植物学报 ›› 2016, Vol. 51 ›› Issue (5): 659-666.doi: 10.11983/CBB16120

• 技术方法 • 上一篇    下一篇

长江流域野生拟南芥种群QTL作图平台的建立

康菊清1,2,*(), 孙田舒2, 张慧婷2, 施逸豪2   

  1. 1陕西师范大学生命科学学院, 西安 710119
    2北京大学生命科学学院, 北京 100871
  • 收稿日期:2016-05-30 接受日期:2016-07-05 出版日期:2016-09-01 发布日期:2016-09-27
  • 通讯作者: 康菊清 E-mail:kangjq@snnu.edu.cn
  • 作者简介:

    # 共同第一作者

  • 基金资助:
    国家自然科学基金青年项目(No.31400203)和陕西省自然科学基础研究计划青年人才项目(No.2016JQ3030)

Quantitative Trait Loci Mapping Platform of Natural Populations of Arabidopsis thaliana along the Yangtze River in China

Juqing Kang1,2*, Tianshu Sun2, Huiting Zhang2, Yihao Shi2   

  1. 1College of Life Science, Shaanxi Normal University, Xi’an 710119, China
    2College of Life Sciences, Peking University, Beijing 100871, China
  • Received:2016-05-30 Accepted:2016-07-05 Online:2016-09-01 Published:2016-09-27
  • Contact: Kang Juqing E-mail:kangjq@snnu.edu.cn
  • About author:

    # Co-first authors

摘要:

对模式植物的研究不仅能揭示众多具有普遍规律的生物现象, 而且能为其它植物物种, 特别是与人类生活紧密相关的经济植物提供具有借鉴与参考意义的研究方法。QTL遗传作图是寻找那些影响不同地域植物自然变异等位基因的传统且有效的工作方法。对不同分化时长和不同遗传背景的植物种群, 有针对性地开发特异的分子标记, 一直是QTL遗传作图工作的重要内容。该研究利用二代测序技术得到的全基因组重测序结果, 根据其中鉴定到的结构变异(SV)多态性设计引物, 开发了针对分化时间短、多态性位点少的中国长江流域野生拟南芥(Arabidopsis thaliana)种群的QTL作图分子标记平台, 得到了有效适用的结果, 该方法不仅在模式植物拟南芥中适用, 而且也适用于其它植物。

Abstract:

Studies on model plants have not only explored the mechanism of many life phenomenology but also provide research methods for other plants, especially economic plants. Quantitative trait loci (QTL) mapping is an effective method for identifying the alleles contributing to natural variation among populations that might be involved in adaptation in different environments. Exploring enough effective markers for specific mapping populations overcoming the differences of diverging time and genetic background was always the important and challenging part in these works. Here we explored efficient mapping markers by using SVs based on resequencing data of populations of Arabidopsis thaliana along the Yangtze River, a plant group that recently diverged and lacks sufficient genetic diversities. This research approach combining next-generation sequencing and traditional QTL mapping to identify the genetic basis of natural variation is effective for Arabidopsis and for other plants.

表1

4个长江流域野生拟南芥种群的基本信息"

Populations Location Latitude (N) Longitude (E) Altitude (m)
AHqsx Qianshanxian, AnHui 30º44'46'' 117º37'26'' 150
CQtlx Tongliangxian, ChongQing 29º49'24'' 106º03'23'' 263
JXjjs Jiujiangshi, JiangXi 29º35'41'' 115º54'44'' 80
SXcgx Chengguxian, ShaanXi 32º55'56'' 107º12'39'' 607

图1

长江流域4个野生拟南芥种群个体重测序数据中SVs分布的维恩图 种群个体框内的数字为相应的个体在重测序结果中检测到的SVs数目"

图2

基于SVs多态性设计的243个分子标记在拟南芥基因组上的定位 每条染色体上的白色标识为每一个分子标记所在的基因座位"

图3

琼脂糖凝胶电泳检测CQtlx、SXcgx和Col生态型中PCR扩增产物片段的长度 Ctl: 种群CQtlx; Scg: 种群SXcgx"

图4

64个CQtlx-SXcgx分子标记在基因组上的定位 每条染色体上的白色标识为每一个分子标记所在的基因座位"

图5

拟南芥CQtlx-SXcgx QTL遗传作图平台的应用举例 CQtlx: F2作图群体(CQtlx × SXcgx)中母方杂交亲本CQtlx5; SXcgx: F2作图群体(CQtlx × SXcgx)中父方杂交亲本SXcgx42; 1-46: F2作图群体的不同个体"

表2

拟南芥重测序检测SVs的PCR扩增和琼脂糖电泳后的验证结果"

SVs’ number called in
resequencing data
Total number In CQtlx5 In SXcgx42 Shared among populations Unique in one
population
246* 122 209 85 161
Verified results by PCR CQtlx vs Col SVs’ number verified Predicted in resequencing data Not predicted in resequencing data False positive False negative
116* 85 31 30.33% 26.72%
SXcgx vs Col SVs’ number verified Predicted in resequencing data Not predicted in resequencing data False positive False negative
134* 128 6 35.89% 4.47%
CQtlx vs SXcgx SVs’ number verified Predicted in resequencing data Not predicted in resequencing data False positive False negative
76* 70 6 56.52% 7.89%
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