Skip to main content

ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Breeding
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1445734

Genetic Diversity and Population Structure Analysis of 418 Tomato Cultivars Based on Single Nucleotide Polymorphism Markers

Provisionally accepted
Xu Wei Jie Xu Wei Jie *Chao Gong Chao Gong Mai Pei ting Mai Pei ting li zhen xing li zhen xing Baojuan Sun Baojuan Sun Tao Li Tao Li *
  • Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China

The final, formatted version of the article will be published soon.

    Tomato (Solanum lycopersicum) is a highly valuable fruit crop. However, due to the lack of scientific and accurate variety identification methods and unified national standards, production management is scattered and non-standard, resulting in mixed varieties. This poses considerable difficulties for the cataloging and preservation of germplasm resources as well as the identification, promotion, and application of new tomato varieties. To better understand the genetic diversity and population structure of representative tomato varieties, we collected 418 tomato varieties from the past 20 years and analyzed them using genome-wide single nucleotide polymorphism (SNP) markers. We initially assessed the population structure, genetic relationships, and genetic profiles of the 418 tomato germplasm resources utilizing simplified genome sequencing techniques. A total of 3,374,929 filtered SNPs were obtained and distributed across 12 chromosomes. Based on these SNP loci, the 418 tomatoes samples were divided into six subgroups. The population structure and genetic relationships among existing tomato germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Rigorous selection criteria identified 15 additional high-quality DNA fingerprints from 50 validated SNP loci, effectively enabling the identification of the 418 tomato varieties, which were successfully converted into KASP (Kompetitive Allele Specific PCR) markers. This study represents the first comprehensive investigation assessing the diversity and population structure of a large collection of tomato varieties. Overall, it marks a considerable advancement in understanding the genetic makeup of tomato populations. The results broadened our understanding of the diversity, phylogeny, and population structure of tomato germplasm resources. Furthermore, this study provides a scientific basis and reference data for future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding in tomatoes.

    Keywords: Genetic relationship1, population structure2, SNPs3, DNA fingerprint4, SNP markers5

    Received: 08 Jun 2024; Accepted: 08 Nov 2024.

    Copyright: © 2024 Jie, Gong, ting, xing, Sun and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Xu Wei Jie, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong Province, China
    Tao Li, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong Province, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.