遗传 ›› 2024, Vol. 46 ›› Issue (8): 640-648.doi: 10.16288/j.yczz.24-068

• 研究报告 • 上一篇    下一篇

“酉芯一号”在地方鸡遗传多样性和结构分析中的应用效力研究

王梦燏1,2(), 周成浩2(), 薛倩2,3, 殷建玫2, 蒋一秀2, 张会永2, 李国辉2, 韩威1,2()   

  1. 1.中国农业科学院家禽研究所,扬州 225125
    2.江苏省家禽科学研究所,扬州 225125
    3.江苏省家禽科学研究所科技创新有限公司,扬州 225125
  • 收稿日期:2024-03-14 修回日期:2024-06-12 出版日期:2024-08-20 发布日期:2024-06-24
  • 通讯作者: 韩威,博士,研究员,研究方向:家禽遗传资源保护、评价与利用。E-mail: hanwei830@163.com
  • 作者简介:王梦燏,硕士研究生,专业方向:动物遗传育种与繁殖原理与技术。E-mail: 2664935435@qq.com;
    周成浩,博士,助理研究员,研究方向:家禽遗传资源保护、评价与利用。E-mail: 604242123@qq.com
    第一联系人:

    王梦燏和周成浩并列第一作者。

  • 基金资助:
    国家重点研发计划项目(2021YFD1200302);江苏省种业振兴揭榜挂帅项目(JBGS[2021]029);江苏省自然科学基金面上项目(BK20221285)

Application effectiveness of “Youxin-1” in genetic diversity and structure analysis of local chickens

Mengyu Wang1,2(), Chenghao Zhou2(), Qian Xue2,3, Jianmei Yin2, Yixiu Jiang2, Huiyong Zhang2, Guohui Li2, Wei Han1,2()   

  1. 1. Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
    2. Poultry Institute of Jiangsu Province, Yangzhou 225125, China
    3. Science and Technology Innovation Co., Ltd., Poultry Institute of JiangsuProvince, Yangzhou 225125, China
  • Received:2024-03-14 Revised:2024-06-12 Published:2024-08-20 Online:2024-06-24
  • Supported by:
    National Key Research and Development Program of China(2021YFD1200302);Seed Industry Revitalization Project of Jiangsu Province(JBGS[2021]029);Natural Science Foundation Project of Jiangsu Province(BK20221285)

摘要:

我国地方鸡品种资源丰富,且在长期的选择进化过程中形成了各异的种质特性。科学评估群体遗传多样性,明确品种间遗传结构,对地方鸡品种资源的保护与创新利用具有重要价值。为了评估23K SNP芯片“酉芯一号”在地方鸡遗传多样性和遗传结构分析中的应用效力,本文利用RADseq鉴定21个地方鸡种基因组遗传变异,并研发23K芯片“酉芯一号”。基于两组SNP数据集计算各品种的遗传统计量,开展相关性、拟合及系统发育分析,以评估芯片的应用效力。结果表明,基于两组SNP数据集计算的观察杂合度(Ho)、多态信息含量(PIC)、近交系数(FROH)和遗传分化系数(Fst),在21个地方鸡种中趋势基本一致。琅琊鸡(LA)、瓢鸡(PJ)、文昌鸡(WC)的遗传多样性较为丰富;边鸡(BJ)、狼山鸡(LS)、固始鸡(GS)、东乡绿壳蛋鸡(DX)和北京油鸡(BY)的遗传多样性相对匮乏,两组Ho、PIC、FROH和平均Fst的相关系数分别为0.794、0.901、0.926和0.984,均达到极显著水平(P<0.01),且拟合度较高(P<0.001),R2分别为0.644、0.827、0.916和0.927。针对两组SNP数据集,采用邻接法(NJ)和极大似然法(ML)构建的进化树较为合理,将21个地方鸡种总体上分为6大类,与品种的形成历史和地理分布相吻合;23K芯片对5个新增品种亦实现有效聚类,没有出现个体偏离。利用不同密度的SNP估算遗传统计量会存在一定差异,需要进行数据和分析方法的标准化,23K芯片在地方鸡遗传多样性和结构分析中具有较好的效力。

关键词: RADseq, SNP芯片, 遗传多样性, 遗传结构

Abstract:

China’s local chicken breeds are rich in resources, and have formed different germplasm characteristics in the process of long-term selection and evolution. Scientific assessment of population genetic diversity and identification of inter-breed genetic structure are of great value to the protection and innovative utilization of local chicken breed resource. In order to evaluate the application effectiveness of 23K SNP chip “Youxin-1” in the analysis of genetic diversity and genetic structure of local chickens, we used RADseq to identify genomic genetic variation of 21 local chicken breeds and developed 23K chip “Youxin-1”. The genetic statistics of each variety were calculated based on two sets of SNP data, and correlation, fitting and phylogenetic analysis were carried out to evaluate the application effectiveness of the chip. The results showed that the observed heterozygosity (Ho), polymorphism information content (PIC), inbred coefficient (FROH) and genetic differentiation coefficient (Fst) calculated based on the two SNP data sets were basically consistent in the 21 local chicken breeds. The genetic diversity of Langya chicken (LA), Piao chicken (PJ) and Wenchang chicken (WC) was relatively rich. The genetic diversity of Bian chickens (BJ), Langshan chickens (LS), Gushi chickens (GS), Dongxiang blue-eggshell chickens (DX) and Beijing fatty chickens (BY) was relatively poor, and the correlation coefficients of Ho, PIC, FROH and average Fst in the two groups were 0.794, 0.901, 0.926 and 0.984, respectively, all reaching extremely significant levels (P<0.01) with a high degree of fit (P<0.001) and R2 were 0.644, 0.827, 0.916 and 0.927. For the two sets of SNP data, the evolutionary tree constructed by neighbor-joining (NJ) method and maximum likelihood (ML) method was reasonable, and the 21 local chicken breeds were generally divided into six categories, which was consistent with the formation history and geographical distribution of the varieties. The 23K chip also realized reasonable clustering of the five new varieties without individual deviation. There are some differences in the estimation of genetic statistics using SNP with different densities, and data standardization is needed. 23K chip has good efficacy in the analysis of genetic diversity and structure of local chickens.

Key words: RADseq, SNP chip, genetic diversity, genetic structure