Small RNAs have emerged as critical regulators in the expression and function of eukaryotic genomes at the post‐transcriptional level. To elucidate the functions of microRNA (miRNAs) and endogenous ...small‐interfering RNAs (siRNAs) in tomato fruit ripening process, the deep sequencing and bioinformatics methods were combined to parse the small RNAs landscape in three fruit‐ripening stages (mature green, breaker and red‐ripe) on a whole genome. Two species‐specific miRNAs and two members of TAS3 family were identified, 590 putative phased small RNAs and 125 cis‐natural antisense (nat‐siRNAs) were also found in our results which enriched the tomato small RNAs repository and all of them showed differential expression patterns during fruit ripening. A large amount of the targets of the small RNAs were predicted to be involved in fruit ripening and ethylene pathway. Furthermore, the promoters of the conserved and novel miRNAs were found to contain the conserved motifs of TATA‐box and CT microsatellites which were also found in Arabidopsis and rice, and several species‐specific motifs were found in parallel.
Recently, long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in model plants, such as Arabidopsis, rice, and maize. However, the presence of lncRNAs and how they ...function in fleshy fruit ripening are still largely unknown because fleshy fruit ripening is not present in the above model plants. Tomato is the model system for fruit ripening studies due to its dramatic ripening process. To investigate further the role of lncRNAs in fruit ripening, it is necessary and urgent to discover and identify novel lncRNAs and understand the function of lncRNAs in tomato fruit ripening. Here it is reported that 3679 lncRNAs were discovered from wild-type tomato and ripening mutant fruit. The lncRNAs are transcribed from all tomato chromosomes, 85.1% of which came from intergenic regions. Tomato lncRNAs are shorter and have fewer exons than protein-coding genes, a situation reminiscent of lncRNAs from other model plants. It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening. In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit. Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.
Main conclusion
NOR-like1 regulates tomato fruit size by targeting
SlARF9
,
SlGRAS2
,
SlFW3
.2, and
SlFW11
.3 genes involved in cell division and cell expansion.
Fruit size is an important ...agricultural character that determines the yield of crops. Here, we found that NAC transcription factor NOR-like1 regulated fruit size by regulating cell layer number and cell area in tomato. Over-expressing
NOR-like1
gene in tomato reduced fruit weight and size, whereas the knock-out of
NOR-like1
increased fruit weight and size. At the molecular level, NOR-like1 binds to the promoter of
SlGRAS2
,
SlFW3
.2, and
SlFW11
.3 to repress their transcription, while it also binds to the promoter of
ARF9
to activate its transcription
.
Overall, these results expand the biological function of NOR-like1 and deepen our understanding of the transcriptional network that regulates tomato fruit size.
Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA ...methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses.
In this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm.
In this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions.
RNA editing plays a key posttranscriptional role in gene expression. Existing studies on cytidine-to-uridine RNA editing in plants have focused on maize (Zea mays), rice (Oryza sativa), and ...Arabidopsis (Arabidopsis thaliana). However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is fruit ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato (Solanum lycopersicum) fruit ripening-related factors. A rapid virus-induced gene silencing assay indicated that the organelle RNA recognition motif-containing protein SlORRM4 affected tomato fruit ripening. Knocking out SlORRM4 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy delayed tomato fruit ripening by lowering respiratory rate and ethylene production. Additionally, the expression of numerous genes associated with fruit ripening and mitochondrial functions changed significantly when SlORRM4 was knocked out. Moreover, the loss of SlORRM4 function significantly reduced RNA editing of many mitochondrial transcripts, leading to low-level expression of some core subunits that are critical for mitochondrial complex assembly (i.e. Nad3, Cytc1, and COX II). Taken together, these results indicate that SlORRM4 is involved in RNA editing of transcripts in ripening fruit that influence mitochondrial function and key aspects of fruit ripening.
SlORRM4 is necessary for timely fruit ripening, mitochondrial health, and RNA editing in tomato.
RNA editing plays a key posttranscriptional role in gene expression. Existing studies on ...cytidine-to-uridine RNA editing in plants have focused on maize (
Zea mays
), rice (
Oryza sativa
), and Arabidopsis (
Arabidopsis thaliana
). However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is fruit ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato (
Solanum lycopersicum
) fruit ripening-related factors. A rapid virus-induced gene silencing assay indicated that the organelle RNA recognition motif-containing protein SlORRM4 affected tomato fruit ripening. Knocking out SlORRM4 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy delayed tomato fruit ripening by lowering respiratory rate and ethylene production. Additionally, the expression of numerous genes associated with fruit ripening and mitochondrial functions changed significantly when
SlORRM4
was knocked out. Moreover, the loss of
SlORRM4
function significantly reduced RNA editing of many mitochondrial transcripts, leading to low-level expression of some core subunits that are critical for mitochondrial complex assembly (i.e. Nad3, Cytc1, and COX II). Taken together, these results indicate that SlORRM4 is involved in RNA editing of transcripts in ripening fruit that influence mitochondrial function and key aspects of fruit ripening.
