生物技术通报2025，Vol.41Issue(2)：65-76,12.DOI:10.13560/j.cnki.biotech.bull.1985.2024-0728
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
摘要
Abstract
[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 re-sequencing 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 1 559 InDel loci with insertion/deletion length>30 bp and sequencing depths>10×were identified from re-sequencing 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 1.816 5.The Shannon's Information index(I)ranged from 0.272 8 to 0.746 4,with an average value of 0.634 6.The polymorphism information content(PIC)valued from 0.132 9 to 0.425 1,with an average value of 0.342 2.While the variation range of Nei's gene diversity index(H)was 0.143 1 to 0.514 3,with an average value of 0.441 2.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 the Ⅳ-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,which helps for deepening the analysis of pineapple genetic diversity,improving the construction of genetic map,and accelerating the process of molecular marker assisted breeding.关键词
菠萝/重测序/InDel标记/遗传多样性分析Key words
pineapple/re-sequencing/InDel markers/genetic diversity analysis引用本文复制引用
贺涵,徐泽,刘传和,喻梦凡,袁梦萍,魏岳荣,杨敏,邝瑞彬,周陈平,吴夏明..基于重测序的菠萝基因组InDel标记的开发[J].生物技术通报,2025,41(2):65-76,12.基金项目
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) （XTXM202203-XT202212）
