Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India

Anim Biotechnol. 2023 Dec 13:1-15. doi: 10.1080/10495398.2023.2290521. Online ahead of print.ABSTRACTThe 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...

Source: Animal Biotechnology - December 13, 2023 Category: Biotechnology Authors: Nidhi Sukhija Anoop Anand Malik Joel M Devadasan Aishwarya Dash Kangabam Bidyalaxmi D Ravi Kumar M Kousalaya Devi Anjali Choudhary K K Kanaka Rekha Sharma Shashi Bhushan Tripathi Saket Kumar Niranjan Jayakumar Sivalingam Archana Verma Source Type: research