Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection

Abstract

The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima’s D, CLR, iHS, varLD, ROH, and F_ST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.

Keywords:

• Cattle
• coat color
• pigmentation
• selection signature

CRediT authorship contribution statement

Divya Rajawat: Methodology, Writing – original draft. Manjit Panigrahi: Conceptualization, Methodology, Writing – review & editing. Sonali Sonejita Nayak: Writing – review & editing. Kanika Ghildiyal: Writing – review & editing. Anurodh Sharma: Review & editing. Harshit Kumar: editing. Subhashree Parida: Writing – review & editing. Bharat Bhushan, G.K. Gaur, Triveni Dutt, and B.P. Mishra: Resources, Supervision.

Disclosure statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Data availability statement

The WIDDE database and the Dryad repository both contain the genotypic data used for this study (http://widde.toulouse.inra.fr/widde/). The genotypic information for the 72 Tharparkar animals utilized in this work is accessible with the corresponding author, and due to some institutional liabilities, we can disclose this dataset on request.

Additional information

Funding

This research work has been funded by the National Agricultural Science Fund (NASF).