Analysis of the D-loop, Phe-tRNA, 12S-rRNA (bar2) mitochondrial gene in black-bone chickens compared to other chickens from gene banks
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Abstract
Black chickens are an economically important animal species that are extensively grown, having high nutritional value and therapeutic characteristics, which work as an antioxidant and play a role in immunological function. They are popular among health-conscious individuals. Black-bone chicken is a variety of chicken breeds raised in Thailand, while black chickens are expensive compared to other chicken breeds, especially Indonesian black chickens which are black throughout the body even the feathers, bones and meat. So, there is a demand for pure breed Indonesian black chickens. However, there is a lack of information on the genetic diversity of black-bone chickens raised in Thailand. This study aimed to find the genetic diversity of the D-loop, Phe-tRNA and 12S-rRNA (bar2) genes located in the mitochondria. The 14 Indonesian black chickens grown in Thailand were compared to 70 samples of chicken data from the GenBank database to identify genetic markers that differ in different chicken breeds. The analysis was performed using PCR and then the PCR product was analyzed to determine the base sequence. The haplotypes were determined using DnaSP6 and the phylogenetic tree was constructed using MEGA 11. The results found that most Indonesian black chickens had nucleotide sequences of their target genes that were uniquely different from those of other chickens (outgroup). On the other hand, they had nucleotide sequences that were closest to the Silkie chickens, based on the results shown in the phylogenetic tree. The results of the haplotype found that Indonesian black chickens were divided into 7 haplotypes, indicating the high genetic diversity of Indonesian black chickens in Thailand. It also was found that the sequence at position 812 bp had a specific sequence in haplotypes 1-7 of Indonesian black chickens with T bases, while haplotypes 8-14 of chickens from the GenBank database had all C bases. In future study, the nucleotide sequence of Indonesian chickens at the 812 bp location, specifically the SNPs, can be utilized as a molecular marker to identify and select black chickens.
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