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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. [ABSTRACT FROM AUTHOR]

Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis–antenna proteins, nitrogen metabolism, plant–pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5′-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, the biosynthesis of secondary metabolites, the biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomatoes to enhance drought tolerance. [ABSTRACT FROM AUTHOR]

Tomato as a fresh fruit has a large market share in China, but few new materials have been developed for such cultivar breeding in recent years. This study aims to create innovative breeding materials for fresh fruit tomatoes with consistent genetic backgrounds and take advantage of beneficial genes from wild germplasm resources. An introgression line (IL) population was constructed using freshly cultivated tomato S. lycopersicum 1052 and wild tomato S. pennellii LA0716 through hybridization and five consecutive backcrossings, with molecular marker-assisted selection techniques during seedling stages. A total of 447 cleaved amplified polymorphic sequences (CAPS) and 525 simple sequence repeat (SSR) markers were used to screen polymorphic markers among the two parental lines, resulting in 216 polymorphic CAPS and 236 polymorphic SSR markers, with 46.5% parental polymorphism. Then, 200 molecular markers uniformly distributed over the entire genome were further selected, and 107 ILs were finally obtained from 541 BC5 candidate plants. The physical distance between adjacent markers was 6.3~10.0 cm, with an average interval of 7.29 cm, and the IL population constructed covered the whole genome of S. pennillii LA0716, with an average introgression segment of 31.5 cm. Moreover, phenotype data of major agronomic traits in BC5 progeny after selfing two times, were analyzed for quantitative trait locus (QTL) mapping, and a total of 11 QTLs distributed on 6 chromosomes were identified, including 3 QTLs regulating plant height, 1 QTL regulating leaf size, 1 QTL regulating fruit color, 4 QTLs regulating fruit weight, and 2 QTLs regulating soluble solids content in ripening fruits. The IL population constructed in this study provided good materials for fresh fruit tomato breeding with improved yield and quality in the future. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 (fw6.3HG) was overdominant to the small-fruit allele fw6.3RG. The soluble solids content was also increased by fw6.3HG. 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. [ABSTRACT FROM AUTHOR]

The formation of locule gel is an important process in tomato and is a typical characteristic of berry fruit. In this study, we examined a natural tomato mutant that produces all-flesh fruit (AFF) in which the locule tissue remains in a solid state during fruit development. We constructed different genetic populations to fine-map the causal gene for this trait and identified SlMBP3 as the locus conferring the locule gel formation, which we rename as AFF. We determined the causal mutation as a 416-bp deletion in the promoter region of AFF , which reduces its expression dosage. Generally, this sequence is highly conserved among Solanaceae, as well as within the tomato germplasm. Using BC6 near-isogenic lines, we determined that the reduced expression dosage of AFF did not affect the normal development of seeds, whilst producing unique, non-liquefied locule tissue that was distinct from that of normal tomatoes in terms of metabolic components. Combined analysis using mRNA-seq and metabolomics indicated the importance of AFF in locule tissue liquefaction. Our findings provide insights into fruit-type differentiation in Solanaceae crops and also present the basis for future applications of AFF in tomato breeding programs. [ABSTRACT FROM AUTHOR]

Leaf veins play an important role in plant growth and development, and the bundle sheath (BS) is believed to greatly improve the photosynthetic efficiency of C4 plants. The OBV mutation in tomato (Solanum lycopersicum) results in dark veins and has been used widely in processing tomato varieties. However, physiological performance has difficulty explaining fitness in production. In this study, we confirmed that this mutation was caused by both the increased chlorophyll content and the absence of bundle sheath extension (BSE) in the veins. Using genome-wide association analysis and map-based cloning, we revealed that OBV encoded a C2H2L domain class transcription factor. It was localized in the nucleus and presented cell type-specific gene expression in the leaf veins. Furthermore, we verified the gene function by generating CRISPR/Cas9 knockout and overexpression mutants of the tomato gene. RNA sequencing analysis revealed that OBV was involved in regulating chloroplast development and photosynthesis, which greatly supported the change in chlorophyll content by mutation. Taken together, these findings demonstrated that OBV affected the growth and development of tomato by regulating chloroplast development in leaf veins. This study also provides a solid foundation to further decipher the mechanism of BSEs and to understand the evolution of photosynthesis in land plants. [ABSTRACT FROM AUTHOR]

