Development and Application of Insertion-deletion （InDel） Markers in Tomato Based on Whole-genome Re-sequencing Data

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

Abstract

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

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

Figures/Tables 9

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

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

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

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

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

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

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

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

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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