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首页 > 过刊浏览>2019年第20卷第5期 >1325-1333. DOI:10.13430/j.cnki.jpgr.20190121001
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基于丹霞梧桐转录组数据的 EST-SSR 标记开发
作者:
作者单位:

1.中南林业科技大学风景园林学院;2.广东省韶关市野生动植物保护办公室

基金项目:

国家林业局野生植物保护项目和韶关市野生动植物保护办公室项目(2016ZWZY06)


Characterization and Development of EST-SSR Markers from Transcriptome Datasets of Firminana danxiaensis
Author:
Affiliation:

1.College of landscape architecture,Central south university of forestry and technology;2.Shaoguan Department of Wildlife Conservation

Fund Project:

State Forestry Administration of Wildlife protection project and Shaoguan department of wildlife conservation

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    摘要:

    以丹霞梧桐转录组序列为基础，开发丹霞梧桐 EST-SSR 标记位点，并利用其对丹霞梧桐群体进行遗传多样性分析，评价丹霞梧桐群体的遗传多样性水平，为丹霞梧桐的合理利用和保护提供依据。应用 Primer 3.0、GenAlEx6.3、FSTAT 和MS-tools 等软件进行引物设计和相关遗传参数分析。17, 858 个 SSR 位点分布于 79, 920 个 unigene 序列，SSR 位点密度为 1/4.78kb。SSR 重复基序中，三核苷酸（43.64%）为优势核苷酸，其次为四核苷酸（23.52%）和二核苷酸（15.54%）。三核苷酸和二核苷酸优势重复基序分别为 AAG/CTT 和 AG/CT。以 16 个样本为材料，从设计的 73 对引物中共筛选出 16 对多态性 EST-SSR引物，多态性信息含量（PIC）的平均值为 0.546，所开发位点具有较高的多态性。主成分分析（PCA）表明，这些位点具有很好地鉴别不同地区样本，甚至单株的能力。三个群体的遗传多样性参数对比结果表明，丹霞梧桐群体具有中等程度的遗传多样性，其期望杂合度（He）的变化范围为 0.550-0.605。地质、历史气候变化及人为干扰等因素可能是造成丹霞梧桐群体偏离哈代-温伯格平衡的主要原因。本研究所开发的 EST-SSR 多态性位点可为丹霞梧桐遗传结构分析和分子辅助育种等相关研究奠定良好基础。

    Abstract:

    The microsatellite markers in Firminana danxiaensis were developed by taking use of from the transcriptome dataset. These markers were subjected for analyzing the genetic diversity of extant populations to provide basis for rational utilization and the protection of Firminana danxiaensis. Primer 3.0, GenAlEx6.3, FSTAT and MS-tools were deployed to explore primers and analyze the genetic parameters. As a result, 17,858 SSRs were identified from 79,920 unigenes with a frequency of 1/4.78kb. Trinucleotide, tetranucleotide and dinucleotide accounted for 43.64%, 23.52% and 15.54%, respectively. AAG/CTT and AG/CT were the most abundant repeat motif for trinucleotide and dinucleotide, respectively. Out of seventy-three primers that were tested in 16 genotypes, 16 primers were polymorphic with an average value of polymorphic information content (PIC) 0.546. The principal component analysis (PCA) showed that these loci are efficient to identify individuals from different regions and each individuals. A moderate genetic diversity among three Firminana danxiaensis populations and the expected heterozygosity (He) varied from 0.550 to 0.605 were observed. The geology, historical climate change and human disturbance may be the main reasons for Firminana danxiaensis deviated from Hardy-Weinberg equilibrium. Taken together, these newly developed EST-SSR markers will lay foundation for unlocking the genetic structure and the marker-assisted breeding of Firminana danxiaensis.

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武星彤,陈璐,王敏求,等.基于丹霞梧桐转录组数据的 EST-SSR 标记开发[J].植物遗传资源学报,2019,20(5):1325-1333.

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  • 收稿日期:2019-01-21
  • 最后修改日期:2019-07-19
  • 录用日期:2019-04-03
  • 在线发布日期: 2019-09-17
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