生物技术通报2026，Vol.42Issue(10)：27-36,10.DOI:10.13560/j.cnki.biotech.bull.1985.2026-0100
基于重测序的番茄全基因组InDel分子标记开发与应用
Development and Application of Insertion-deletion(InDel)Markers in Tomato Based on Whole-genome Re-sequencing Data
摘要
Abstract
[Objective]This study aims to develop a set of genome-wide,highly polymorphic insertion-deletion(InDel)markers that are easily detectable via conventional agarose gel electrophoresis,thereby providing efficient and practical technical tools for analyzing genetic diversity in tomato germplasm,constructing DNA fingerprint databases,and conducting cultivar identification.[Method]Target InDel loci were screened from publicly available tomato resequencing data using bioinformatic methods,and primers were designed accordingly.The developed markers were validated,screened,and applied using commercial tomato varieties encompassing four major market types:fresh,flavor,processing and cherry tomatoes.[Result]A total of 84 well-distributed and highly polymorphic InDel markers were successfully developed across the tomato genome.Analysis of 288 tomato varieties revealed pairwise genetic similarity coefficients ranging from 0.369 to 0.994,with an average of 0.667.Both cluster analysis and principal component analysis based on genetic distance consistently classified the tested varieties into four major genetic groups.Cherry tomatoes exhibited the highest genetic diversity and formed a distinct cluster,while fresh and flavor tomatoes shared the closest genetic background,showing overlapping patterns in the clustering.Considering the differential polymorphism of markers across tomato types,core marker sets for identification were refined for fresh,flavor,processing and cherry tomatoes,consisting of 48,36,48,and 48 primer pairs,respectively.DNA fingerprint profiles were subsequently constructed using these core sets.Case studies demonstrated that polymorphic markers between parental lines enabled rapid assessment of hybrid seed purity,and the core marker combinations effectively differentiated between varieties,confirming the practicality and reliability of this marker system.[Conclusion]The genome-wide InDel marker system exhibits high polymorphism and ease of detection.It effectively reveals the genetic diversity and population structure of commercial tomato varieties and has been successfully applied in varietal fingerprint construction,authenticity verification,and hybrid purity testing.This system provides technical support for tomato germplasm resource management,molecular breeding,and plant variety protection.关键词
番茄/InDel标记/群体结构/指纹图谱/品种鉴定/纯度鉴定/全基因组Key words
tomato/InDel markers/population structure/fingerprint/variety identification/purity test/whole-genome引用本文复制引用
苏晓梅,刘淑梅,吕宏君,杨宗辉,侯丽霞..基于重测序的番茄全基因组InDel分子标记开发与应用[J].生物技术通报,2026,42(10):27-36,10.基金项目
山东省重点研发计划农业良种工程(2024LZGC006),东西部科技协作专项(25CXNA026),国家现代农业产业技术体系建设专项资金(CARS-23-G13) （2024LZGC006）
