Male sterility is a valuable trait for hybrid seed production in tomato (Solanum lycopersicum). The mutants male sterile-30 (ms-30) and ms-33 of tomato exhibit twisted stamens, exposed stigmas, and complete male sterility, thus holding potential for application in hybrid seed production. In this study, the ms-30 and ms-33 loci were fine-mapped to 53.3 kb and 111.2 kb intervals, respectively. Tomato PISTILLATA (TPI, syn. SlGLO2), a B-class MADS-box transcription factor gene, was identified as the most likely candidate gene for both loci. TPI is also the candidate gene of tomato male sterile mutant 7B-1 and sl-2. Allelism tests revealed that ms-30, ms-33, 7B-1, and sl-2 were allelic. Sequencing analysis showed sequence alterations in the TPI gene in all these mutants, with ms-30 exhibiting a transversion (G to T) that resulted in a missense mutation (S to I); ms-33 showing a transition (A to T) that led to alternative splicing, resulting in a loss of 46 amino acids in protein; and 7B-1 and sl-2 mutants showing the insertion of an approximately 4.8 kb retrotransposon. On the basis of these sequence alterations, a Kompetitive Allele Specific PCR marker, a sequencing marker, and an Insertion/Deletion marker were developed. Phenotypic analysis of the TPI gene-edited mutants and allelism tests indicated that the gene TPI is responsible for ms-30 and its alleles. Transcriptome analysis of ms-30 and quantitative RT-PCR revealed some differentially expressed genes associated with stamen and carpel development. These findings will aid in the marker-assisted selection for ms-30 and its alleles in tomato breeding and support the functional analysis of the TPI gene.

Tomato (Solanum lycopersicum) is a widely consumed vegetable, and the tomato fruit weight is a key yield component. Many quantitative trait loci (QTLs) controlling tomato fruit weight have been identified, and six of them have been fine-mapped and cloned. Here, four loci controlling tomato fruit weight were identified in an F₂ population through QTL seq.; fruit weight 6.3 (fw6.3) was a major-effect QTL and its percentage of variation explanation (R²) was 0.118. This QTL was fine-mapped to a 62.6 kb interval on chromosome 6. According to the annotated tomato genome (version SL4.0, annotation ITAG4.0), this interval contained seven genes, including Solyc06g074350 (the SELF-PRUNING gene), which was likely the candidate gene underlying variation in fruit weight. The SELF-PRUNING gene contained a single-nucleotide polymorphism that resulted in an amino acid substitution in the protein sequence. The large-fruit allele of fw6.3 (fw6.3_HG) was overdominant to the small-fruit allele fw6.3_RG. The soluble solids content was also increased by fw6.3_HG. These findings provide valuable information that will aid the cloning of the FW6.3 gene and ongoing efforts to breed tomato plants with higher yield and quality via molecular marker-assisted selection.

Plant cuticular wax plays an important role in resistance to environmental stresses. Eceriferum (CER) genes are involved in wax synthesis. However, little information is available for tomato species. In this study, 26 SlCER genes were identified in tomato (S. lycopersicum), and they were classified into four clades. The physicochemical properties and conserved motifs of their proteins were predicted. These SlCERs were mainly expressed in leaves, flowers or fruits, and most SlCERs played roles in response to abiotic stresses, especially drought stress. Furthermore, the changes in haplotypes indicated that SlCERs might have been involved in adapting to the environments for wild species S. pimpinellifolium before domestication. These findings would lay a foundation for future functional studies of SlCERs and also provide insights for anti-stress improvement in tomato in the near future.

Late blight is a destructive disease affecting tomato production. The identification and characterization of resistance (R) genes are critical for the breeding of late blight-resistant cultivars. The incompletely dominant gene Ph-2 confers resistance against the race T₁ of Phytophthora infestans in tomatoes. Herein, we identified Solyc10g085460 (RGA1) as a candidate gene for Ph-2 through the analysis of sequences and post-inoculation expression levels of genes located within the fine mapping interval. The RGA1 was subsequently validated to be a Ph-2 gene through targeted knockout and complementation analyses. It encodes a CC-NBS-LRR disease resistance protein, and transient expression assays conducted in the leaves of Nicotiana benthamiana indicate that Ph-2 is predominantly localized within the nucleus. In comparison to its susceptible allele (ph-2), the transient expression of Ph-2 can elicit hypersensitive responses (HR) in N. benthamiana, and subsequent investigations indicate that the structural integrity of the Ph-2 protein is likely a requirement for inducing HR in this species. Furthermore, ethylene and salicylic acid hormonal signaling pathways may mediate the transmission of the Ph-2 resistance signal, with PR1- and HR-related genes potentially involved in the Ph-2-mediated resistance. Our results could provide a theoretical foundation for the molecular breeding of tomato varieties resistant to late blight and offer valuable insights into elucidating the interaction mechanism between tomatoes and P. infestans.

Parthenocarpy and male sterility are highly desirable traits in tomato breeding and molecular study. The stamen carpelloid mutant generally displays male sterility. A natural mutant displaying carpelloid stamen and parthenocarpy (csp) was identified in our research group. In this study, the csp locus was finely mapped to a 65 kb interval, which contained six putative genes. One of them, Solyc04g081000, encodes the tomato class B MADS box gene TAP3 (syn. SlDEF). Sequencing data revealed that a copia long terminal repeat retrotransposon was inserted in the first intron of the TAP3 gene of the csp mutant. qRT-PCR showed that the expression of TAP3 was significantly down-regulated in the petals and stamens of the csp mutant. A phenotypic analysis of the TAP3 gene-edited mutants and allelism tests indicated that TAP3 was the gene underlying csp, and csp was a novel allelic mutation of TAP3. The results of this study will lay the foundation for a further analysis of the function of TAP3 and provide materials and a basis for a further study of the functional differentiation of tomato B-class genes.

Tomato chlorosis virus (ToCV) is an emerging plant virus that poses a substantial threat to the cultivation of economically vital vegetable crops, particularly tomato (Solanum lycopersicum). Despite its substantial impact on crop yield, resistant or tolerant tomato germplasms have not been well documented, and the genetic basis of resistance to ToCV remains poorly understood. In this study, two wild accessions that were immune to ToCV and five accessions that were highly resistant to ToCV were identified from 58 tomato accessions. Additionally, a novel method was developed for evaluating resistance to ToCV in tomatoes, and it was observed that tomatoes exhibited typical pathological features on days 15 and 30 after ToCV inoculation, referred to as Stage 1 and Stage 2, respectively. Using quantitative trait locus (QTL) sequencing in conjunction with classical QTL approaches, ToCV resistance loci were identified in two F2 populations derived from the crosses between SG11 (susceptible) and LA1028 (resistant) and between SP15 (susceptible) and LA0444 (resistant). Genetic analysis indicated that resistance to ToCV in the wild-type ToCV-resistant tomato accessions LA1028 and LA0444 was quantitative and mainly governed by four loci (Qtc1.1 and Qtc11.1 from LA1028 and Qtc7.1 and Qtc9.1 from LA0444). Subsequently, transcriptome analysis of three resistant accessions (LA2157, LA0444, and LA1028) and two susceptible accessions (SG11 and SP15) revealed unique differentially expressed genes and specific biological processes in the two stages of ToCV infection. This study provides new resistant germplasms and potential genetic resources for ToCV resistance, which can be valuable in tomato molecular breeding programs in obtaining resistant varieties.