The whitefly-transmitted tomato yellow leaf curl virus (TYLCV) is one of the most destructive viral pathogens of cultivated tomato. To combat TYLCV, resistance gene Ty-2 has been introduced into cultivated tomato (Solanum lycopersicum) from wild tomato species Solanum habrochaites by interspecific crossing. Introgression lines with Ty-2 contain a large inversion compared with S. lycopersicum , which causes severe suppression of recombination and has hampered the cloning of Ty-2 so far. Here, we report the fine-mapping and cloning of Ty-2 using crosses between a Ty-2 introgression line and several susceptible S. habrochaites accessions. Ty-2 was shown to encode a nucleotide-binding leucine-rich repeat (NLR) protein. For breeding purposes, a highly specific DNA marker tightly linked to the Ty-2 gene was developed permitting marker-assisted selection. The resistance mediated by Ty-2 was effective against the Israel strain of TYLCV (TYLCV-IL) and tomato yellow leaf curl virus-[China : Shanghai2] (TYLCV-[CN : SH2]), but not against tomato yellow leaf curl Sardinia virus (TYLCSV) and leafhopper-transmitted beet curly top virus (BCTV). By co-infiltration experiments we showed that transient expression of the Rep/C1 protein of TYLCV, but not of TYLCSV triggered a hypersensitive response (HR) in Nicotiana benthamiana plants co-expressing the Ty-2 gene. Our results indicate that the Rep / C1 gene of TYLCV-IL presents the avirulence determinant of Ty-2- mediated resistance. [ABSTRACT FROM AUTHOR]

Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of phenotypic variation (R2), respectively. The qtph1.1 was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40), Solyc01g098390 encoding GA receptor SlGID1a was the putative candidate gene. The SlGID1a gene underlying the qtph1.1 locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the qtph1.1 locus (NIL- qtph1.1) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL- qtph1.1 could not be rescued by exogenous GA3 treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL- qtph1.1 and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height. [ABSTRACT FROM AUTHOR]

Key message: Tomato male sterile-1526 locus was fine-mapped to an interval of 44.6 kb, and a B-class MADS-box gene TM6 was identified as the candidate gene. Male sterile lines have been widely used for hybrid seed production in many crop plants. The tomato male sterile-1526 (ms-1526) mutant displays abnormal stamens and exerted stigmas and is suitable for practical use. In this study, the ms-1526 locus was fine-mapped to a 44.6 kb interval that contained four putative genes. Thereinto, Solyc02g084630 encodes tomato B-class MADS-box gene TM6 (syn. TDR6), which plays an important role in stamen development. Sequencing revealed that there was a 12.7 kb deletion in the ms-1526 region, where the promoter and first four exons of the TM6 gene were absent. ms-1547, an allele of ms-1526, also contained the same deletion in the TM6 gene. And the other allele ms-15 mutant contained a single-nucleotide polymorphism (SNP, C to A) in the coding region of the TM6 gene, which led to a missense mutation (G to W). The codominant insertion/deletion (InDel) marker MS26D and codominant derived cleaved amplified polymorphic sequence (dCAPS) marker MS15C were developed based on the deletion and SNP, respectively. A real-time quantitative reverse-transcription PCR showed that expression of the TM6 gene was barely detectable in the flowers of the ms-1526 and ms-1547 mutants. In addition, other floral organ identity genes, pollen development marker genes, and pistil marker genes were differentially expressed between wild type and mutant flowers. These findings may facilitate functional analysis of the TM6 gene and help in the marker-assisted selection of ms-15 and its alleles in tomato breeding. [ABSTRACT FROM AUTHOR]

Anthocyanin pigments play many roles in plants, including providing protection against biotic and abiotic stresses. Many of the genes that mediate anthocyanin accumulation have been identified through studies of flowers and fruits; however, the mechanisms of genes involved in anthocyanin regulation in seedlings under low-temperature stimulus are less well understood. Genetic characterization of a tomato inbred line, FMTT271, which showed no anthocyanin pigmentation, revealed a mutation in a bHLH transcription factor (TF) gene, which corresponds to the ah (Hoffman's anthocyaninless) locus, and so the gene in FMTT271 at that locus was named ah. Overexpression of the wild type allele of AH in FMTT271 resulted in greater anthocyanin accumulation and increased expression of several genes in the anthocyanin biosynthetic pathway. The expression of AH and anthocyanin accumulation in seedlings was shown to be developmentally regulated and induced by low-temperature stress. Additionally, transcriptome analyses of hypocotyls and leaves from the near-isogenic lines seedlings revealed that AH not only influences the expression of anthocyanin biosynthetic genes, but also genes associated with responses to abiotic stress. Furthermore, the ah mutation was shown to cause accumulation of reactive oxidative species and the constitutive activation of defense responses under cold conditions. These results suggest that AH regulates anthocyanin biosynthesis, thereby playing a protective role, and that this function is particularly important in young seedlings that are particularly vulnerable to abiotic stresses. [ABSTRACT FROM AUTHOR]

