Indigenous chickens (ICs) are known for disease resistance and hardiness. The role of major histocompatibility complex (MHC) in disease resistance is well known. The present study carried out to find out variability at the MHC revealed higher genetic variability at the MHC of ICs over White Leghorn birds. ICs are likely to have new alleles of the LEI0258 marker of MHC. Some alleles were found to be associated with growth, production, survivability and antibody titres to Newcastle disease virus.

To study whether chicken PLIN1 expression is regulated by DNA methylation, we analyzed the promoter methylation status and expression of the PLIN1 gene, and found that chicken PLIN1 expression was significantly positively correlated with abdominal fat percentage, the DNA methylation of CpG5 at position −490 bp of the promoter had a certain impact on PLIN1 expression. These results imply that epigenetic regulation of PLIN1 might be important for hypertrophic growth in chicken adipose development.

Substitution of amino acids due to single nucleotide polymorphisms (SNPs) in pattern recognition receptors leads to altered innate immunity to diseases. The present study shows extensive polymorphisms in coding sequences of TLR (TLR3, TLR1LA) and NLR (NOD1) genes compared to the RLR (MDA5, LGP2) gene. SNPs were higher in Indian chicken breeds (Ghagus and Nicobari) compared to the WLH breed. A computer simulation study revealed a neutral effect of most non-synonymous SNPs on protein function.