中国农业科学 ›› 2022, Vol. 55 ›› Issue (22): 4526-4538.doi: 10.3864/j.issn.0578-1752.2022.22.016

• 畜牧·兽医 • 上一篇    下一篇

中国地方品种黄鸡线粒体DNA D-loop遗传多样性研究

黄勋和1(),翁茁先1,李威娜1,王庆1,何丹林2,罗威2,张细权2,杜炳旺1()   

  1. 1嘉应学院/广东省山区特色农业资源保护与精准利用重点实验室/广东省五华三黄鸡科技创新中心,广东梅州 514015
    2华南农业大学动物科学学院,广州 510642
  • 收稿日期:2021-09-13 接受日期:2021-12-16 出版日期:2022-11-16 发布日期:2022-12-14
  • 通讯作者: 杜炳旺
  • 作者简介:黄勋和,E-mail:hxh826@126.com
  • 基金资助:
    广东省自然科学基金(2014A030307018);广东省公益研究与能力建设项目(2016A030303068);广东省高等教育“冲补强”提升计划重点建设学科(农业资源与环境)建设项目(粤教科函[2018]181号);梅州市应用型科技专项资金项目(2019B0201003);梅州市应用型科技专项资金项目(2019B0201006)

Genetic Diversity of Indigenous Yellow-Feathered Chickens in Southern China Inferred from Mitochondrial DNA D-Loop Region

HUANG XunHe1(),WENG ZhuoXian1,LI WeiNa1,WANG Qing1,HE DanLin2,LUO Wei2,ZHANG XiQuan2,DU BingWang1()   

  1. 1Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas/Guangdong Science and Technology Innovation Centre of Wuhua Yellow Chicken, Meizhou 514015, Gugangdong
    2College of Animal Sciences, South China Agricultural University, Guangzhou 510642
  • Received:2021-09-13 Accepted:2021-12-16 Online:2022-11-16 Published:2022-12-14
  • Contact: BingWang DU

摘要:

【目的】 地方品种黄鸡是中国重要的家禽遗传资源,系统评估其遗传多样性水平,为提高利用率和制定科学的保护策略提供依据。【方法】 对新测的694份样本和下载的589份样本,合计28个中国南方地方品种黄鸡共1 283份的线粒体DNA片段(D-loop,519 bp)遗传多样性进行整合分析,构建单倍型中介网络图,通过单倍型地理分布格局、主坐标分析、分子变异分析和中性检测,确认其内部的群体遗传结构和群体历史。通过分析亚洲和太平洋地方鸡线粒体DNA地理分布格局,推测中国南方地方品种黄鸡稀有单倍型类群的来源。【结果】 从1 283份样本检测到101个变异位点,其中92个为多态位点。定义了169种单倍型,归属于6个单倍型类群A-E和G,其中A-C和E为优势单倍型类群,D和G为稀有单倍型类群,占总体样本比例分别为15.43%、49.26%、18.55%、16.37%、0.31%和0.08%。河南省单倍型类群最丰富(6个);广东省单倍型数量最多(61),浙江省(19)和海南省(12)较少。单倍型类群A和B在28个黄鸡品种中均有分布;D只分布于淮南麻黄鸡、固始鸡、宁都黄鸡和霞烟鸡中;G只分布于固始鸡中。从单倍型类群D的分布频率和单倍型数量来看,中国南方地方品种黄鸡单倍型类群D可能来源于东南亚地区。从单倍型类群G的地理分布和中介网络图来看,河南和南亚的单倍型类群G可能来源于中国西南地区。中国南方地方品种黄鸡总体单倍型多样性和核苷酸多样性分别为0.903±0.005和0.01269±n.d.。河南省和湖南省的单倍型多样性和核苷酸多样性最高,分别为0.916±0.011、0.01358±0.00039和0.913±0.012、0.01345±0.00042;海南省的单倍型多样性最低(0.736±0.076),江西省的核苷酸多样性最低(0.00981±0.00072)。在不同地方品种间,淮南麻黄鸡、固始鸡和郧阳大鸡的单倍型多样性最高,江汉鸡、淮南麻黄鸡和黄郎鸡的核苷酸多样性最高,洪山鸡、广西三黄鸡和萧山鸡的单倍型多样性和核苷酸多样性最低。文昌鸡与河田鸡的遗传关系最近,与历史记载相吻合。地方品种黄鸡群体遗传分化不明显,分子变异主要来源于品种内。中性检测显示黄鸡在品种水平上近期未经历明显种群扩张,但单倍型类群A、B和E经历明显的扩张历史。【结论】 结果表明地方品种黄鸡总体上保留着较高的遗传多样性水平,处于较好的保种状态,但洪山鸡、萧山鸡和广西三黄鸡应加强保护。地方品种黄鸡存在杂交现象,整体上经历了群体扩张历史。东南亚和西南地方鸡对中国南方地方品种黄鸡有一定的遗传贡献。

