A tomato NAC transcription factor, SlNAP1, directly regulates gibberellin-dependent fruit ripening

In tomato (Solanum lycopersicum), the ripening of fruit is regulated by the selective expression of ripening-related genes, and this procedure is controlled by transcription factors (TFs). In the various plant-specific TF families, the no apical meristem (NAM), Arabidopsis thaliana activating factor 1/2 (ATAF1/2), and cup-shaped cotyledon 2 (CUC2; NAC) TF family stands out and plays a significant function in plant physiological activities, such as fruit ripening (FR). Despite the numerous genes of NAC found in the tomato genome, limited information is available on the effects of NAC members on FR, and there is also a lack of studies on their target genes. In this research, we focus on SlNAP1, which is a NAC TF that positively influences the FR of tomato. By employing CRISPR/Cas9 technology, compared with the wild type (WT), we generated slnap1 mutants and observed a delay in the ethylene production and color change of fruits. We employed the yeast one-hybrid (Y1H) and dual-luciferase reporter (DLR) assays to confirm that SlNAP1 directly binds to the promoters of two crucial genes involved in gibberellin (GA) degradation, namely SlGA2ox1 and SlGA2ox5, thus activating their expression. Furthermore, through a yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BIFC) and luciferase (LUC) assays, we established an interaction between SlNAP1 and SlGID1. Hence, our findings suggest that SlNAP1 regulates FR positively by activating the GA degradation genes directly. Additionally, the interaction between SlNAP1 and SlGID1 may play a role in SlNAP1-induced FR. Overall, our study provides important insights into the molecular mechanisms through which NAC TFs regulate tomato FR via the GA pathway.

Genome-Wide Identification and Characterization of Tomato Fatty Acid β-Oxidase Family Genes KAT and MFP

Fatty acids and their derivatives play a variety of roles in living organisms. Fatty acids not only store energy but also comprise membrane lipids and act as signaling molecules. There are three main proteins involved in the fatty acid β-oxidation pathway in plant peroxisomes, including acyl-CoA oxidase (ACX), multifunctional protein (MFP), and 3-ketolipoyl-CoA thiolase (KAT). However, genome-scale analysis of KAT and MFP has not been systemically investigated in tomatoes. Here, we conducted a bioinformatics analysis of KAT and MFP genes in tomatoes. Their physicochemical properties, protein secondary structure, subcellular localization, gene structure, phylogeny, and collinearity were also analyzed. In addition, a conserved motif analysis, an evolutionary pressure selection analysis, a cis-acting element analysis, tissue expression profiling, and a qRT-PCR analysis were conducted within tomato KAT and MFP family members. There are five KAT and four MFP family members in tomatoes, which are randomly distributed on four chromosomes. By analyzing the conserved motifs of tomato KAT and MFP family members, we found that both KAT and MFP members are highly conserved. In addition, the results of the evolutionary pressure selection analysis indicate that the KAT and MFP family members have evolved mainly from purifying selection, which makes them more structurally stable. The results of the cis-acting element analysis show that SlKAT and SlMFP with respect may respond to light, hormones, and adversity stresses. The tissue expression analysis showed that KAT and MFP family members have important roles in regulating the development of floral organs as well as fruit ripening. The qRT-PCR analysis revealed that the expressions of SlKAT and SlMFP genes can be regulated by ABA, MeJA, darkness, NaCl, PEG, UV, cold, heat, and H2O2 treatments. These results provide a basis for the involvement of the SlKAT and SlMFP genes in tomato floral organ development and abiotic stress response, which lay a foundation for future functional study of SlKAT and SlMFP in tomatoes.

Hydrogen Sulfide in the Oxidative Stress Response of Plants: Crosstalk with Reactive Oxygen Species

Growing evidence suggests that exposure of plants to unfavorable environments leads to the accumulation of hydrogen sulfide (H2S) and reactive oxygen species (ROS). H2S interacts with the ROS-mediated oxidative stress response network at multiple levels. Therefore, it is essential to elucidate the mechanisms by which H2S and ROS interact. The molecular mechanism of action by H2S relies on the post-translational modification of the cysteine sulfur group (-SH), known as persulfidation. H2S cannot react directly with -SH, but it can react with oxidized cysteine residues, and this oxidation process is induced by H2O2. Evidently, ROS is involved in the signaling pathway of H2S and plays a significant role. In this review, we summarize the role of H2S-mediated post-translational modification mechanisms in oxidative stress responses. Moreover, the mechanism of interaction between H2S and ROS in the regulation of redox reactions is focused upon, and the positive cooperative role of H2S and ROS is elucidated. Subsequently, based on the existing evidence and clues, we propose some potential problems and new clues to be explored, which are crucial for the development of the crosstalk mechanism of H2S and ROS in plants.

