Exploring the Genomic Landscape: A Comprehensive Analysis of the Genetic Diversity and Population Structure of Thai Tomato Germplasm through Whole-Genome Sequencing (WGS)
Arweewut Yongsuwan,
Wasin Poncheewin,
Wittaya Sastawittaya,
Akarachai Somkul,
Burin Thunnom,
Wanchana Aesomnuk,
Anjana Bhunchoth,
Namthip Phironrit,
Bencharong Phuangrat,
Ratree Koohapitakthum,
Rungnapa Deeto,
Nuchnard Warin,
Samart Wanchana,
Siwaret Arikit,
Orawan Chatchawankanphanich,
Paweena Chuenwarin,
Vinitchan Ruanjaichon
Affiliations
Arweewut Yongsuwan
Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
Wasin Poncheewin
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Wittaya Sastawittaya
Tropical Vegetable Research Center, Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
Akarachai Somkul
Tropical Vegetable Research Center, Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
Burin Thunnom
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Wanchana Aesomnuk
Rice Science Center, Kasetsart University, Nakhon Pathom 73140, Thailand
Anjana Bhunchoth
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Namthip Phironrit
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Bencharong Phuangrat
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Ratree Koohapitakthum
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Rungnapa Deeto
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Nuchnard Warin
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Samart Wanchana
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Siwaret Arikit
Rice Science Center, Kasetsart University, Nakhon Pathom 73140, Thailand
Orawan Chatchawankanphanich
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
Paweena Chuenwarin
Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
Vinitchan Ruanjaichon
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
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.
