ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1582241
An advanced 10K SNP Panel for Genotyping Tomato (Solanum lycopersicum L.) via Targeted Genome Sequencing
Provisionally accepted
Yawo Mawunyo Nevame Adedze1,2*
Yanfen Xu2Song Liu2Yaran Zhao2Changjuan Mo2Renxu Zhang2Jiahui Dong2Haofa Lan2Jingjing Huang2Xingming Chen2Xuefei Gao2Qingzhen Yin3Jianan Zhang2- 1Other, Suqian, China
- 2Molbreeding Biotechnology Co., Ltd., No. 769 Taihang South Street, High-tech Zone, Shijiazhuang 050000, China, Tel: + (86) 400 008 9521 Email: info@molbreeding.com, Shijiazhuang, China
- 3Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences (HAAFS), Shijiazhuang, Hebei Province, China
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Recent breakthroughs in genomics have facilitated the identification of single nucleotide polymorphisms (SNPs) and small insertions-deletions (InDels). With the reduction in sequencing costs, a variety of genotyping tools have emerged for genetic analysis in plants. However, there is a significant need for an effective and affordable tool that combines both foreground and background sites. To meet this requirement in tomatoes, four SNP databases accounting for 12,442 SNPs were integrated with 186 trait-specific markers. A total of 335 tomato samples were used for the genotyping by target sequencing analysis. A series of criteria were performed for site selection and for assessing the sequencing data effectiveness. The panel designated as the GenoBaits Tomato 10K panel ultimately comprised 11,174 background sites, with 74.83% sourced from database 1 upon optimization. The uniformity_50 and capture efficiency of this panel were 98.03% and 74.84%, respectively, while the SNP detection rate was 99.34%. The SNPs with a minor allele frequency (MAF) > 0.05 accounted for 60.57%, and those with MAF > 0.4 represented 20%. The average genome MAF was 0.18, with a gap value of 0.07 Mbp. The GenoBaits Tomato 10K panel has demonstrated its effectiveness in assessing genetic diversity, with minimal impact from trait-specific markers. This panel effectively pinpointed the predefined resistant and susceptible marker alleles associated with 19 key tomato resistance genes in the targeted population. Therefore, future research should validate them in order to unlock the full diagnostic potential of this panel in tomato genetics and breeding.
Keywords: optimization, Efficiency, genetic, diversity, Resistance, Tomato
Received: 24 Feb 2025; Accepted: 15 Apr 2025.
Copyright: © 2025 Adedze, Xu, Liu, Zhao, Mo, Zhang, Dong, Lan, Huang, Chen, Gao, Yin and Zhang. 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: Yawo Mawunyo Nevame Adedze, Other, Suqian, 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.