生物多样性 ›› 2019, Vol. 27 ›› Issue (6): 667-676.DOI: 10.17520/biods.2019013

• 研究报告:动物多样性 • 上一篇    下一篇

利用线粒体COI基因揭示中国乌骨鸡遗传多样性和群体遗传结构

翁茁先1,2,3,黄佳琼2,张仕豪2,余锴纯2,钟福生1,2,3,黄勋和2,3,*(),张彬1,*()   

  1. 1 湖南农业大学动物科学技术学院, 长沙 410128
    2 嘉应学院生命科学学院, 广东梅州 514015
    3 广东省五华三黄鸡科技创新中心, 广东梅州 514015
  • 收稿日期:2019-01-17 接受日期:2019-05-20 出版日期:2019-06-20 发布日期:2019-06-14
  • 通讯作者: 黄勋和,张彬
  • 基金资助:
    广东省公益研究与能力建设项目(2016A030303068);嘉应学院省市共建重点建设项目(嘉院[2017]27号)

Genetic diversity and population structure of black-bone chickens in China revealed by mitochondrial COI gene sequences

Weng Zhuoxian1,2,3,Huang Jiaqiong2,Zhang Shihao2,Yu Kaichun2,Zhong Fusheng1,2,3,Huang Xunhe2,3,*(),Zhang Bin1,*()   

  1. 1 College of Animal Science & Technology, Hunan Agricultural University, Changsha 410128
    2 School of Life Science, Jiaying University, Meizhou, Guangdong 514015
    3 Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, Guangdong 514015
  • Received:2019-01-17 Accepted:2019-05-20 Online:2019-06-20 Published:2019-06-14
  • Contact: Huang Xunhe,Zhang Bin

摘要:

全面了解中国乌骨鸡的遗传背景有利于保护和开发利用其种质资源。本研究测定了中国12个乌骨鸡品种线粒体细胞色素c氧化酶亚基I (cytochrome c oxidase subunit I, COI)基因, 比较分析其遗传多样性和群体遗传结构。255份乌骨鸡样品共检测到22个变异位点, 占分析位点的3.17%; 核苷酸多样性为0.00142-0.00339, 单倍型多样性为0.380-0.757, 其中略阳乌鸡核苷酸多样性最高, 德化黑鸡最低。检测到7个氨基酸变异位点, 来自6个品种共11个个体。定义了24种单倍型, 其中单倍型H1和H3为12个乌骨鸡品种共享, 出现频率分别为115次和64次; 盐津乌骨鸡单倍型数最多, 广西乌鸡最少。中性检验与错配分析显示实验种群未经历显著的群体扩张事件。分子变异分析显示81.06%的变异来自群体内; 品种间遗传距离为0.002-0.004, 品种间遗传分化系数Fst值为-0.035至0.594, 雪峰乌骨鸡与其他种群间的遗传分化程度最高。邻接树显示, 乌骨鸡未能独立形成分支, 不能从家鸡和红原鸡中有效区分开来。中国乌骨鸡中介网络图将24个单倍型分为3条进化主支, 呈现出一定的品种特异性, 由无量山乌骨鸡、云南盐津乌骨鸡和雪峰乌骨鸡组成单倍型H8、H9、H11、H12游离于这3条进化主支之外。增加其他家鸡和红原鸡COI基因的中介网络图主体结构与中国乌骨鸡的相同。结果表明中国乌骨鸡品种遗传多样性较低, 但品种间遗传分化显著, 可能是从当地家鸡中选育而来, 需要加强种质资源的保护。

关键词: 乌骨鸡, 线粒体COI基因, 遗传变异, 遗传分化

Abstract:

Comprehensively evaluating the genetic diversity of Chinese black-bone chickens will facilitate conservation and utilization initiatives for this invaluable genetic resource. Mitochondrial cytochrome c oxidase subunit I (COI) gene sequences were obtained from 12 black-bone chicken breeds in China. These sequences were then used to analyze the genetic variation and population structure. A total of 22 mutation sites were detected from 255 individuals representing 3.17% of all sites. The nucleotide diversity and haplotype diversity ranged from 0.00142 to 0.00339 and from 0.380 to 0.757, respectively. Lueyang black chicken has the highest level of genetic diversity and Dehua the lowest. Seven amino acid variations were detected from 11 individuals from six breeds. A total of 24 haplotypes were defined, where haplotype H1 and H3 are shared by 12 black-bone chicken breeds with a frequency of 115 and 64, respectively. Yanjin had the greatest number of haplotypes, while Guangxi has the fewest. Neutrality tests and mismatch distribution analysis revealed that these populations have not experienced significant population expansion. Most of the genetic variations observed were intra-population variation (81.06%) as indicated in AMOVA analysis. Pairwise fixation indexes Fst values among 12 populations range from -0.035 to 0.594, and genetic distance ranges from 0.002 to 0.004. The genetic differentiation indexes between Xuefeng and other populations was the greatest. Black-bone chickens cannot be separated from domestic chickens and red junglefowls within the neighbor-joining tree. The median-joining network of black-bone chickens is classified into three main clusters with the characteristic of specific breeds, while haplotype H8, H9, H11 and H12 existing in Wuliangshan, Yanjin, Xuefeng are not directly related to the three main clusters. The median-joining network of black-bone chickens and additional domestic chickens and red junglefowls does not change the main structure of the tree. The results presented here indicate that the genetic diversity of Chinese black-bone chickens is low but significant genetic differentiation is evident. The Chinese black-bone chickens may be selected in situ from domestic chickens. Overall, the results suggest that more attention should be paid to germplasm resource protection of these fascinating breeds.

Key words: black-bone chicken, mitochondrial COI, genetic variation, genetic divergence