The epigenetic basis of resilience refers to how environmental factors (like stress, trauma, diet, or social support) physically alter the way your genes behave, without changing your underlying DNA sequence.

The findings, published in Scientific Reports, a Nature Portfolio journal, demonstrate that indigenous chicken breeds possess distinct DNA methylation patterns that regulate genes associated with adaptability, offering fresh insights into why native birds outperform commercial poultry under challenging environmental conditions despite their relatively lower production potential.

The study was led by Dr Malarmathi Muthusamy of the Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Namakkal, under Tanuvas. The research brought together scientists from Tanuvas, the University of Georgia and Berry College in the US, ICAR-Krishi Vigyan Kendra, Pudukkottai, under Tamil Nadu Agricultural University (TNAU), and the University of Jos, Nigeria.

The researchers compared the genome-wide DNA methylation profiles of four indigenous Indian chicken breeds – Aseel, Kadaknath, Nicobari and Naked Neck – with those of commercial broiler and layer chickens. Using Oxford Nanopore long-read sequencing, they mapped two key epigenetic modifications, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), which regulate gene activity without altering the DNA sequence.

The analysis identified between 11.9 million and 44.5 million methylation sites across the six breeds, with each exhibiting a distinct methylation landscape. More than 6,979 differentially methylated regions (DMRs) were detected in every indigenous breed when compared with commercial broilers and layers, highlighting substantial differences in the regulation of genes governing adaptation, productivity and physiological functions.

Principal component analysis clearly distinguished indigenous breeds from commercial strains based on their methylation profiles, while the researchers observed consistently higher methylation levels in native chickens across multiple genomic regions, indicating stronger epigenetic regulation linked to environmental resilience.

“Our findings reveal that each breed possesses a unique methylation landscape shaped by its evolutionary and environmental history. These epigenetic signatures provide valuable insights into the mechanisms that enable indigenous chickens to survive and perform under diverse production systems,” the researchers said.

The study identified several genes associated with economically important traits, including heat tolerance (CDC37 and ELOVL5), egg production (RUNX1 and CBFA2T3), feed intake (CUX1), pigmentation (SLC31A1), and growth and carcass quality (FGF14, PTK7 and LDB2). Other genes, including LINGO1, EFNB1 and NFIA, were associated with behavioural traits, while SIK1 and Rasd1 were linked to osmotic stress adaptation.

The researchers also documented breed-specific epigenetic signatures. Aseel exhibited methylation changes in genes associated with muscle development and behavioural characteristics. Kadaknath showed distinct methylation patterns linked to pigmentation and production traits. Nicobari displayed signatures associated with adaptation to humid coastal environments, while Naked Neck demonstrated methylation changes in genes involved in heat tolerance and stress response.

The findings assume significance for India’s poultry sector as rising temperatures, disease outbreaks and climate variability continue to challenge commercial production systems. “Tamil Nadu, one of the country’s leading poultry-producing States with major broiler and layer clusters in Namakkal, Hosur, Erode and Salem, could leverage these findings to develop breeding programmes that combine the productivity of commercial lines with the resilience of indigenous germplasm. The identified methylation markers could serve as potential epigenetic biomarkers for future breeding programmes,” the researchers said.

They added that integrating epigenetic, genomic, transcriptomic, phenotypic and ecological data would be essential to validate these markers and translate them into practical breeding strategies. The researchers also opined that the study advanced the understanding of epigenetic regulation in poultry and establishes a scientific framework for conserving indigenous chicken breeds while accelerating the development of climate-resilient commercial birds.

At a time when sustainable livestock production is becoming central to food security, the findings position India’s native poultry germplasm as a valuable resource for breeding programmes aimed at balancing productivity with resilience to a changing climate.