基于重测序的番茄全基因组InDel分子标记开发与应用

doi:10.13560/j.cnki.biotech.bull.1985.2026-0100

摘要/Abstract

摘要：

目的开发覆盖番茄全基因组、多态性高且便于琼脂糖凝胶电泳检测的InDel分子标记，为番茄种质资源遗传多样性分析、DNA指纹图谱构建及品种鉴定等提供高效实用的技术工具。方法基于已公开的番茄重测序数据，通过生物信息学方法筛选符合目标的InDel变异位点并设计引物。利用涵盖普通鲜食番茄、口感番茄、加工番茄及樱桃番茄4大类型的商业品种，对所开发标记进行多态性验证、筛选与应用分析。结果成功开发84个在番茄全基因组均匀分布且多态性良好的InDel标记。利用该标记体系对288份番茄品种进行分析，结果显示品种间遗传相似系数变幅为0.369-0.994，平均值为0.667。基于遗传距离的聚类分析和主成分分析将供试番茄品种划分为4大类群，其中樱桃番茄表现出最高的遗传多样性并形成独立分支，普通鲜食番茄与口感番茄遗传背景最为相近，在聚类图中呈交叉混合分布。根据标记在不同类型番茄中的多态性差异，分别筛选出适用于普通鲜食番茄、口感番茄、加工番茄和樱桃番茄的核心鉴定标记组合，分别包含48、36、48和48对引物，并据此构建了品种DNA指纹图谱。应用案例表明，利用亲本间多态性标记可实现杂交种纯度的快速鉴定，利用核心标记组合可有效区分不同品种，证实了该标记体系的实用性与可靠性。结论开发的全基因组InDel标记体系多态性高、检测简便，能够有效揭示番茄商业品种的遗传多样性与群体结构，并成功应用于品种指纹图谱构建、真实性鉴定及杂交种纯度检测，可为番茄种质资源管理、分子育种及品种权保护提供技术支撑。

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

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.

Key words: tomato, InDel markers, population structure, fingerprint, variety identification, purity test, whole-genome

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.

SU Xiao-mei, LIU Shu-mei, LYU Hong-jun, YANG Zong-hui, HOU Li-xia. Development and Application of Insertion-deletion （InDel） Markers in Tomato Based on Whole-genome Re-sequencing Data[J]. Biotechnology Bulletin, 2026, 42(10): 27-36.

图/表 9

表1 不同类型番茄遗传多样性信息

Table 1 Genetic diversity parameters of different tomato types

群体类型 Group type	平均次要等位基因频率 Mean MAF	平均观测杂合度 Mean Ho	平均期望杂合度 Mean He	平均多态信息含量 Mean PIC
普通鲜食番茄 Fresh tomato （B）	0.207 4	0.254 8	0.264 0	0.208 8
口感番茄 Flavor tomato （K）	0.168 0	0.242 7	0.232 4	0.190 1
加工番茄 Processing tomato （P）	0.205 1	0.179 7	0.282 3	0.227 2
樱桃番茄 Cherry tomato （Y）	0.279 1	0.337 0	0.360 6	0.284 9
总计 Total	0.279 8	0.253 6	0.369 3	0.294 5

图1 84个InDel标记在番茄参考基因组的位置（SL4.0）

Fig. 1 Physical positions of 84 InDel markers on the tomato reference genome (SL4.0)

表2 不同类型番茄间遗传距离矩阵

Table 2 Genetic distance matrix among different tomato types

群体类型 Group type	普通鲜食番茄 Fresh tomato （B）	口感番茄 Flavor tomato （K）	加工番茄 Processing tomato （P）	樱桃番茄 Cherry tomato （Y）
普通鲜食番茄 Fresh tomato （B）	0.213 2	—	—	—
口感番茄 Flavor tomato （K）	0.261 9	0.185 5	—	—
加工番茄 Processing tomato （P）	0.315 3	0.345 7	0.259 9	—
樱桃番茄 Cherry tomato （Y）	0.412 2	0.429 0	0.420 8	0.296 8

图2 基于84个InDel标记构建的288个番茄品种UPGMA系统发育树B：普通鲜食番茄；K：口感番茄；P：加工番茄；Y：樱桃番茄。下同

Fig. 2 Phylogenetic tree of 288 tomato varieties based on 84 InDel markers using the UPGMA methodB: Fresh tomato. K: Flavor tomato. P: Processing tomato. Y: Cherry tomato. The same below

图3 基于84个InDel标记的288份番茄品种主成分分析（PCA）PC1：解释21.60%的遗传变异；PC2：解释11.58%的遗传变异

Fig. 3 Principal component analysis (PCA) of 288 tomato varieties based on 84 InDel markersPC1: Explained 21.60% of the total genetic variation; PC2: explained 11.58% of the total genetic variation

图4 InDel位点数对番茄品种的鉴定效率

Fig. 4 Efficiency of tomato variety identification using different numbers of InDel markers

图5 基于核心标记的4种类型番茄指纹图谱指纹图谱中不同颜色分别表示与参考基因组一致的纯合型（a，蓝色）、杂合型（h，白色）、纯合变异型（b，红色）

Fig. 5 DNA fingerprints of four tomato types based on core markersIn the fingerprint, different colors represent the homozygous type consistent with the reference genome (a, blue), heterozygous type (h, white) and variant homozygous type (b, red), respectively

图6 基于36个核心标记的2个口感番茄品种真实性鉴定红框表示2个品种间具有差异的标记

Fig. 6 Authenticity identification of two flavor tomato varieties based on a core set of 36 markersThe red box indicates polymorphic markers between the two varieties. M: 100 bp DNA marker

图7 基于分子标记的‘品番1933’杂交种纯度鉴定P1：母本，P2：父本；红色箭头表示杂株；红色数字表示可用于纯度鉴定的标记

Fig. 7 Purity identification of the hybrid 'Pinfan 1933' based on molecular markersP1: The female parent. P2: The male parent. The red arrows indicate the off-type plants. The red numbers indicate the markers that can be used for purity identification

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