关键词: 黄鸡, 线粒体DNA D-loop, 遗传变异, 遗传分化, 群体历史

Abstract:

【Objective】 Indigenous yellow-feathered chicken is an important poultry genetic resource in China. The genetic diversity of these chickens was evaluated to facilitate scientific protection policies and to improve their use.【Method】 A total of 1283 mitochondrial DNA fragments (mtDNA D-loop, 519 bp) were investigated including 694 de novo and 589 previously published units from 28 indigenous yellow-feathered chicken breeds from southern China. These data were subsequently used to calculate the genetic diversity, to construct median-joining networks of haplotypes, and to investigate geographical distribution patterns of haplotypes by using principal coordinate analysis, analysis of molecular variance, and neutral test. The origin of rare haplogroups was inferred from the geographical distribution pattern of mitochondrial DNA haplogroups of Asian and Pacific indigenous chickens.【Result】One hundred and one mutation sites were detected in 1 283 samples, of which 92 were polymorphic. One hundred and sixty-nine haplotypes, belonging to haplogroups A-E and G, were defined. The predominant haplogroups were A (15.43%), B (49.26%), C (18.55%), and E (16.37%), while D (0.31%) and G (0.08%) were the rare haplogroups within the total samples. Chickens from Henan Province covered all six haplogroups; Chickens from Guangdong Province had the largest number of haplotypes (64), whereas those from Zhejiang (19) and Hainan (12) Provinces had the lowest. Haplogroups A and B occurred in all 28 breeds. Haplogroup D existed only in Huainan yellow, Gushi, Ningdu yellow and Xiayan chickens, whereas haplogroup G only occurred in Gushi chickens. The distribution frequency of haplogroup D and the number of haplotypes indicated that haplogroup D of indigenous yellow-feathered chickens in southern China could originated from Southeast Asia. The evidence from geographical distribution and median-joining networks of haplogroup G indicated that haplogroup G of chickens from Henan Province and South Asia could originated from Southwest China. The indigenous yellow-feathered chickens in southern China had a total haplotype diversity of 0.903±0.005 and nucleotide diversity of 0.01269±n.d. Indigenous yellow-feathered chickens from Henan and Hunan Provinces had the highest level of haplotype diversity of 0.916±0.011 and 0.01358±0.00039, respectively, and the nucleotide diversity of 0.913±0.012 and 0.01345±0.00042, respectively. The lowest level of haplotype diversity was found in Hainan Province (0.736±0.076), and the lowest level of nucleotide diversity was found in Jiangxi Province (0.00981±0.00072). Huainan yellow, Gushi and Yunyang da chickens retained the highest level of haplotype diversity; Jianghan, Huainan yellow and Huanglang chickens had the highest level of nucleotide diversity, whereas the haplotype diversity and nucleotide diversity in Hongshan, Guangxi yellow and Xiaoshan chickens were the lowest. Wenchang chickens were genetically close to Hentian chickens, which was consistent with their breeding history. The population genetic structure of yellow-feathered chickens was less clear, and the molecular variance component of within-population was significantly higher than others. The neutral test indicated that the yellow-feathered chickens in southern China did not sustain obvious population expansion at the breed level, with the exception of haplogroups A, B and E.【Conclusion】 The results suggested that yellow-feathered chickens had a good conservation status with high level of genetic diversity, although Hongshan, Xiaoshan and Guangxi yellow chickens required further protection. Hybridization between chickens was common in yellow-feathered chickens, which had experienced population expansion. Indigenous chickens from Southeast Asia and Southwest China had substantial genetic contributions to indigenous yellow-feathered chickens in southern China.

Key words: yellow-feathered chicken, mitochondrial DNA D-loop, genetic variation, genetic divergence, demographic history