DNA Variation in a Diversity Panel of Tomato Genetic Resources

Abstract

A diversity panel of 190 National Plant Germplasm System (NPGS) tomato (Solanum lycopersicum) accessions was genotyped using genotyping by sequencing. These originated from 31 countries and included fresh market, ornamental, processing, breeders’ lines, landraces, and home gardening types, as well as six different accessions of the economically valuable cultivar San Marzano. Most of the 34,531 discovered single nucleotide polymorphisms were rare and therefore excluded from downstream analyses. A total of 3713 high-quality, mapped single nucleotide polymorphisms that were present in at least two accessions were used to estimate genetic distances and population structure. Results showed that these phenotypically and geographically diverse NPGS tomato accessions were closely related to each other. However, a subset of divergent genotypes was identified that included landraces from primary centers of diversity (South America), secondary centers of diversity (Italy, Taiwan, and France), and genotypes that originated from wild species through 20th century breeding for disease resistance (e.g., ‘VFNT Cherry’). Extreme variant accessions produce cultivated fruit traits in a background that contains many wild or primitive genes. These accessions are promising sources of novel genes for continued crop improvement.

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

“…Neither grouping was able to differentiate between fruit types or regions of origin. This indicates an extreme closeness among the cultivars, possibly resulting from early domestication and selective breeding [16,37,[49][50][51]. AMOVA analysis using a SNP subset yielded consistent results, showing only 0.7% variation attributable to population differences.…”

“…The genetic diversity and population structure of tomatoes are pivotal in plant breeding for devising efficient breeding programs and ensuring sustainable production of tomatoes [8]. Despite numerous studies addressing this aspect, until recent times, Thai varieties were overlooked [17,37,38]. Consequently, our comprehension of the genetic diversity and resources within Thai tomatoes remains considerably restricted.…”