Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes

Abstract

Background and Aim: India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India. Materials and Methods: Two mitochondrial markers, namely, cytochrome c oxidase subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares. Results: Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds. Conclusion: Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens.

A Comparable genetic diversity between chicken ecotypes of different zones using DNA barcoding

“…Although ISM ecotypes have a relatively wider length range (563-611 bp) compared to TA ecotype (570-607 bp). The average sequence length was shorter than what was reported by Xun-he et al (2016) 28 31 found that the sequence length of cytochrome c oxidase subunit I length for two native Indian chicken breeds averaged 608 and 756 bp. However, it is also important to note that due to the fact that the molecular evolution rate fluctuate among various segments of the genome and across taxa, there no species-specific standard sequence length.…”

“…To our surprise, both ecotypes have the same number of sites 548 bp (Table 1) 31 found that the total number of sites of two native Indian chicken populations was 596 and 647 of which merely 3 and 4 polymorphic sites were detected. Yu-Shi et al (2011) 33 on 26 individuals of two newly discovered chicken breeds found only 10 variation sites, of which only 6 sites were single polymorphism sites while 4 were simple information sites.…”

“…Haplotype diversity (Hd) and nucleotide diversity (π) are both of principle importance for assessment of genetic diversity of either population or breed. 31 Haplotype diversity implies the distinctiveness of a certain haplotype in a particular population. Therefore, the higher Hd's mean and π the richer genetic diversity in population.…”

Sık Kullanılan Bazı Hücre Hatları için Kalite Kontrol: Mikoplazma Kontaminasyon Tespiti, Sitokrom B ve Sitokrom Oksidaz Alt Birim I Genlerinin DNA Dizi Analizlerinin Gerçekleştirilmesi

“…Günümüzde, PCR ile DNA analizi, ilgi konusu genlerin bölgelerinin amplifiye edilmesine izin verdiği için, türlerin tanımlanmasında rutin olarak kullanılan bir yöntem haline gelmiştir [25][26][27] .…”

“…Türlerin tanımlanmasında uluslararası olarak önerilen iki mitokondriyal bölge bulunmaktadır: sitokrom B (CYTB) ve sitokrom c oksidaz alt birim I geni (COI). CYTB ve COI bölgeleri evrensel primerler tarafından tanınan bazı stabil dizilere, kimliklendirmeyi sağlayacak birtakım dizi çeşitliliklerine sahiptir, bu nedenle bu nükleotid dizileri türe özgü bilgiler içerir 9,27 .…”