliding windows, resulting in 63,728 CNVRs in Dataset-I and 48,869 CNVRs in Dataset-II. These numbers surpass previous reports, attributed to refined resolution, larger sample sizes, and advanced detection algorithms. Principal component analysis (PCA) and admixture analyses leveraged by CVerror (https://github.com/chau-mau/CVerror) revealed clustering patterns, demonstrating genetic uniqueness among Indian breeds while highlighting admixture with transboundary populations. Phylogenetic analysis using custom pipeline named Plink2Phylo (https://github.com/kkokay07/pq-genetics/tree/main/Plink2Phylo; Kanaka 2025), identified distinct evolutionary nodes, with Uttarakhand Hill and Black Bengal showing unique clustering patterns, affirming rich genetic diversity. This research provides a comprehensive framework for understanding CNVR-based genetic diversity in Indian goats, positioning them within the global genetic landscape.

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印度山羊品种的基因组拷贝数多样性扩展到世界范围的品种

拷贝数变异（拷贝数变异，Copy number variation, CNVs）是一种以缺失或插入超过50个碱基对为特征的遗传性染色体结构变化，由于其在形态、代谢和适应性状中具有重要作用，是遗传多样性研究的一个新兴领域。尽管全球对不同物种的克隆变异进行了探索，但对山羊，特别是印度品种的关注有限。本研究利用来自印度山羊品种的全基因组重测序（WGRS）数据，与跨境和全球品种/群体（包括野生近缘品种）进行比较，研究拷贝数变异区（CNVRs）作为遗传多样性和群体结构的标记。数据集i分析了来自本土品种的103个序列和代表黑孟加拉山羊和Beetal山羊的9个公开的跨界序列，而数据集ii分析了来自全球品种和野生近缘品种的262个全基因组序列。使用CNVcaller识别cnvr，利用跨滑动窗口的标准化读取深度，在Dataset-I中产生63,728个cnvr，在Dataset-II中产生48,869个cnvr。由于精细的分辨率、更大的样本量和先进的检测算法，这些数字超过了以前的报告。主成分分析（PCA）和CVerror （https://github.com/chau-mau/CVerror）利用的混合分析揭示了聚类模式，显示了印度品种之间的遗传独特性，同时突出了跨界种群的混合。系统发育分析使用自定义管道命名为Plink2Phylo (https://github.com/kkokay07/pq-genetics/tree/main/Plink2Phylo；Kanaka 2025)，确定了不同的进化节点，北阿坎德山和黑孟加拉显示出独特的集群模式，肯定了丰富的遗传多样性。这项研究为了解印度山羊基于cnvr的遗传多样性提供了一个全面的框架，将它们定位在全球遗传格局中。

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来源期刊

Small Ruminant Research 农林科学-奶制品与动物科学

CiteScore

3.10

自引率

11.10%

发文量

210

审稿时长

12.5 weeks

期刊介绍： Small Ruminant Research publishes original, basic and applied research articles, technical notes, and review articles on research relating to goats, sheep, deer, the New World camelids llama, alpaca, vicuna and guanaco, and the Old World camels. Topics covered include nutrition, physiology, anatomy, genetics, microbiology, ethology, product technology, socio-economics, management, sustainability and environment, veterinary medicine and husbandry engineering.