园艺学报 ›› 2023, Vol. 50 ›› Issue (1): 15-26.doi: 10.16420/j.issn.0513-353x.2021-0935

• 研究论文 • 上一篇    下一篇


汤雨晴, 杨惠栋, 闫承璞, 王斯妤, 王雨亭, 胡钟东*(), 朱方红*()   

  1. 江西省农业科学院园艺研究所,南昌 330200
  • 收稿日期:2022-08-25 修回日期:2022-12-02 出版日期:2023-01-25 发布日期:2023-01-18
  • 通讯作者: *(
  • 基金资助:

Development and Application of Jinlan Pummelo(Citrus maxima)InDel Markers Based on Genome Re-sequencing

TANG Yuqing, YANG Huidong, YAN Chengpu, WANG Siyu, WANG Yuting, HU Zhongdong*(), ZHU Fanghong*()   

  1. Horticultural Institute,Jiangxi Academy of Agricultural Sciences,Nanchang 330200,China
  • Received:2022-08-25 Revised:2022-12-02 Online:2023-01-25 Published:2023-01-18
  • Contact: *(


基于重测序进行金兰柚全基因组InDel标记开发。利用二代测序技术对‘金兰柚’进行全基因组重测序,运用BWA软件将测序得到的片段与参考基因组序列进行比对,利用严格的参数筛选杂合InDel,结合Primer 3.0设计扩增引物,进行PCR扩增并利用琼脂糖凝胶电泳验证,以重测序材料‘金兰柚’和47份柚品种检测其有效性。在全基因组范围内共筛选出81对扩增条带清晰的引物。筛选出的多态性标记涵盖了整个‘金兰柚’基因组,平均每条染色体上9个。选取的24对 InDel 标记可以将48份柚品种有效区分,最少使用2对引物就可将‘金兰柚’与其他47份柚品种完全区分。利用UPGMA构建48份柚品种的聚类树状图,在遗传相似系数为0.611的阈值处可将48个柚品种分为3大类群。本研究中的InDel标记带型简单易读,适宜柚DNA指纹图谱构建和品种鉴定,可为柚名优品种保护、原产地溯源管理等提供科学依据。

关键词: 柚, 重测序, InDel标记


This study developed a genome-wide InDel marker map of Jinlan pummelo(Citrus maxima)genome. The next generation sequencing(NGS)technology was applied to produce the deep resequencing data of the individual,and was mapped to the reference genome using BWA-MEM. The pipeline with strict parameters improved accuracy and effectiveness of heterozygous InDel markers. The primers designment was performed by using Primer 3.0. The agarose gel electrophoresis of polymerase chain reaction(PCR)product was used to validate the effectiveness of primers. A total of 81 effective paired primers were identified. The corresponding markers covered nearly the whole genome of Jinlan pummelo,with an average number of nine InDel markers per chromosome. Of these markers,24 markerswere succussed in distinguishing the 48 pummelo individuals,which showed that two paired markers could distinguish Jinlan pummelo and other 47 pummelo individuals. Finally,UPGMA was used to construct the phylogeny of 48 pummelo,which was divided into three groups at threshold 0.611 of genetic similarity coefficient. This study suggested that the genome-wide InDel markers developed using deep resequencing was suitable for the identification of the different germplasms of pummelo,and provides a basis in variety protection and origin traceability management.

Key words: pummelo, re-sequencing, InDel marker