4个优质鸡群体mtDNA D-loop区遗传多样性分析

Genetic Diversity Analysis of Mitochondrial DNA D-loop Region in Four High Quality Chicken Breeds

本研究旨在利用线粒体DNA(mtDNA)D-loop区序列分析清远麻鸡群体1、清远麻鸡群体2、阳山鸡和清远黄羽乌鸡4个优质鸡群体mtDNA D-loop区遗传多样性。根据GenBank中红原鸡mtDNA序列(登录号:NC_007235.1)针对D-loop区设计特异性引物,PCR扩增并测序后对序列进行分析,统计单倍型数、多态位点数、单倍型多样度、核苷酸多样度和核苷酸平均差异数等,利用Mega 5.10软件计算品种间进化分歧,并构建系统进化树。结果显示,获得了4个优质鸡群体D-loop区长约591 bp序列,经比对后对其中的549 bp进行分析,A、T、C和G碱基含量分别为27.2%~27.3%、30.1%~30.4%、29.5%~29.8%和12.8%~12.9%,G+C平均含量为42.5%,共发现92处单核苷酸多态位点,其中单一多态位点14个、简约信息位点78个,转换和颠换分别占89.13%(82/92)和10.87%(10/92);单倍型多样度为0.682~0.835,核苷酸多样度为0.00849~0.01167;共存在32种单倍型,可分为A、B、C和E共4个分支,其中B(51.2%)和E(37.6%)为优势分支。基于单倍型构建系统进化树发现,4个优质鸡群体可以归为4大分支,与单倍型分类结果一致。表明4个优质鸡群体均具有中等以上多样性,揭示4个优质鸡群体在进化过程中存在两个及两个以上的母系来源。

This study was conducted to elucidate the genetic diversity of mitochondrial DNA(mtDNA)D-loop region in Qingyuan partridge chicken group 1,Qingyuan partridge chicken group 2,Yangshan chicken and Qingyuan Yellow feather black-bone chicken.The specific primers were designed according to mtDNA D-loop region of Gullus gullus spadiceus(accession No.:NC_007235.1)in GenBank.The sequence was analyzed after PCR amplification and sequencing,and the haplotype number,polymorphism number,haplotype diversity,nucleotide diversity and nucleotide mean difference were counted.The evolution divergence among breeds was calculated by Mega 5.10 software,and the phylogenetic tree was constructed.The results showed that the length of mtDNA D-loop region in four high quality chicken breeds was 591 bp,and 549 bp were used for subsequent analysis.The content of A,T,C and G were 27.2%to 27.3%,30.1%to 30.4%,29.5%to 29.8%and 12.8%to 12.9%,respectively,and the average content of G+C was 42.5%.There were 92 polymorphic sites which contained 14 singleton variable sites and 78 parsimony informative sites,and the percentage of transitions and transversions were 89.13%(82/92)and 10.87%(10/92),respectively.The haplotype diversity ranged from 0.682 to 0.835,and the nucleotide diversity ranged from 0.00849 to 0.01167.There were 32 haplotypes in all sequences,which could be divided into clades A,B,C and E,however,most of the individuals belonged to clades B(51.2%)and E(37.6%).The phylogenetic tree results showed that four high quality chicken breeds could be classified as 4 branches which were consistent with the haplotypes classification results.The results indicated that the four high quality chicken populations from Qingyuan had relatively high haplotype and nucleotide diversity and likely shared two or more common maternal lineages.