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Bulletin of Botanical Research ›› 2019, Vol. 39 ›› Issue (6): 899-907.doi: 10.7525/j.issn.1673-5102.2019.06.013

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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)

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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