Tohru Ariizumi

Cytoplasmic male sterility (CMS) is a trait wherein plants cannot develop normal male organs because of mitochondrial genes. In potatoes (Solanum tuberosum), reports on the relevant mitochondrial genes remain scarce. Many potato cultivars express pollen sterility caused by mitochondria, thereby limiting their use as male parents in breeding. Therefore, identifying the causal genes is crucial for potato breeding. In this study, we focused on the T/β cytoplasm type, the most prevalent cytoplasm of potato worldwide, to explore mitochondrial genes involved in CMS in potatoes. We identified a novel gene, open reading frame 320 (orf320) from potato with T/β type cytoplasm by comparing the mitochondrial genomes. The accumulation level of orf320 transcripts was drastically reduced in the anthers of a fertile potato cultivar compared with those of a sterile cultivar. Functional analysis of tomatoes showed that overexpression of orf320 with a mitochondrial transit peptide induced male sterility phenotype accompanying abnormal anther development and pollen abortion. Furthermore, an investigation of orf320 in 124 potato cultivars revealed that this gene is tightly associated with the T/β type cytoplasm and is absent from cultivars with other cytoplasm types. These findings provide evidence that orf320 is a candidate CMS-causing gene in male sterility of T/β type cytoplasm, offering valuable insights for future potato breeding.

Tomato (Solanum lycopersicum) is a globally important crop, typically requiring pollination for fruit set. Seedless fruit production—fruit set without pollination (parthenocarpy)—is a desirable trait for horticulture, but its molecular mechanisms are not fully understood. Research on tomato fruit set has largely focused on phytohormones such as auxin and gibberellins (GAs), while the role of jasmonic acid (JA) remains unclear. Here, we identified a novel seedless mutant, Sldad1 (Solanum lycopersicum defective in anther dehiscence1) with a mutation in JA biosynthesis induced by ethyl methanesulfonate mutagenesis in the ‘Micro-Tom’ background. The wild type SlDAD1 was found to be specifically transcribed in the stamen filament, particularly 2 d before anthesis, with JA levels correlating to its transcript abundance, as visualized by imaging mass spectrometry. Notably, JA also accumulated in the ovary and ovule before anthesis. The Sldad1 mutant produced seedless fruit without any manual pollination or emasculation and seeded fruit via self-pollination. The mutant showed increased cell expansion, elevated GA levels, and higher transcripts of SlGA20ox3, while treatment to inhibit GA biosynthesis suppressed Sldad1-induced fruit set. Overall, our findings suggest that JA synthesized in the filament accumulates in the ovule before anthesis, thereby preventing tomato fruit set, at least in part, through the modulation of GA metabolism.

Cytoplasmic male sterility (CMS) in plants is caused by incompatibility between nuclear and cytoplasmic genetic information. Fertility can be restored through the action of fertility restorer (RF) genes, which are usually present in the nucleus. CMS lines of tomato (Solanum lycopersicum) caused by mitochondrial gene orf137 have been developed from asymmetric cell fusions, and in these lines, cultivated tomato served as a nuclear donor and its wild relative, S. acaule, as a cytoplasm donor. Although RF genes are present in wild relatives of tomato, no genetic or genomic information on the RF genes is yet available. This study reports an RF genetic locus, RF1, on chromosome 1 of S. pimpinellifolium LA1670 and S. lycopersicum var. cerasiforme LA1673, which was revealed by bulked segregant analysis and sequencing. An additional RF locus, RF2, was identified on chromosome 2 of LA1670. The genomic sequence of S. cheesmaniae LA0166 was assembled using high-fidelity, long-read sequencing technology. Sequence comparisons identified further candidate RF genes on chromosome 1 of S. cheesmaniae LA0166. These results suggested that multiple gene loci control the fertility restoration trait in wild relatives of tomato.

Cytoplasmic male sterility (CMS) in plants is caused by incompatibility between nuclear and cytoplasmic genetic information. Fertility can be restored through the action of fertility restoration ( RF ) genes, which are usually present in the nucleus. CMS lines of tomato ( Solanum lycopersicum ) have been developed from asymmetric cell fusions, in these lines, cultivated tomato served as a nuclear donor and its wild relative, S. acaule , as a cytoplasm donor. Although RF genes are present in wild relatives of tomato, no genetic or genomic information on the RF genes is yet available. This study reports an RF genetic locus, RF1 , on chromosome 1 of S. pimpinellifolium LA1670 and S. lycopersicum var. cerasiforme LA1673 that was revealed by bulked segregant analysis and sequencing. An additional RF locus, RF2 , was identified on chromosome 2 of LA1670. A transgenic approach identified two other candidate genes that also restored fertility. The genomic sequence of S. cheesmaniae LA0166 was assembled using high-fidelity, long-read sequencing technology. Sequence comparisons identified further candidate RF genes on chromosome 1 of S. cheesmaniae LA0166. These results suggested that multiple gene loci control the fertility restoration trait in wild relatives of tomato.

