Heterosis and combining ability are two important considerations in the utilization of heterosis, which can be used to generate excellent hybrid resource candidates and is very important in conventional hybrid breeding. In this study, the combining ability, heritability, and heterosis of eight major agronomic traits were analyzed in 10 tomato parents and 45 crosses between them. As well as TY-301, a recognized and official excellent variety that is currently selling well on the market was used as a control to conduct a control heterosis analysis, with the goal of selecting ideal parents with high combining ability and new hybrids with commodity value, high yield, early maturity, and high quality. The results showed that both additive and nonadditive genetic effects are involved in the expression of the traits and that the additive genetic effect is dominant in trait inheritance. Although general combining ability (GCA) and specific combining ability (SCA) were not correlated, and the strength of heterosis depends on SCA, the sum of the parental GCA values (GCAsum) did predict heterosis for some traits with higher predictive accuracy than did SCA. Compared with heterosis, GCAsum can better predict hybrid performance. Finally, the parent 17,969 was the breeding material with the best comprehensive trait performance, especially in yield. We screened a high-yielding candidate combination 17,927 × 17,969 and a precocious and good taste candidate combination 17,666 × 17,927. This information may play an important role in the selection of superior parents and hybrid combinations based on combining ability and heterosis analysis.

Understanding the genetic background of elite cultivated tomato germplasm resources in crossbreeding and revealing the genetic basis of complex traits are vital for better-targeted germplasm expansion and the creation of strong hybrids. Here, we obtained approximately 21 million single-nucleotide polymorphisms (SNPs) based on the sequencing of 212 cultivated tomato accessions and the population structure of which was revealed. More importantly, we found that target genes distributed on chromosomes 1, 5, 9, and 11 may be actively selected in breeding. In particular, the significant signals related to soluble sugar content (chr1_94170222, chr1_96273188, chr9_4167512, and chr11_55592768), fruit firmness (chr5_4384919 and chr5_5111452) and gray leaf spot resistance (chr11_8935252 and chr11_9707993) were also detected on the corresponding chromosomes, respectively. Overall, we reported 28 significant association signals for nine agronomic traits based on a mixed linear model (MLM), including 114 genes. Among these signals, 21 contained potential novel genes for six fruit traits. These novel candidate genes located in genomic regions without previously known loci or on different chromosomes explained approximately 16% of the phenotypic variance on average in cultivated tomatoes. These findings could accelerate the identification and validation of novel and known candidate genes and QTLs, improving the understanding of the genetic structure of complex quantitative traits. These results also provide a basis for tomato breeding and improvement.

Tomato leaf mold disease caused by Cladosporium fulvum (C. fulvum) is one of the most common diseases affecting greenhouse tomato production. Cf proteins can recognize corresponding AVR proteins produced by C. fulvum, and Cf genes are associated with leaf mold resistance. Given that there are many physiological races of C. fulvum and that these races rapidly mutate, resistance to common Cf genes (such as Cf-2, Cf-4, Cf-5, and Cf-9) has decreased. In the field, Ont7813 plants (carrying the Cf-13 gene) show effective resistance to C. fulvum; thus, these plants could be used as new, disease-resistant materials. To explore the mechanism of the Cf-13-mediated resistance response, transcriptome sequencing was performed on three replicates each of Ont7813 (Cf-13) and Moneymaker (MM; carrying the Cf-0 gene) at 0, 9, and 15 days after inoculation (dai) for a total of 18 samples. In total, 943 genes were differentially expressed, specifically in the Ont7813 response process as compared to the Moneymaker response process. Gene ontology (GO) classification of these 943 differentially expressed genes (DEGs) showed that GO terms, including “hydrogen peroxide metabolic process (GO_Process)”, “secondary active transmembrane transporter activity (GO_Function)”, and “mismatch repair complex (GO_Component)”, which were the same as 11 other GO terms, were significantly enriched. An analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that many key regulatory genes of the Cf-13-mediated resistance response processes were involved in the “plant hormone signal transduction” pathway, the “plant–pathogen interaction” pathway, and the “MAPK signaling pathway–plant” pathway. Moreover, during C. fulvum infection, jasmonic acid (JA) and salicylic acid (SA) contents significantly increased in Ont7813 at the early stage. These results lay a vital foundation for further understanding the molecular mechanism of the Cf-13 gene in response to C. fulvum infection.

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.