Genome-Wide Identification of SNPs and Their Annotation in Indian Gir Cattle

Pub Date : 2024-07-23 DOI:10.3103/s0095452724040042

Anjali Choudhary, M. Joel Devadasan, Nidhi Sukhija, K. K. Kanaka, D. Ravi Kumar, M. R. Vineeth, T. Surya, Archana Verma, S. K. Niranjan, Jayakumar Sivalingam

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Abstract

The study was carried out in Gir cattle for identification of genome wide SNPs and then to annotate the identified high-quality SNPs to the milk production traits. A total of 99 517 SNPs were identified with respect to the Bos indicus reference genome. Upon annotation of SNPs identified with respect to Bos indicus reference genome, 984 SNPs located in 175 candidate genes related with milk production traits, notably Acetyl-CoA carboxylase β gene, which affects milk composition traits by regulation of fatty acid oxidation in the mitochondria; Growth hormone receptor gene which have role in milk yield and its composition traits; LEP gene, involved in energy partitioning and metabolism, were among others. This study provides the first analysis of ddRAD sequences to discover SNPs in Indian Gir cattle breed, aligned to indicine reference genome. The variants mined in this study can be incorporated in existing SNP chips and thus, play an important role in understanding the genetic structure of our cattle in order to design appropriate breed improvement programmes.

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印度吉尔牛全基因组 SNPs 鉴定及其注释

摘要该研究在吉尔牛中进行了全基因组SNPs的鉴定，然后将鉴定出的高质量SNPs注释到产奶性状中。研究共鉴定出 99 517 个 SNPs，这些 SNPs 均来自于麝香牛参考基因组。在对参考基因组中的 SNPs 进行注释后，发现 984 个 SNPs 位于 175 个与产奶性状相关的候选基因中，特别是乙酰-CoA 羧化酶 β 基因，该基因通过调节线粒体中的脂肪酸氧化影响牛奶成分性状；生长激素受体基因，该基因在产奶量及其成分性状中发挥作用；LEP 基因，该基因参与能量分配和代谢。本研究首次通过分析 ddRAD 序列发现了印度吉尔牛品种的 SNPs，并与 indicine 参考基因组进行了比对。本研究中发现的变异可纳入现有的 SNP 芯片，从而在了解我国牛的遗传结构以设计适当的品种改良计划方面发挥重要作用。

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