• Exploring the Genomic Landscape: A Comprehensive Analysis of the Genetic Diversity and Population Structure of Thai Tomato Germplasm through Whole-Genome Sequencing (WGS)

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06/12/2024 by   

Metadata

Document Title

Exploring the Genomic Landscape: A Comprehensive Analysis of the Genetic Diversity and Population Structure of Thai Tomato Germplasm through Whole-Genome Sequencing (WGS)

Author

Yongsuwan A., Poncheewin W., Sastawittaya W., Somkul A., Thunnom B., Aesomnuk W., Bhunchoth A., Phironrit N., Phuangrat B., Koohapitakthum R., Deeto R., Warin N., Wanchana S., Arikit S., Chatchawankanphanich O., Chuenwarin P., Ruanjaichon V.

Affiliations

Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Center of Excellence on Agricultural Biotechnology—(AG-BIO/MHESI), Bangkok, 10900, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand; Tropical Vegetable Research Center, Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Rice Science Center, Kasetsart University, Nakhon Pathom, 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand

Source Title

Horticulturae

ISSN

23117524

Year

2024

Volume

10

Issue

6

Open Access

All Open Access, Gold

Publisher

Multidisciplinary Digital Publishing Institute (MDPI)

DOI

10.3390/horticulturae10060602

Abstract

Tomatoes (Solanum lycopersicum L.) represent a valuable crop species cultivated on a global scale, with Thailand playing a notable role in Southeast Asia’s agricultural landscape. However, a comprehensive understanding of the genetic underpinnings, population dynamics, and genetic correlations among tomato cultivars within Thailand remains relatively nascent. This study conducted an extensive analysis of 283 tomato accessions sourced from Thailand’s largest germplasm repository, employing approximately 2.4 million single-nucleotide polymorphisms (SNPs) obtained through whole-genome sequencing (WGS). The results of the genetic diversity assessment demonstrate a consistent delineation of groups, as indicated by UPGMA clustering, revealing five distinct clusters, while population structure analysis unveils twelve subpopulations. These findings underscore the limited genetic reservoir within Thai tomato germplasm, providing valuable insights for germplasm management strategies and offering a promising avenue for the refinement of breeding programs aimed at enhancing tomato genetics. © 2024 by the authors.

Industrial Classification

Agriculture | Fishing and Hunting | Forestry

Knowledge Taxonomy Level 1

Biological Sciences

Knowledge Taxonomy Level 3

Plant breeding

License

CC BY

Rights

Authors

Publication Source

Scopus

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