Genome-Wide InDel Marker Development and Genetic Diversity Analysis of 52 Tomato Germplasm Accessions.

Chenjiao Huang, Di Ge, Yaxuan Zhang, Zhiye Ge, Yicheng Wu, Qianrong Zhang, Yunxia Zhao, Chonghui Ji

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Article in Plants (Basel, Switzerland), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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8 authors.

Chenjiao HuangCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Di GeCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Yaxuan ZhangCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Zhiye GeCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Yicheng WuCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Qianrong ZhangFujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China.

Yunxia ZhaoInstitute of Horticulture, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China.

Chonghui JiCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.ORCID 0000-0003-2724-0859

Funding

Fujian Provincial Department of Science and Technology 2023J01072Ningxia Academy of Agriculture and Forestry Sciences NKYGZL-2026-10

6 · The paper itself

Abstract

To address the challenges of narrow genetic backgrounds and low phenotypic selection efficiency in tomato breeding, comparative genomics was applied. Based on the genomic sequences of five tomato varieties ('Micro-Tom', 'Moneymaker', 'M82', 'Heinz 1706', and 'LA2093'), a total of 285,796 InDel loci were preliminarily identified. Based on these loci, a total of 255 pairs of molecular markers were developed. Subsequently, based on InDel length, polymorphism, and electrophoretic performance, 63 InDel markers with stable amplification, clear polymorphic bands, and coverage across all 12 chromosomes were rigorously selected. These markers were subsequently used to analyze the genetic diversity of 52 tomato germplasm resources. The polymorphism information content (PIC) values of the markers ranged from 0.074 to 0.402, with an average of 0.2804. Cluster analysis based on InDel genotyping data divided the 52 germplasm samples into four distinct groups with significant genetic differentiation, which was validated in conjunction with previously collected phenotypic data from the 52 tomato germplasm resources. Furthermore, a set of core InDel primer combinations (24 pairs) was selected to construct unique DNA fingerprint profiles for each germplasm group. Overall, the InDel markers developed in this study provide an efficient tool for evaluating genetic diversity in tomato germplasm and offer a reliable molecular basis for germplasm identification, heterosis prediction, and marker-assisted breeding, thereby facilitating the development of improved tomato cultivars.

Indexed as

genetic diversityInDel makersmolecular markerstomato germplasm

Identifiers

PMID41977777

DOI10.3390/plants15071118

PMCPMC13074326

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