Estimation of Genetic Diversity in Nigerian Local Chickens Using Mitochondrial Cytochrome C Oxidase Subunit 1 (COI) Gene Sequences
This study evaluated the genetic diversity of Nigerian indigenous chickens using sequences obtained from the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of fifty local chickens of five distinct phenotypic groups (Normal Feather, Naked Neck, Frizzle Feather, Crested Feather, and Ptilopody) were randomly sampled from Kwara State, Nigeria. Blood samples were collected from fifteen chickens according to feather type for genomic DNA extraction and sequencing using mitochondrial cytochrome C oxidase 1 (COI) primers.
Sequence alignment and diversity analyses were carried out using MEGA 11.0 and DnaSP V6 software, respectively. Among the 358 nucleotide sites examined, only three variable positions were identified, all of which had mutations that occurred at alignment positions 13, 14, and 15. The sequences had haplotype diversity of 0.154 and nucleotide diversity of 0.00135, which were very low, indicating limited mitochondrial genetic variation among the sampled indigenous chicken phenotypes. Neutrality analyses generated negative but statistically non-significant values for Tajima’s D (−1.652), Fu and Li’s D* (−2.025), and Fu and Li’s F* (−2.189). These findings indicated that the mitochondrial COI marker has limited discriminatory power for detecting genetic differences among Nigerian local chicken phenotypes but recommend future investigations with a larger population so as to obtain a more comprehensive understanding of genetic diversity and population structure in Nigerian local chickens.
Keywords: Genetic diversity, Nigerian local chicken, mitochondrial cytochrome c oxidase1, haplotype diversity.
