Genetic Background and Agronomic Trait Assessment in 212 Tomato (Solanum lycopersicum L.) Based on Phenotypic and SNP: Implications for Breeding and Germplasm Utilization

To comprehensively evaluate 212 tomato accessions and gain an in-depth understanding of their genetic background, 17 major agronomic traits were assessed, and whole-genome resequencing was performed on all materials. The results indicated that the genetic diversity of quantitative traits was abundant, with the genetic diversity index (H′) ranging from 0.79 to 2.03. In contrast, the genetic diversity of qualitative traits was relatively low, with the H′ falling between 0.363 and 0.936. The relationships between phenotypes were intricate and characterized by information redundancy. The top five principal components captured 69.014% of the phenotypic information. The F and D score-based comprehensive evaluation methods demonstrated strong consistency (r = 0.955 **). Among the 17 accessions ranked in the top 20 by both scores, 12 belonged to the large-fruit yellowish late-ripening type with distinct genetic backgrounds. These preliminary efforts not only provide an idea, a framework and a dataset for the integrated analysis of phenotypic evaluation, phenotypic clustering and population structure, but also lay a foundation for future inter-data network research, as well as potential material support for subsequent breeding efforts.