The epigenetic landscape of adaptability reveals key methylation differences in indigenous Indian and commercial chickens

DNA methylation is an epigenetic mechanism that regulates gene function and plays a crucial role in adaptability traits. Unlike commercial chickens, which have been bred for uniform production performance, desi chickens experience varying environmental pressures, shaping their genetic diversity and survival strategies through organized methylation patterns. We compared global DNA methylation profiles between indigenous (Al, Kn, Nb, and Nn) and commercial chickens (Br and Ly) to identify epigenetic factors. In this study, a single cytosine base modification was observed globally in all six breeds, ranging from 11,935,490 to 44,572,168. Each indigenous and commercial chicken breed exhibited a unique methylation pattern. Further analysis revealed that more than 6979 differentially methylated regions (DMRs) were identified in each indigenous breed compared to the commercial layer and broiler. The identified DMR-associated genes (DMGs) revealed various adaptational processes in each breed. The chicken breeds studied showed different levels of methylation across various genes, indicating breed-specific differences. They were inferred as epigenetic markers for traits, which makes them differ between the breeds, like cognitive behavioral (LINGO1, EFNB1 and NFIA), feed intake (CUX1), thermal stress adaptation (CDC37 and ELOVL5), egg production (RUNX1, and CBFA2T3), hyperpigmentation (SLC31A1), osmotic stress adaptation (SIK1 and Rasd1), growth and carcass quality (LINGO1, PTK7, GPHN, LDB2 and FGF14) and feathering pattern (EFNB1). This study extends our understanding of the epigenetic regulatory mechanisms across different chicken breeds and highlights the value of the environmental adaptability of indigenous germplasm. Finally, we suggest that validating these markers by integrating transcriptomic, phenotypic, and ecological data will be critical for the comprehensive integration of epigenetic and phenotypic data into breeding and conservation biology.