Genetic Diversity of Mitochondrial DNA (mtDNA) D-Loop Sequences in Six Improved Tropically Adapted Chicken Breeds (iTABs) in Imo State, Nigeria

Abstract

The improved tropically adapted chicken breeds (iTABs) are low-input-high-output chickens suitable for smallholder poultry (SHP). Six iTABs (Fulani, FUNAAB Alpha, Kuroiler, Noiler, Sasso and Shika Brown) were introduced, and were raised under semi-intensive management system and tested under the African Chicken Genetic Gains project in Nigeria. The objective of this study was to evaluate the genetic diversity of these iTABs tested in Imo State Nigeria using mitochondrial DNA (mtDNA), Blood samples were collected from 77 chickens belonging to these six populations of iTABs in the ratio (12:12:14:13:13:13), for Noiler, FUNAAB Alpha, Shika Brown, Kuroiler, Sasso and Fulani chickens, respectively. Genomic DNA was extracted from seventy-seven birds randomly selected from the six iTABs. A 450-bp mtDNA D-loop region was sequenced. The highest (H=5) and the lowest (H=2) number of haplotypes were found within Noiler, and Shika Brown/Fulani, respectively. Among the six populations, haplotype and nucleotide diversity was 0.558±0.063 and 0.0064±0.0013, respectively. A total of 8 haplotypes were identified from 15 polymorphic sites. These haplotypes clustered into three clades with 87.89% of the total maternal genetic variations occurring within population. Fulani and Shika Brown had the least (0.000) genetic distance. Tajima’s D was negative among populations and within Noiler, Kuroiler, Sasso and Fulani populations but was only statistically significant within the Noiler population. Diversity indices of this study revealed that mtDNA polymorphism was on the average both within populations and among populations. The results indicate the existence of two distinct maternal lineages from Southeast Asia, south central and Southeast China evenly distributed among the iTABs. The average genetic diversity observed within population can be utilized for the long-term genetic improvement and stabilization of the breeds.