干旱区生态环境知识资源中心(Arid): Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India

Arid

DOI	10.1080/10495398.2023.2290521
	Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India
	Sukhija, Nidhi; Malik, Anoop Anand; Devadasan, Joel M.; Dash, Aishwarya; Bidyalaxmi, Kangabam; Kumar, D. Ravi; Devi, M. Kousalaya; Choudhary, Anjali; Kanaka, K. K.; Sharma, Rekha; Tripathi, Shashi Bhushan; Niranjan, Saket Kumar; Sivalingam, Jayakumar; Verma, Archana
通讯作者	Sivalingam, J
来源期刊	ANIMAL BIOTECHNOLOGY
ISSN	1049-5398
EISSN	1532-2378
出版年	2024
卷号	35 期号:1
英文摘要	The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.
英文关键词	ddRAD-seq Gir Tharparkar selection signatures SNPs
类型	Article
语种	英语
开放获取类型	hybrid
收录类别	SCI-E
WOS记录号	WOS:001126643100001
WOS关键词	FERTILITY TRAITS ; CELL-ADHESION ; SHEEP BREEDS ; REVEALS ; IDENTIFICATION ; ASSOCIATION ; HITCHHIKING ; ADAPTATION ; PROTEIN ; SNPS
WOS类目	Agriculture, Dairy & Animal Science ; Biotechnology & Applied Microbiology
WOS研究方向	Agriculture ; Biotechnology & Applied Microbiology
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/402820
推荐引用方式 GB/T 7714	Sukhija, Nidhi,Malik, Anoop Anand,Devadasan, Joel M.,et al. Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India[J],2024,35(1).
APA	Sukhija, Nidhi.,Malik, Anoop Anand.,Devadasan, Joel M..,Dash, Aishwarya.,Bidyalaxmi, Kangabam.,...&Verma, Archana.(2024).Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India.ANIMAL BIOTECHNOLOGY,35(1).
MLA	Sukhija, Nidhi,et al."Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India".ANIMAL BIOTECHNOLOGY 35.1(2024).