基于线粒体DNA D-loop区的肉鸡品种遗传多样性和起源分析

【目的】探讨不同生长速度鸡品种（配套系）线粒体DNA D-loop区全序列遗传多样性和起源特性,为肉鸡品种选育和溯源提供理论依据。【方法】以不同生长速度的8个黄羽肉鸡配套系（中快速型5个、慢速型3个）、2个地方鸡种（固始鸡、藏鸡）、2个引进鸡种（隐性白羽鸡、安卡鸡）、1个白羽肉鸡（罗斯308）、817杂交肉鸡以及1个高产蛋鸡配套系（大午褐壳蛋鸡）共计15个鸡种为研究对象,采集血液提取DNA后进行PCR扩增,对15个鸡种共683个个体mtDNA D-loop区全序列进行测序,使用DnaSP 5.10软件分析各个鸡种遗传多样性和单倍型特点,使用MEGA 4.0软件计算种间遗传距离,构建不同单倍型与红色原鸡之间NJ系统发育树,分析起源和亲缘关系。【结果】15个鸡种线粒体D-loop区全序列大小为1 231—1 232bp,序列长度为1 231 bp的个体在859 bp处存在C碱基缺失。683个个体共检测到45个变异位点,组合为53个单倍型,可以分为A、B、C和E共4个单倍型群,其中中快速型肉鸡、817杂交肉鸡以及高产蛋鸡均是E单倍型为优势单倍型（≥48.89%）;慢速型黄羽肉鸡中鸿光黑鸡优势单倍型为B单倍型,京海黄鸡优势单倍型为A单倍型,雪山鸡4种单倍型相对均衡,3个慢速型黄羽肉鸡配套系E单倍型比例≤38.46%;地方鸡种中固始鸡的单倍型为A和C型,藏鸡的单倍型为A和B型。15个鸡种单倍型多样度（Hd）分布在0.496—0.853,核苷酸多样度（Pi）分布在0.00146—0.00673,遗传多样性相对丰富的品种（配套系）是新兴矮脚黄鸡、雪山鸡、京海黄鸡和罗斯308;遗传多样性程度相对较低的品种（配套系）是藏鸡、高产蛋鸡、安卡鸡、新兴麻鸡4号和墟岗黄鸡1号。15个鸡种Kiumura双参数距离范围为0.0016—0.0113,其中罗斯308种内遗传距离最大,而817杂交肉鸡和高产蛋鸡的种内遗传距离最小;种间遗传距离最大为高产蛋鸡与藏鸡之间,最小为高产蛋鸡与817杂交肉鸡之间;中快速型黄羽肉鸡配套系相互之间遗传距离相对较小,而与慢速型黄羽肉鸡配套系以及地方鸡种之间遗传距离相对较大;京海黄鸡和鸿光黑鸡均是与藏鸡遗传距离最小。聚类分析显示,A、B单倍型群与红色原鸡滇南亚种交叉聚为一枝;E单倍型与红色原鸡印度亚种交叉聚为一枝;C单倍型群与红色原鸡印度亚种、滇南亚种、指名亚种以及印尼亚种交叉聚为一枝。【结论】不同生长速度鸡种之间线粒体D-loop区遗传多样性程度差异较大;E单倍型与肉鸡生长速度具有较强的相关性,中快速型群体均以E单倍型为优势单倍型,而慢速型群体E单倍型比例均低于40%;我国家鸡群体具有多个红色原鸡母系起源,显示其在中性选择下被驯化。研究结果为肉鸡品种选育和溯源以及资源化开发利用提供了理论依据。

Genetic Diversity and Origin Characteristics of Chicken Species Based on Mitochondrial DNA D-loop Region

【Objective】 The purpose of this study was to investigate the genetic diversity and origin characteristics of the whole sequence of mitochondrial DNA D-loop region in chicken breeds (complete set line) with different growth rates, so as to provide a theoretical basis for breeding and traceability of broiler breeds. 【Method】 15 broiler breeds with different growth rates were used as research materials, including eight yellow-feathered broiler lines (5 medium-fast and 3 slow lines), two local chicken breeds (Gushi chicken and Tibetan chicken), two introduced chicken breeds (Recessive White and Anka), one white-feathered broiler (Ross 308), 817 hybrid broiler and one commercial layer line (Dawu Brown Eggshell Hens). Chicken blood was collected, and DNA was PCR amplified. The full sequences of mtDNA D-loop region of 683 individuals from 15 chicken breeds were sequenced, and the genetic diversity and haplotype characteristics of each chicken breed were analyzed using DnaSP 5.10 software. The genetic distance between breeds was calculated using MEGA 4.0 software, and then a phylogenetic tree was constructed between different haplotypes and the red original chicken. 【Result】The full sequence size of the D-loop region of 15 chicken breeds ranged from 1 231 to 1 232 bp, and individuals with sequence length of 1 231 bp had C-base deletion at 859 bp. 45 variant loci were detected in 683 individuals, which were combined into 53 haplotypes and could be divided into four haplotype groups, including A, B, C and E. Among them, the medium-fast broilers, 817 hybrid broilers and high-yielding laying hens were all haplotype E as the dominant haplotype (≥48.89%); the dominant haplotypes were B haplotypes for Hongguang black chickens, A haplotypes for Jinghai yellow chickens, and four haplotypes were relatively balanced for Xueshan chickens (the proportion of E haplotypes ≤38.46% for three chicken breeds); the haplotypes of local chicken breeds were A and C haplotypes for Gushi chickens and A and B haplotypes for Tibetan chickens. The genetic diversity of the 15 chicken breeds ranged from 0.496 to 0.853 for Hd and from 0.00146 to 0.00673 for Pi. The relatively rich genetic diversity was found in the Xinxing Dwarf Yellow Chicken, Xueshan Chicken, Jinghai Yellow Chicken and Ross 308; the relatively low genetic diversity was found in the Tibetan Chicken, the High Laying Chicken, the Anka Chicken, the Xinxing partridge Chicken No. 4 and the Xugang Yellow Chicken No. 1. The range of Kiumura two-parameter distance of 15 chicken breeds was 0.0016-0.0113, among which the intra-breed genetic distance of Ross 308 was the largest while the intra-breed genetic distance of 817 hybrid broiler and high-yielding chicken was the smallest; the inter-breed genetic distance was the largest between high-yielding chicken and Tibetan chicken, and the smallest between high-yielding chicken and 817 hybrid broiler; the genetic distance between medium-fast broiler was relatively small while the genetic distance between medium-fast broiler, slow-fast and local chicken breeds was relatively large; the genetic distance between Jinghai and local chicken breeds was relatively large. Cluster analysis showed that the haplotypes A, B, and gallus gallus spadiceus were clustered in one group. Haplotype E and gallus gallus murghi were clustered in another group. Haplotype C was clustered with four subspecies of jungle fowl, including gallus gallus murghi, gallus gallus spadiceus, gallus gallus gallus and gallus gallus bankiva. 【Conclusion】The genetic diversity of mitochondrial D-loop region varied among different chicken breeds; E haplotypes were strongly correlated with broiler growth rate, and E haplotypes were the dominant haplotypes in all medium and fast populations, while the proportion of E haplotypes in slow populations was less than 40%; the national chicken population had multiple red proto-chicken maternal origins, indicating that it was domesticated under neutral selection. The results of the study provided a theoretical basis for broiler breed selection and tracing as well as resource exploitation.