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园艺学报 ›› 2022, Vol. 49 ›› Issue (4): 778-790.doi: 10.16420/j.issn.0513-353x.2021-0347

• 研究论文 • 上一篇    下一篇

基于重测序的长豇豆基因组InDel标记开发及应用

杨易1, 黎庭耀1, 李国景2, 陈汉才1, 沈卓1, 周轩1, 吴增祥1, 吴新义2, 张艳1,*()   

  1. 1.广东省农业科学院蔬菜研究所,广东省蔬菜新技术研究重点实验室,广州 510640
    2.浙江省农业科学院蔬菜研究所,杭州 310021
  • 收稿日期:2021-11-01 修回日期:2022-01-18 出版日期:2022-04-25 发布日期:2022-04-24
  • 通讯作者: 张艳 E-mail:893251473@qq.com
  • 基金资助:
    广东省重点领域研发计划项目(2020B020220002);广东省科技计划项目(2018A050506051)

Development and Application of Insertion-Deletion(InDel)Markers in Asparagus Bean Based on Whole Genome Re-sequencing Data

YANG Yi1, LI Tingyao1, LI Guojing2, CHEN Hancai1, SHEN Zhuo1, ZHOU Xuan1, WU Zengxiang1, WU Xinyi2, ZHANG Yan1,*()   

  1. 1. Guangdong Key Laboratory for New Technology Research of Vegetables,Vegetable Research Institute,Guangdong Academy of Agricultural Sciences,Guangzhou 510640,China
    2. Vegetable Research Institute,Zhejiang Academy of Agricultural Sciences,Hangzhou 310021,China
  • Received:2021-11-01 Revised:2022-01-18 Online:2022-04-25 Published:2022-04-24
  • Contact: ZHANG Yan E-mail:893251473@qq.com

摘要:

选取3份长豇豆种质资源进行全基因组重测序,利用重测序数据挖掘InDel位点,根据这些位点开发分子标记,并验证这些标记的有效性和应用价值。经过严格筛选,获得981个易于凝胶电泳检测的长度大于30 bp且多态性高的InDel位点,挑选其中在基因组上均匀分布的165个设计引物并进行验证。用6份长豇豆材料对165对引物进行初筛,其中162对可获得PCR扩增产物,共扩增出673条条带;85对引物表现出多态性,多态性带333条(占总带数的49.48%)。利用85个多态性高的标记对173份长豇豆资源进行基因分型和遗传多样性分析,共检测到333个等位位点;多态性信息含量(PIC)为0.01 ~ 0.37,平均值为0.29;基因多样性指数变异范围为0.01 ~ 0.50,平均值为0.36,表明现有长豇豆资源遗传背景相对狭窄。通过聚类分析,173份长豇豆被分为2个类群,成功将不同类型长豇豆划分到不同亚群。另外,选用亲本间多态性标记用于6个杂交组合的F1代真实性鉴定,鉴定出5个真实杂交种。本研究所开发的多态性 InDel 标记在长豇豆遗传多样性分析、杂交种纯度鉴定、遗传连锁图谱构建、基因定位和分子标记辅助选择育种等方面具有很好的应用前景。

关键词: 长豇豆, InDel标记, 遗传多样性, F1代真实性鉴定

Abstract:

Based on resequencing data on three asparagus bean accessions,a set of InDel markers were developed and validated. Nine hundred and eight-one highly polymorphic InDel loci were screened out with insert or deletion bases longer than 30 bp suitable for PAGE gel electrophoresis detection. Among them,165 markers with uniform distribution across the genome were selected and checked in six asparagus bean inbreed lines. The results showed that 162 primer pairs yielded 673 amplification bands,and 85 primer pairs exhibited polymorphism yielded 333 polymorphic bands,accounted for 49.48% in the total amplification bands. These 85 polymorphic InDel markers were further used for genetic diversity analyzing in 173 asparagus bean accessions,and a total of 333 loci were generated. The polymorphism information content(PIC)value ranged from 0.01 to 0.37,with an average value of 0.29,while the gene diversity index value ranged from 0.01 to 0.50,with an average value of 0.36,indicating a relatively narrowed genetic diversity among these accessions. Population structure analysis revealed that there are two groups existed in these accessions. Further,these markers helped to identified five real hybrids from six hybrid combinations. Taken together,the polymorphic InDel markers developed in this study can be widely used for asparagus bean genetic analysis and molecular marker assisted selection breeding.

Key words: asparagus bean, InDel marker, genetic diversity analysis, F1 identification

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