Utilitarian selection signatures co-localized with copy number variation regions in Indian goat breeds revealed through whole-genome re-sequencing

This study investigates the selection signatures of 11 Indigenous goat breeds from diverse eco-topographies of India, using whole-genome re-sequencing data from 103 individuals. We identified population-wide copy number variation regions (as well as selection signatures through a variance-stabilizing transformation approach for utility traits. A total of 32 711 polymorphic sites were analyzed, revealing 327 significant and 32 highly significant signatures under selection. Key genes identified in selection signatures include GHR, PLAG1, and MTOR, which play crucial roles in growth, development, and reproductive traits across different utility groups. Notable reproduction-related genes such as ITPR3, ESRRG, and SOX6 were found to be associated with fertility, hormone regulation, and reproductive system. Network analysis revealed ESR1 as a central hub gene forming significant interactions with RUNX2, HDAC2, and BCL2, indicating its vital role in muscle development and metabolism. The MTOR signaling pathway emerged as another crucial hub, connecting with DEPDC5 and SESN1, suggesting its importance in nutrient sensing and metabolic regulation for production traits. Gene ontology analysis of the selection signatures revealed pathways for functional categories between meat, milk, and fiber-producing breeds, reflecting the genetic architecture underlying their specialized phenotypes. Identified selection signatures and hub genes can be used in marker-assisted and genomic selection to improve growth, reproduction, and adaptability in indigenous goats, aiding precision breeding and conservation programs.