Genetic diversity of red-plumaged native chicken ecotype from northern Kerala using mitochondrial DNA D-loop sequence analysis

Indigenous chickens play a vital role in rural livelihoods, particularly in developing countries, due to their resilience and adaptability to diverse agro-climatic conditions. While the Tellicherry breed is the only officially recognized chicken breed from Kerala, several other distinct ecotypes persist, including a red-plumaged ecotype. This study aimed to characterize this ecotype's genetic diversity and population structure, which is crucial for its conservation and improvement through targeted b reeding programs. The mitochondrial DNA (mtDNA) D-loop region of thirty native red chickens conserved at the AICRP Poultry Farm was sequenced. Analysis revealed fifteen distinct haplotypes, predominantly aligning with haplogroups A and E, commonly associated with South Asian domestic chicken populations. The moderate nucleotide diversity (☐ = 0.00315) and high haplotype diversity (Hd = 0.910) indicate a genetically diverse population with multiple maternal lineages. Phylogenetic analysis confirmed the clustering of these haplotypes within established South Asian haplogroups, underscoring their potential conservation value. These findings emphasize the importance of genetically characterizing local chicken ecotypes to preserve genetic diversity and support sustainable rural poultry production.