Genomic advancements in goat breeding: enhancing productivity, disease resistance, and sustainability in India's rural economy.

Goats are vital to the rural economy of India, contributing significantly to livelihoods, nutrition, and agricultural sustainability. With a population of 148.88 million, India holds the world's largest goat population, comprising 41 recognized indigenous breeds. These goats provide milk, meat, and fiber, particularly in marginal environments. The genomic advancements in goat research have revolutionized the understanding of genetic diversity, adaptation, and trait improvement. Whole-genome sequencing (WGS), single nucleotide polymorphism (SNP) arrays and transcriptomics have unveiled genetic markers associated with production, disease resistance, and reproductive traits. Genomic tools such as the Illumina Goat SNP50K BeadChip and high-throughput sequencing technologies have facilitated the identification of selection signatures and quantitative trait loci (QTL), influencing economically important traits like milk yield, meat quality, and prolificacy. Notably, genes such as DGAT1, GHR, BMPR1B, and HSP70 have been linked to production efficiency, reproductive performance, and climate resilience. Genome-wide association studies (GWAS) and genomic selection (GS) have enabled precision breeding, enhancing genetic gains and reducing inbreeding risks. The application of RNA sequencing has provided insights into gene expression patterns governing lactation, growth, and reproductive efficiency. Epigenomic studies, focusing on DNA methylation and histone modifications, have highlighted regulatory mechanisms underpinning prolificacy and muscle development. Conservation genomics has played a pivotal role in safeguarding native breeds by assessing genetic diversity and mitigating inbreeding depression. Indicine goat breeds, such as Jamunapari, Beetal, Barbari, and Black Bengal, exhibit unique genetic adaptations to diverse agro-climatic conditions, emphasizing the need for their conservation. Emerging technologies, including CRISPR-Cas9 gene editing, hold promise for precision breeding to enhance productivity and disease resistance. Integrating genomics with artificial intelligence (AI) and big data analytics is poised to revolutionize goat breeding and management. Future efforts should focus on expanding genomic databases, developing breed-specific reference genomes, and promoting genomic literacy among farmers to ensure sustainable goat production and improve rural livelihoods in India.