Genetic diversity and population structure analysis of 418 tomato cultivars based on SNP markers

Abstract Tomato (Solanum lycopersicum) is a highly valuable fruit crop. However, due to the lack of scientific and accurate variety identification methods and nationally unified standards, scattered and non-standardized management in production has led to mixed varieties that have caused significant difficulties in the cataloging and preservation of germplasm resources and the identification, promotion, and application of new tomato varieties. In order to better understand the genetic diversity and population structure of representative tomato varieties, we have collected a total of 418 representative tomato varieties in the past 20 years and analyzed them based on genome-wide single nucleotide polymorphism (SNP) markers. In this study, we evaluated the population structure, genetic relationships, and genetic fingerprints of 418 germplasm resources of tomatoes using simplified genome sequencing technology. A total of 196,612,427 single nucleotide polymorphisms (SNPs) were identified. Furthermore, 418 samples of tomatoes were divided into six subgroups, and the population structure and genetic relationships among existing tomato germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Through several stringent selection criteria, 15 additional streamlined, high-quality DNA fingerprints were filtered out of the validated 50 SNP loci and verified as being able to effectively identify the 418 tomato varieties. Among them, 46 SNP loci were successfully converted into KASP markers. In general, this study marks the first comprehensive investigation that measures the diversity and population structure of a substantial collection of tomato varieties. These results have greatly broadened our understanding of the diversity, phylogeny, and population structure of tomato germplasm resources. The results may provide a scientific basis and reference data for the future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding in tomatoes.