Ogura-type cytoplasmic male sterility (Ogura-CMS) has been widely used in the hybrid breeding industry for cruciferous vegetables. Turnip ( Brassica rapa ssp. rapifera ) is one of the most important local cruciferous vegetables in China, cultivated for its fleshy root as a flat disc. Here, morphological characteristics of an Ogura-CMS line ‘BY10-2A’ and its maintainer fertile (MF) line ‘BY10-2B’ of turnip were investigated. Ogura-CMS turnip showed a reduction in the size of the fleshy root, and had distinct defects in microspore development and tapetum degeneration during the transition from microspore mother cells to tetrads. Defective microspore production and premature tapetum degeneration during microgametogenesis resulted in short filaments and withered white anthers, leading to complete male sterility of the Ogura-CMS line. Additionally, the mechanism regulating Ogura-CMS in turnip was investigated using inflorescence transcriptome analyses of the Ogura-CMS and MF lines. The de novo assembly resulted in a total of 84,132 unigenes. Among them, 5,117 differentially expressed genes (DEGs) were identified, including 1,339 up- and 3,778 down-regulated genes in the Ogura-CMS line compared to the MF line. A number of functionally known members involved in anther development and microspore formation were addressed in our DEG pool, particularly genes regulating tapetum programmed cell death (PCD), and associated with pollen wall formation. Additionally, 185 novel genes were proposed to function in male organ development based on GO analyses, of which 26 DEGs were genotype-specifically expressed. Our research provides a comprehensive foundation for understanding anther development and the CMS mechanism in turnip.

Cytoplasmic male sterility (CMS) is a widely used trait in angiosperms caused by perturbations in nucleus-mitochondrion interactions that suppress the production of functional pollen. MicroRNAs (miRNAs) are small non-coding RNAs that act as regulatory molecules of transcriptional or post-transcriptional gene silencing in plants. The discovery of miRNAs and their possible implications in CMS induction provides clues for the intricacies and complexity of this phenomenon. Previously, we characterized an Ogura-CMS line of turnip (Brassica rapa ssp. rapifera) that displays distinct impaired anther development with defective microspore production and premature tapetum degeneration. In the present study, high-throughput sequencing was employed for a genome-wide investigation of miRNAs. Six small RNA libraries of inflorescences collected from the Ogura-CMS line and its maintainer fertile (MF) line of turnip were constructed. A total of 120 pre-miRNAs corresponding to 89 mature miR-NAs were identified, including 87 conversed miRNAs and 33 novel miRNAs. Among these miRNAs, the expression of 10 differentially expressed mature miRNAs originating from 12 pre-miRNAs was shown to have changed by more than twofold between inflorescences of the Ogura-CMS line and inflorescences of the MF line, including 8 down-and 2 up-regulated miRNAs. The expression profiles of the differentially expressed miRNAs were confirmed by stem-loop quantitative real-time PCR. In addition, to identify the targets of the identified miR-NAs, a degradome analysis was performed. A total of 22 targets of 25 miRNAs and 17 targets of 28 miRNAs were identified as being involved in the reproductive development for Ogura-CMS and MF lines of turnip, respectively. Negative correlations of expression patterns between partial miRNAs and their targets were detected. Some of these identified targets, such as squamosa promoter-binding-like transcription factor family proteins, auxin response factors and pentatricopeptide repeat-containing proteins, were previously

