Mapping genome-wide diversity and population dynamics in Indian chicken breeds for targeted conservation and breeding

1. Genetic improvement and widespread use of artificial selection may have impacted the genetic make-up of Indian chicken breeds. The genetic architecture of contemporary chicken population of India needs to be assessed for future improvement and conservation programmes. This study utilised whole-genome sequences in 180 chicken samples from 16 indigenous breeds, along with the Red Jungle Fowl and the commercial White Leghorn. 2. A panel of 76 978 genome-wide single-nucleotide polymorphisms (SNP) was selected for comparative genome analysis after stringent screening. Breeds originating from the eastern regions of India exhibited higher genomic diversity, indicative of a rich repository of distinct germplasm. Conversely, the Uttara breed, from the northern hilly areas, display considerable genetic differentiation with diminished diversity compared to others, underscoring conservation concerns. The average coefficient (F_IS) of 0.084 caution the need to mitigate risks associated with inbreeding. 3. The study revealed that the analysis of 76 978 genome-wide SNP will serve as a cornerstone in refining conservation strategies, to design interventions with greater precision. 4. The contribution of Red Jungle Fowl to the gene pool of all native breeds was supported by this study. Genetic structuring indicated a relationship among breeds based on geographical proximity, underscored by varying levels of admixture.