•All 13 SlGRFs were analyzed comprehensively in tomato.•STTM396a/396a-88 effectively down-regulated miR396a and miR396b in tomato.•Destruction of miR396 decreased the size and cell size of tomato ...cotyledon.•Blockage of miR396 significantly increased the size and cell size of tomato sepal.•Degradation of miR396 obviously elevated weight and cell size of tomato fruit.
Despite many studies about functions of miR396 were concentrated on cotyledon and leaf growth and development, only few researches were focused on flower and fruit, especially for fleshy fruit, for example, tomato fruit. Here, the roles of miR396 throughout the growth and development of tomato plant were explored with combining bioinformatics and transgene-mediated methods. In tomato, miR396 had two mature types (miR396a and miR396b), and miR396a expressed significantly higher than miR396b in cotyledon, flower, sepal and fruit. Generally, plant growth and development were regulated by miR396 via growth-regulating factors (GRFs). In tomato, all 13 SlGRFs were analyzed comprehensively, including phylogeny, domain and expression patterns. To investigate the roles of miR396 further, STTM396a/396a-88 was over-expressed in tomato, which induced miR396a and miR396b both dramatical down-regulation, and the target GRFs general up-regulation. As a result, the flowers, sepals and fruits all obviously became bigger. Most significantly, the sepal length of transgenic lines #3 and #4 at 39 days post-anthesis was separately increased 75% and 81%, and the fruit weight was added 45% and 39%, respectively. Overall, these results revealed novel roles of miR396 in regulating flower and fruit development, and provided a new potential way for improving tomato fruit yield.
China is the world leader in peach production and export. Peaches are prone to rapid deterioration after harvest, especially when honey peach export chain always is longer and complex. Both ...traceability and Hazard Analysis and Critical Control Point (HACCP) are considered as the effective tools to improve quality control and chain transparency. This paper presents an effort to develop and evaluate a multi-sensors-managed traceability system for honey peach export chain. The key traceable information and quality control point were identified based on the principles of HACCP; a traceability system, integrated multi-sensors and a HACCP based quality control plan, was developed to monitor identified traceable information in real-time and provide the quality evaluation and control decision; The system was evaluated and validated at a sampled honey peach export chain from Shandong, China to Singapore. The results show that the critical ambient parameters (CAPs) in the honey peach export chain are temperature, relative humidity (RH), O2, CO2 and ethylene. The temperature influences the change of RH, CO2 and ethylene. The traceability system can improve the transparency and quality control by tracing the CAPs in honey peach export chain and provide the tracking service. The quality loss of honey peach export chain decreased from 25% to 30% to below 13% based two years’ statistics with the system application.
•A traceability system integrated multi-sensors and principles of HACCP was developed and evaluated.•The critical ambient parameters include temperature, relative humidity, O2, CO2, and ethylene.•The critical ambient parameters and quality indexes are monitored and analyzed.•The system was evaluated and validated at a sampled honey peach export chain from China(Shandong)-Singapore.•Improving quality control and transparency in honey peach export chain.
In flowering plants, sepals play important roles in the development of flowers and fruit, and both processes are regulated by MADS-box (MADS) transcription factors (TFs). SlMADS1 was previously ...reported to act as a negative regulator of fruit ripening. In this study, expression analysis shown that its transcripts were very highly expressed during the development of sepals. To test the role of SlMADS1, we generated KO-SlMADS1 (knock-out) tomato mutants by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9) technology and over-expression of SlMADS1 (OE-SlMADS1). The sepals and individual cells of KO-SlMADS1 mutants were significantly elongated, compared with the wild type (WT), whereas the sepals of OE-SlMADS1 tomatoes were significantly shorter and their cells were wider. RNA-seq (RNA-sequencing) of sepal samples showed that ethylene-, gibberellin-, auxin-, cytokinin- and cell wall metabolism-related genes were significantly affected in both KO-SlMADS1 and OE-SlMADS1 plants with altered sepal size. Since SlMACROCALYX (MC) is known to regulate the development of tomato sepals, we also studied the relationship between SlMC and SlMADS1 and the result showed that SlMADS1 interacts directly with SlMC. In addition, we also found that manipulating SlMADS1 expression alters the development of tomato plant leaves, roots and plant height. These results enrich our understanding of sepal development and the function of SlMADS1 throughout the plant.
•SlMADS1 is highly expressed during the development of sepals.•The sepals and individual cells of KO-SlMADS1 mutants are significantly elongated and the inverse phenotypes are detected in OE-SlMADS1 lines.•SlMADS1 interacts with MACROCALYX (MC).•Manipulating SlMADS1 expression alters the sepal length of tomato fruit.
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