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植物研究 ›› 2019, Vol. 39 ›› Issue (6): 899-907.doi: 10.7525/j.issn.1673-5102.2019.06.013

• 研究报告 • 上一篇    下一篇

基于简化基因组技术的云南蓝果树群体遗传分析

张珊珊, 康洪梅, 杨文忠   

  1. 云南省林业科学院, 云南省森林植物培育与开发利用重点实验室/国家林业局云南珍稀濒特森林植物保护和繁育国家林业局重点实验室, 昆明 650201
  • 收稿日期:2019-02-14 出版日期:2019-11-05 发布日期:2019-11-16
  • 通讯作者: 杨文忠 E-mail:wzyang2004@126.com
  • 作者简介:张珊珊(1984-),女,博士,副研究员,主要从事保护生物学的研究工作。
  • 基金资助:
    国家自然科学基金项目(31960278,31660164);国家科技基础资源调查专项项目(2017FY100100);国家林业和草原野生植物保护管理项目(2016YB1038,2017YB1010);云南省林业科学院创新基金项目(QN2018-05);云南省应用基础研究青年项目(2016FD079)

Population Genetic Analysis of Nyssa yunnanensis by Reduced-representation Sequencing Technique

ZHANG Shan-Shan, KANG Hong-Mei, YANG Wen-Zhong   

  1. Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry, Kunming 650201
  • Received:2019-02-14 Online:2019-11-05 Published:2019-11-16
  • Supported by:
    National Natural Science Foundation of China(31960278,31660164);National Science and Technology Fundamental Resources Investigation Project(2017FY100100);State Forestry and Grassland Administration of China(2016YB1038,2017YB1010);Innovation Fund Project of Yunnan Academy of Forestry(QN2018-05);Youth Project of Applied Basic Research in Yunnan Province(2016FD079)

摘要: 极小种群野生植物云南蓝果树是国家和云南省实施极小种群野生植物保护工程的代表性物种。为有效保护其遗传资源,本研究通过二代测序技术,对其进行简化基因组测序,开发一批特异性高的单核苷酸多态性标记,分析现存群体的遗传结构和遗传多样性。经过遗传变异检测,本次研究中共获得SNP位点98 498个,通过样品最低测序深度>2,样品缺失率<0.5,次要基因型频率(MAF)>0.05筛选以后,得到有效SNP位点6 309个。基于过滤后的SNP,运用生物信息学分析方法,对云南蓝果树完成了群体的遗传分析,其中:系统进化树分析将云南蓝果树划分为3大类,研究分析了云南蓝果树各分类的私人等位基因数目(Private)、平均观测杂合度(Ho)、平均期望杂合度(He)、核苷酸多样性(π)和平均近交系数(FIS)5个遗传多样性参数;群体结构和主成分分析进一步证明了,云南蓝果树现存植株之间亲缘关系较远,遗传多样性差异较大,具有很高的遗传资源保存价值。本研究结果将为基于遗传管理的云南蓝果树就地保护、遗传资源保存和种群重建等保护工程提供科学依据。

关键词: 云南蓝果树, 简化基因组测序, SNP, 群体遗传分析, 遗传管理

Abstract: Nyssa yunnananesis, a plant species with extremely small populations(PSESP), has become the flagship species in national and provincial conservation programs of PSESP. For effectively preserving the existing genetic resources, the recently developed technology restriction-site associated DNA sequencing(RAD-seq), which is based on next-generation sequencing(NGS), was used to develop a batch of highly specific single nucleotide polymorphism(SNP) markers and analyze genetic structure and genetic diversity of existing populations. After detection of genetic variation, a total of 98 498 SNPs were got. Under these conditions, the minimum sequencing depth of samples>2, sample missing rate < 0.5 and MAF > 0.05 screening from all 98 498 SNPs, 6 309 effective SNPs were obtained. Population genetics analysis of N.yunnananesis was analyzed using bioinformatic method with screening SNPs. Results demonstrated that the phylogenetic tree was divided into three clusters, in which the genetic diversity parameters, such as private, the nucleotide diversity(π), observed heterozygosity(Ho), expected heterozygosity(He) and inbreeding coefficient(FIS) were elucidated. Population structure and PCA analysis further proved that N.yunnananesis had far relationships and quite different genetic diversity between the existing plants. Therefore, preserving genetic resources was of very high value. This study will give scientific evidences to protection engineering in particular the in-situ conservation, genetic resource preservation and population reestablishment with genetic management related methods and techniques.

Key words: Nyssa yunnanensis, restriction-site associated DNA sequencing, SNP, population genetic analysis, genetic management

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