Ebb-and-flow subirrigation is a promising strategy to increase water use efficiency, avoid waterlogging or drought conditions, and promote the overall growth of vegetable crops. The aim of this study was to evaluate the seedling growth, root morphology, activities of root-softening enzymes, and transcript profiling of those enzyme-related genes in tomato under top sprinkle irrigation and ebb-and-flow subirrigation. The results showed that ebb-and-flow subirrigation could significantly improve stem diameter, root fresh weight, root dry weight, root volume, and root diameter of tomato by 9.42%, 45.92%, 44.82%, 15.61%, and 9.41%, as compared with top sprinkle irrigation, respectively. The ebb-and-flow subirrigation also maintained the root activity and photosynthetic rate of tomato seedlings. The activities of superoxidase dismutase, peroxidase, catalase, glutathione reductase, and ascorbate peroxidase of tomato roots under ebb-and-flow subirrigation were remarkably increased, while the malondialdehyde content was decreased compared with the plants grown under top sprinkle irrigation. Correlation analysis among activities of root-softening enzymes and transcriptomic profiling of their biosynthesis-related genes revealed that 10 genes might be responsible for regulation of studied enzymes. Overall, ebb-and-flow subirrigation could significantly promote the growth of tomato seedlings, so as to maintain high activity and promote the cultivation of high-quality and strong seedlings.

Background Tomato (Solanum lycopersicum) is both an important agricultural product and an excellent model system for studying plant-pathogen interactions. It is susceptible to bacterial wilt caused by Ralstonia solanacearum (Rs), and infection can result in severe yield and quality losses. To investigate which genes are involved in the resistance response to this pathogen, we sequenced the transcriptomes of both resistant and susceptible tomato inbred lines before and after Rs inoculation. Results In total, 75.02 Gb of high-quality reads were generated from 12 RNA-seq libraries. A total of 1,312 differentially expressed genes (DEGs) were identified, including 693 up-regulated and 621 down-regulated genes. Additionally, 836 unique DEGs were obtained when comparing two tomato lines, including 27 co-expression hub genes. A total of 1,290 DEGs were functionally annotated using eight databases, most of which were found to be involved in biological pathways such as DNA and chromatin activity, plant-pathogen interaction, plant hormone signal transduction, secondary metabolite biosynthesis, and defense response. Among the core-enriched genes in 12 key pathways related to resistance, 36 genotype-specific DEGs were identified. RT-qPCR integrated analysis revealed that multiple DEGs may play a significant role in tomato response to Rs. In particular, Solyc01g073985.1 (NLR disease resistance protein) and Solyc04g058170.1 (calcium-binding protein) in plant-pathogen interaction are likely to be involved in the resistance. Conclusion We analyzed the transcriptomes of both resistant and susceptible tomato lines during control and inoculated conditions and identified several key genotype-specific hub genes involved in a variety of different biological processes. These findings lay a foundation for better understanding the molecular basis by which resistant tomato lines respond to Rs.

Ebb-and-flow subirrigation (EFI) is a water-saving and environmentally friendly irrigation method that can effectively improve water use efficiency and promote plant growth. In this study, we elucidated the effects of ebb-and-flow subirrigation on the protein levels in tomato roots in comparison with top sprinkle irrigation (TSI) and used an integrated approach involving tandem mass tag (TMT) labeling, high-performance liquid chromatography (HPLC) fractionation, and mass-spectrometry (MS)-based analysis. A total of 8510 quantifiable proteins and 513 differentially accumulated proteins (DAPs) were identified, of which the expressions of 283 DAPs were up-regulated, and 230 DAPs were down-regulated in the EFI vs. TSI treatment comparison. According to proteomic data, we performed a systematic bioinformatics analysis of all the identified proteins and DAPs. The DAPs were most significantly associated with the terms ‘metabolic process’, ‘anchored component of membrane’, ‘oxidoreductase activity’, ‘phenylpropanoid biosynthesis’, and ‘biosynthesis of secondary metabolites’ according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG) analysis. The 272 DAPs were classified into 12 subcellular components according to their subcellular localization. Furthermore, the activities of SOD, POD, CAT, GR, and APX in tomato roots were remarkably increased under EFI, while the MDA content was decreased compared with TSI. Correlation analysis among activities of enzymes and their related DAPs showed that 30 DAPs might be responsible for the regulation of these enzymes. The results showed that ebb-and-flow subirrigation could induce a series of DAPs responses in tomato roots to be adapted to the new mode of water supply.