Molecular characterisation of mtDNA D-loop in three indigenous chicken populations in Southwestern Nigeria

The detailed knowledge of population structure among and within breeds of chickens is essential for conservation and strategies. It is therefore important to evaluate the existing chicken genetic resources using genomic approaches. In most species, the mitochondrial DNA D-loop region is the most variable part of the mitochondrial DNA molecule because of the lack of coding constraints. The analysis of mtDNA D-loop sequences revealed several single nucleotide polymorphisms in the chicken population studied. This study was carried out on indigenous chickens in different geographical zones in South-West region of Nigeria. Nigerian indigenous female chickens consisting of normal feathered (50), frizzle feathered (25) and naked neck (25) constituted base materials for this study, blood samples  was collected from the wing veins of each birds and then transferred immediately to FTA card. Following this, the samples were transferred to the ACUTIG Genetics Laboratory, for DNA extraction. Genomic DNA was isolated and amplified with mitochondrial DNA D-loop primers and then sequenced. Data collected were analysed with various molecular software. The calculated Polymorphic information content (PIC) and heterozygosity ranged from 0.43-0.97 and 0.03-0.45 in all the chickens examined with mitochondrial DNA D-loop markers respectively. Single nucleotide polymorphism  (SNPs) observed in normal feathered, naked neck and frizzle feathered chickens were 20, 19 and 17 with major allele frequency (MAF) having the lowest and the highest values of  0.55 in SNPs (677A>G) and 0.97 in SNPs (5A>T, 321C>T, 346T>C); 0.64  in SNPs (151T>C, 201C>T, 209C>T, 227C>T, 240C>T, 245T>C, 294T>C, 430T>C , 670A>G) and 0.93  in SNPs (194C>T, 196G>A, 314C>T, 342A>G); and 0.71 in SNPs (677G>A) and 0.93 in SNPs (5A>T) respectively. Networking analysis revealed two haplogroup. The study identified high mtDNA D-loop variation resulting from high mtDNA D-loop polymorphisms in Southwestern Nigeria indigenous chicken populations. Furthermore, the population of indigenous chickens in this study showed low level of heterozygosity and as such may be homogenous in nature which is an indicative of their potentials for genetic improvement via selection or crossbreeding.