基于重测序的菠萝基因组InDel标记的开发  

Development of Insertion-deletion Markers in Ananas comosus of Genome Based on Re-sequencing Data

作　　者：贺涵 刘传和[1] 喻梦凡 袁梦萍 魏岳荣[1] 杨敏 邝瑞彬[1] 周陈平 吴夏明 徐泽 HE Han;LIU Chuan-he;YU Meng-fan;YUAN Meng-ping;WEI Yue-rong;YANG Min;KUANG Rui-bin;ZHOU Chen-ping;WU Xia-ming;XU Ze(Institute of Fruit Tree Research,Guangdong Academy of Agricultural Sciences/Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization,Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Science and Technology Research on Fruit Tree,Guangzhou 510640)

机构地区：[1]广东省农业科学院果树研究所农业农村部南亚热带果树生物学与遗传资源利用重点实验室广东省果树科学与技术研究重点实验室,广州510640

出　　处：《生物技术通报》2025年第2期65-76,共12页Biotechnology Bulletin

基　　金：广东省农业科学院创新中心课题(XTXM202203-XT202212);国家重点研发计划项目(2023YFD2300800);广东省农村科技特派员项目(KTP20210395,KTP20240379);广州市科技计划项目(2023E04J0562)。

摘　　要：【目的】基于菠萝种质的基因组重测序数据研发菠萝InDel分子标记,为菠萝种质资源的创新利用奠定理论基础。【方法】选取4份代表性菠萝种质进行基因组重测序,鉴定插入/缺失长度大于30 bp的InDel位点。根据InDel位点信息设计InDel标记引物,选择扩增条带清晰、分离效果好的引物用于菠萝种质遗传多样性分析。【结果】在4份菠萝种质中鉴定到插入/缺失长度大于30 bp、测序深度大于10×的InDel位点1559个。基于InDel位点的上下游序列信息,在全基因组范围内设计候选InDel标记引物372对,其中264对引物表现出稳定的多态性,多态性比例为70.97%。采用50对多态性高的核心标记引物分析58份菠萝种质的遗传多样性。共检测到等位位点103个;各标记的平均有效等位位点数(Ne)为1.8164个;Shannon's多样性指数(I)的变异范围为0.2728-0.7464,平均值为0.6346;多态性信息含量(PIC)为0.1329-0.4251,平均值为0.3422;Nei’s基因多样性指数(H)变异范围为0.1431-0.5143,平均值为0.4412。通过聚类分析在遗传距离0.75处将58份菠萝种质分为4个类群,其中第Ⅳ类群可进一步分为2个亚群。采用群体结构分析将58份种质划分为2个稳定群体,其中POP-1群体与聚类分析获得的第Ⅳ-2亚群重合,主要由纯种卡因类种质组成。【结论】研发的50个菠萝核心InDel标记能精准区分不同菠萝品种,对于深化菠萝遗传多样性分析、完善遗传图谱构建和加速分子标记辅助育种进程具有重要意义。【Objective】The goal is to develop InDel molecular markers based on genome re-sequencing data,laying a theoretical foundation for innovative utilization of pineapple resources.【Method】Four representative pineapple accessions were selected for genome resequencing to identify InDel loci with insertion/deletion lengths>30 bp.The InDel marker primers were designed based on the sequence information of these InDel loci,and those having clear amplification bands and favorable separation effects were selected for further analysis of genetic diversity.【Result】The 1559 InDel loci with insertion/deletion length>30 bp and sequencing depths>10×were identified from resequencing data of four pineapple accessions.Based on the upstream and downstream sequences of these InDel loci,372 pairs of InDel marker primers were designed across the entire genome,of which 264 pairs showed stable polymorphism,with a polymorphism ratio of 70.97%.The 50 of the 264 polymorphic InDel markers were assigned as core markers,further used for the genetic diversity analyzing of 58 pineapple accessions.A total of 103 alleles were identified,and the average effective numbers of alleles(Ne)for each marker are 1.8165.The Shannon’s Information index(I)ranged from 0.2728 to 0.7464,with an average value of 0.6346.The polymorphism information content(PIC)valued from 0.1329 to 0.4251,with an average value of 0.3422.While the variation range of Nei’s gene diversity index(H)was 0.1431 to 0.5143,with an average value of 0.4412.Through cluster analysis,58 pineapple accessions were classified into 4 groups at a genetic distance of 0.75,with group IV can be further divided into 2 subgroups.The 58 pineapple accessions can also be divided into two stable populations through structure analysis,with the POP-1 population overlapping with theⅣ-2 subgroup obtained from cluster analysis,mainly composed of smooth cayenne germplasms.【Conclusion】The 50 core InDel markers developed in this study can accurately distinguish different pineapple accessions,whic

关 键 词：菠萝 重测序 INDEL标记 遗传多样性分析 

分 类 号：S668.3[农业科学—果树学]