Skip to main content
ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #420799
Research Project: Harnessing Genomic Technologies Toward Improving Vegetable Health in Field and Controlled Environments

Location: Vegetable Research

Title: Genetic diversity and population structure of tomato (Solanum lycopersicum)

Author
item ALATAWI, IBTISAM - University Of Arkansas
item XIONG, HAIZHENG - University Of Arkansas
item ALKABKABI, HANAN - University Of Arkansas
item CHIWINA, KENANI - University Of Arkansas
item LUO, QUN - University Of Arkansas
item Ling, Kai Shu
item QU, YUEJUN - University Of Arkansas
item DU, RENJIE - University Of Arkansas
item SHI, AINONG - University Of Arkansas

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2024
Publication Date: 12/26/2024
Citation: Alatawi, I., Xiong, H., Alkabkabi, H., Chiwina, K., Luo, Q., Ling, K., Qu, Y., Du, R., Shi, A. 2024. Genetic diversity and population structure of tomato (Solanum lycopersicum). Agronomy. 15(1):22. https://doi.org/10.3390/agronomy15010022.
DOI: https://doi.org/10.3390/agronomy15010022

Interpretive Summary: Tomato is a globally valued horticultural crop and a major vegetable in the U.S. Enhancing the genetic makeup of tomatoes has long been a priority for plant breeders, with a focus on improving traits such as yield, disease resistance, fruit quality, and environmental adaptability. In collaboration with scientists in University of Arkansas, ARS scientist in Charleston, SC applied the genotyping-by-sequencing technology on a core collection of tomato germplasm (276 accessions) from the USDA's National Plant Germplasm System and conducted single nucleotide polymorphism analysis to understand the genetic diversity and population structure within these accessions. The results from model-based ancestry analysis, phylogenetic tree construction, and principal component analysis supported these accessions as representing three well-differentiated genetic populations. Understanding the genetic diversity and population structure of this valuable tomato germplasm provides critical insights to enhance breeding strategy and ensure the conservation of essential genetic resources.

Technical Abstract: This study aimed to determine gene pool structure in the tomato (Solanum lycopersicum) along with the relationships of populations in different regions. To do so, it leveraged 276 diverse cultivated accessions representing 35 countries, obtained via the USDA tomato germplasm collection. Single nucleotide polymorphisms (SNPs) in these accessions were detected by sequencing, and genetic diversity, population structure, and phylogenetic relationships were estimated from the SNP alleles. The results of model-based ancestry analysis, phylogenetic tree construction, and principal component analysis supported these accessions as representing three well-differentiated genetic populations. Phylogenetic analyses traced the accessions back to their regions of origin, highlighting Central and South America as the primary center of domestication, with secondary centers in Europe and North America. This study provides a comprehensive analysis of the genetic variation in and relationships among cultivated tomato genotypes. The findings are of benefit to curators, researchers, and breeders in understanding, utilizing, conserving, and managing the collection, and in thereby contributing more efficiently to international tomato research.