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

Abstract

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 F_ST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and F_ST 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.

Keywords:

• ddRAD-seq
• Gir
• Tharparkar
• selection signatures
• SNPs

Acknowledgements

The authors thank the Director, ICAR-National Dairy Research Institute, and the Director, ICAR-National Bureau of Animal Genetic Resources, for their support in carrying out this research work. The authors express their sincere thanks to Dr. Parameswari B., Senior Scientist (Plant Pathology), and Dr. Neeraj Kulshreshtha, Principal Scientist (Plant Breeding) and Head, Regional Centre, Sugarcane Breeding Institute Regional Centre, Karnal, Haryana, for providing computational facilities for this work.

Disclosure statement

On behalf of all authors, the corresponding authors state that there is no conflict of interest.

Data availability statement

All data generated or analysed during this study are included in this manuscript.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.