Late blight is the most devastating potato disease and it also causes serious yield loss in tomato. Several disease resistance genes ( R genes) to late blight have been cloned from potato in the past decade. However, the resistance mechanisms remain elusive. Tomato and potato belong to the botanical family Solanaceace and share remarkably conserved genome structure. Since tomato is a model system in genetic and plant pathology research, we used tomato to develop a powerful mutant screening system that will greatly facilitate the analysis of the signaling pathway of resistance to Phytophthora infestans. First we proved that the R3a transgenic tomatoes developed specific hypersensitive cell death response (HR) to P. infestans strains carrying the corresponding avirulence gene Avr3a, indicating that the signaling pathway from the R3a-Avr3a recognition to HR is conserved between potato and tomato. Second, we generated transgenic tomatoes carrying both R3a and Avr3a genes, with the latter under the control of a glucocorticiod-inducible promoter. Dexamethasone induced expression of Avr3a and resulted in localized HR. This versatile system can be used to construct a mutant library to screen surviving mutants whose resistance signal transduction was interrupted, providing the basis to identify key genes involved in the resistance to late blight in Solanaceae. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum L.) is one of the most popular cultivated vegetables worldwide. Tomato leaves are determinate organs with important functions affecting plant growth and development. In addition to the other leaf phenotypes, folded leaves have recently been observed in several tomato varieties. In the present study, an F2 population was generated from a cross between tomato inbred lines 14g-677 (i.e., folded leaves) and 14g-683 (i.e., wild-type leaves). A genetic analysis of the folded-leaf trait in 199 F2 individuals revealed this leaf phenotype is controlled by a single recessive gene, which was designated as fl. This gene was initially localized to chromosome 11 based on insertion/deletion (InDel) markers and a bulked segregant analysis (BSA). According to a genetic map consisting of new markers and recombinants, the fl gene was mapped between the SNP-1 and dcaps-10 markers at the distal end of the long arm of tomato chromosome 11. The physical distance between the two markers was approximately 62.2 kb. The annotation and functional characterization of the genes in this region indicated fl may be ARF4, which encodes an auxin response factor. A sequence analysis revealed that the ARF4 of line 14g-677 is missing a single C in the third exon region. Furthermore, a quantitative real-time polymerase chain reaction detected an approximate fourfold difference in ARF4 transcript abundance between lines 14g-677 and 14g-683. Thus, a mutation to ARF4 is likely responsible for the folded-leaf phenotype of tomato mutants. [ABSTRACT FROM AUTHOR]

Key message: Tomato male sterile-1526 locus was fine-mapped to an interval of 44.6 kb, and a B-class MADS-box gene TM6 was identified as the candidate gene. Male sterile lines have been widely used for hybrid seed production in many crop plants. The tomato male sterile-1526 (ms-1526) mutant displays abnormal stamens and exerted stigmas and is suitable for practical use. In this study, the ms-1526 locus was fine-mapped to a 44.6 kb interval that contained four putative genes. Thereinto, Solyc02g084630 encodes tomato B-class MADS-box gene TM6 (syn. TDR6), which plays an important role in stamen development. Sequencing revealed that there was a 12.7 kb deletion in the ms-1526 region, where the promoter and first four exons of the TM6 gene were absent. ms-1547, an allele of ms-1526, also contained the same deletion in the TM6 gene. And the other allele ms-15 mutant contained a single-nucleotide polymorphism (SNP, C to A) in the coding region of the TM6 gene, which led to a missense mutation (G to W). The codominant insertion/deletion (InDel) marker MS26D and codominant derived cleaved amplified polymorphic sequence (dCAPS) marker MS15C were developed based on the deletion and SNP, respectively. A real-time quantitative reverse-transcription PCR showed that expression of the TM6 gene was barely detectable in the flowers of the ms-1526 and ms-1547 mutants. In addition, other floral organ identity genes, pollen development marker genes, and pistil marker genes were differentially expressed between wild type and mutant flowers. These findings may facilitate functional analysis of the TM6 gene and help in the marker-assisted selection of ms-15 and its alleles in tomato breeding. [ABSTRACT FROM AUTHOR]