SUMMARY: Knotted1‐like homeodomain (KNOX) proteins are essential in regulating plant organ differentiation. Land plants, including tomato (Solanum lycopersicum), have two classes of the KNOX protein family, namely, class I (KNOX I) and class II KNOX (KNOX II). While tomato KNOX I proteins are known to stimulate chloroplast development in fruit, affecting fruit coloration, the role of KNOX II proteins in this context remains unclear. In this study, we employ CRISPR/Cas9 to generate knockout mutants of the KNOX II member, SlKN5. These mutants display increased leaf complexity, a phenotype commonly associated with reduced KNOX II activity, as well as enhanced accumulation of chloroplasts and chlorophylls in smaller cells within young, unripe fruit. RNA‐seq data analyses indicate that SlKN5 suppresses the transcriptions of genes involved in chloroplast biogenesis, chlorophyll biosynthesis, and gibberellin catabolism. Furthermore, protein–protein interaction assays reveal that SlKN5 physically interacts with three transcriptional repressors from the BLH1‐clade of BEL1‐like homeodomain (BLH) protein family, SlBLH4, SlBLH5, and SlBLH7, with SlBLH7 showing the strongest interaction. CRISPR/Cas9‐mediated knockout of these SlBLH genes confirmed their overlapping roles in suppressing chloroplast biogenesis, chlorophyll biosynthesis, and lycopene cyclization. Transient assays further demonstrate that the SlKN5–SlBLH7 interaction enhances binding capacity to regulatory regions of key chloroplast‐ and chlorophyll‐related genes, including SlAPRR2‐like1, SlCAB‐1C, and SlGUN4. Collectively, our findings elucidate that the KNOX II SlKN5‐SlBLH regulatory modules serve to inhibit fruit greening and subsequently promote lycopene accumulation, thereby fine‐tuning the color transition from immature green fruit to mature red fruit.

We present a near-complete genome assembly of tomato ( Solanum lycopersicum ) cultivar Micro-Tom, which has been recognized as a model cultivar for fruit research. The genome DNA of Micro-Tom, provided by the National BioResource Project (NBRP) Tomato of Japan, was sequenced to obtain 72 Gb of high-fidelity long reads. These reads were assembled into 140 contigs, spanning 832.8 Mb, with an N50 length of 39.6 Mb. The contigs were aligned against the tomato reference genome sequence SL4.0 to establish a chromosome-level assembly. The genome assembly of Micro-Tom contained 98.5% complete BUSCOs and a total of 31,429 genes. Comparative genome structure analysis revealed that Micro-Tom possesses a cluster of rDNA genes spanning a 15 Mb stretch at the short arm of chromosome 2. This region was not found in the genome assemblies of previously sequenced tomato cultivars, possibly because of the inability of previous technologies to sequence such repetitive DNA. In conclusion, the near-complete genome assembly of Micro-Tom reported in this study would advance the genomics and genetics research on tomato and facilitate the breeding of improved tomato cultivars.

Fruit set is the process by which the ovary develops into a fruit and is an important factor in determining fruit yield. Fruit set is induced by two hormones, auxin and gibberellin, and the activation of their signaling pathways, partly by suppressing various negative regulators. Many studies have investigated the structural changes and gene networks in the ovary during fruit set, revealing the cytological and molecular mechanisms. In tomato (Solanum lycopersicum), SlIAA9 and SlDELLA/PROCERA act as auxin and gibberellin signaling repressors, respectively, and are important regulators of the activity of transcription factors and downstream gene expression involved in fruit set. Upon pollination, SlIAA9 and SlDELLA are degraded, which subsequently activates downstream cascades and mainly contributes to active cell division and cell elongation, respectively, in ovaries during fruit setting. According to current knowledge, the gibberellin pathway functions as the most downstream signal in fruit set induction, and therefore its role in fruit set has been extensively explored. Furthermore, multi-omics analysis has revealed the detailed dynamics of gene expression and metabolites downstream of gibberellins, highlighting the rapid activation of central carbon metabolism. This review will outline the relevant mechanisms at the molecular and metabolic levels during fruit set, particularly focusing on tomato.

Parthenocarpy, the pollination-independent fruit set, can raise the productivity of the fruit set even under adverse factors during the reproductive phase. The application of plant hormones stimulates parthenocarpy, but artificial hormones incur extra financial and labour costs to farmers and can induce the formation of deformed fruit. This study examines the performance of parthenocarpic mutants having no transcription factors of SlIAA9 and SlTAP3 and sldella that do not have the protein-coding gene, SlDELLA, in tomato (cv. Micro-Tom). At 0 day after the flowering (DAF) stage and DAFs after pollination, the sliaa9 mutant demonstrated increased pistil development compared to the other two mutants and wild type (WT). In contrast to WT and the other mutants, the sliaa9 mutant with pollination efficiently stimulated the build-up of auxin and GAs after flowering. Alterations in both transcript and metabolite profiles existed for WT with and without pollination, while the three mutants without pollination demonstrated the comparable metabolomic status of pollinated WT. Network analysis showed key modules linked to photosynthesis, sugar metabolism and cell proliferation. Equivalent modules were noticed in the famous parthenocarpic cultivars ‘Severianin’, particularly for emasculated samples. Our discovery indicates that controlling the genes and metabolites proffers future breeding policies for tomatoes.

In the evolutionary history of plants, variation in cis-regulatory elements (CREs) resulting in diversification of gene expression has played a central role in driving the evolution of lineage-specific traits. However, it is difficult to predict expression behaviors from CRE patterns to properly harness them, mainly because the biological processes are complex. In this study, we used cistrome datasets and explainable convolutional neural network (CNN) frameworks to predict genome-wide expression patterns in tomato (Solanum lycopersicum) fruit from the DNA sequences in gene regulatory regions. By fixing the effects of trans-acting factors using single cell-type spatiotemporal transcriptome data for the response variables, we developed a prediction model for crucial expression patterns in the initiation of tomato fruit ripening. Feature visualization of the CNNs identified nucleotide residues critical to the objective expression pattern in each gene, and their effects were validated experimentally in ripening tomato fruit. This cis-decoding framework will not only contribute to the understanding of the regulatory networks derived from CREs and transcription factor interactions, but also provides a flexible means of designing alleles for optimized expression.

MitoTALEN, a mitochondrial genome editing technology, demonstrated that the mitochondrial gene orf137 is responsible for inducing cytoplasmic male sterility in tomato.