Research Projects

Improving economically important traits like growth rate, wool quality, milk yield, and disease resistance in India’s diverse sheep breeds is essential for enhancing productivity and supporting small-scale farmers. However, traditional breeding approaches in India have limitations in targeting these complex, polygenic traits effectively. By using advanced genomic tools such as Genome-Wide Association Studies (GWAS) and selection signature analyses, this study aims to identify critical genetic variants linked to these traits. Findings from this study will guide the development of SNP panels, laying the groundwork for future genomic selection to optimize breeding strategies and support sustainable sheep farming across diverse agro-climatic regions in India. The project has four main objectives: (1) to conduct a GWAS to identify genetic variants associated with traits such as growth rate, wool quality, milk yield, and gastrointestinal nematode (GIN) resistance; (2) to detect genomic signatures of selection related to adaptation and production traits, identifying regions of the genome under selection pressure; (3) to perform functional annotation and pathway analysis of identified genetic variants, connecting them to key biological functions and pathways; and (4) to develop trait-specific SNP panels for implementation in marker-assisted selection and integration into genomic selection programs. The study hypothesizes that indigenous sheep breeds harbour unique genetic variations associated with economically important and adaptive traits, reflecting selection pressures from their native environments. The project’s methodology includes sampling and phenotyping approximately 700–800 sheep from seven indigenous breeds (Malpura, Magra, Patanwadi, Mecheri, Nilgiri, Gaddi, and Muzaffarnagari) for GWAS, and five additional breeds (Bonpala, Kendrapada, Madras Red, Nellore, and Marwari) from different agroclimatic zones of India for selection signature analyses. High-quality DNA will be extracted and genotyped using high-density SNP arrays or whole-genome sequencing. Rigorous quality control, followed by GWAS to pinpoint significant SNPs associated with growth, wool, milk, and disease resistance traits. Parallel selection signature analyses will reveal genomic regions under adaptive selection. The project will then proceed to functional annotation and pathway analysis of candidate genes and genomic regions identified in both GWAS and selection signature analyses. Finally, the design of trait-specific SNP panels for economically important traits will offer an efficient tool for marker-assisted selection. This project will serve as a foundation for future genomic selection in Indian sheep, driving significant advancements in breeding efficiency and productivity.