Genome-wide identification and analysis of the GGCT gene family in wheat

BACKGROUND

γ-glutamylcyclotransferase (GGCT), an enzyme to maintain glutathione homeostasis, plays a vital role in the response to plant growth and development as well as the adaptation to various stresses. Although the GGCT gene family analysis has been conducted in Arabidopsis and rice, the family genes have not yet been well identified and analyzed at the genome-wide level in wheat (Triticum aestivum L.).

RESULTS

In the present study, 20 TaGGCT genes were identified in the wheat genome and widely distributed on chromosomes 2A, 2B, 2D, 3A, 4A, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B, and 7D. Phylogenetic and structural analyses showed that these TaGGCT genes could be classified into three subfamilies: ChaC, GGGACT, and GGCT-PS. They exhibited similar motif compositions and distribution patterns in the same subgroup. Gene duplication analysis suggested that the expansion of TaGGCT family genes was facilitated by segmental duplications and tandem repeats in the wheat evolutionary events. Identification of diverse cis-acting response elements in TaGGCT promoters indicated their potential fundamental roles in response to plant development and abiotic stresses. The analysis of transcriptome data combined with RT-qPCR results revealed that the TaGGCTs genes exhibited ubiquitous expression across plant organs, with highly expressed in roots, stems, and developing grains. Most TaGGCT genes were up-regulated after 6 h under 20% PEG6000 and ABA treatments. Association analysis revealed that two haplotypes of TaGGCT20 gene displayed significantly different Thousand-kernel weight (TKW), Kernel length (KL), and Kernel width (KW) in wheat. The geographical and annual distribution of the two haplotypes of TaGGCT20 gene further revealed that the frequency of the favorable haplotype TaGGCT20-Hap-I was positively selected in the historical breeding process of wheat.

CONCLUSION

This study investigated the genome-wide identification, structure, evolution, and expression analysis of TaGGCT genes in wheat. The motifs of TaGGCTs were highly conserved throughout the evolutionary history of wheat. Most TaGGCT genes were highly expressed in roots, stems, and developing grains, and involved in the response to drought stresses. Two haplotypes were developed in the TaGGCT20 gene, where TaGGCT20-Hap-I, as a favorable haplotype, was significantly associated with higher TKW, KL, and KW in wheat, suggesting that the haplotype is used as a function marker for the selection in grain yield in wheat breeding.

Characterization of the FLA Gene Family in Tomato (Solanum lycopersicum L.) and the Expression Analysis of SlFLAs in Response to Hormone and Abiotic Stresses

Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating plant growth, development, and response to abiotic stress. However, the characterization and function of FLAs in tomato are currently unknown. In this study, members of the tomato FLA family are characterized and analyzed in relation to their response to phytohormonal and abiotic stresses. The results show that a total of 24 FLA members were characterized in tomato. The structural domain analysis showed that these members have a high protein similarity. The expression profiles of different tissues indicated that the genes of most members of the tomato FLA gene family are highly expressed in roots, but to a lower extent in fruits. qRT-PCR analysis revealed that all 24 tomato FLA genes are responsive to ABA and MeJA. SlFLAs showed a positive response to salt and cold stress. SlFLA1, SlFLA12, and SlFLA14 are significantly induced under darkness. SlFLA1 and SlFLA3 are significantly induced under drought stress. This study provides a basis for a further understanding of the role of tomato FLA homologous genes in plant response to abiotic stress and lays the foundation for further research on the function of FLAs in tomato.

Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator?

Recognized as a pivotal developmental transition, flowering marks the continuation of a plant's life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.

Brassinosteroids is involved in methane-induced adventitious root formation via inducing cell wall relaxation in marigold

BACKGROUND

Methane (CH₄) and brassinosteroids (BRs) are important signaling molecules involved in a variety of biological processes in plants.

RESULTS

Here, marigold (Tagetes erecta L. 'Marvel') was used to investigate the role and relationship between CH₄ and BRs during adventitious root (AR) formation. The results showed a dose-dependent effect of CH₄ and BRs on rooting, with the greatest biological effects of methane-rich water (MRW, CH₄ donor) and 2,4-epibrassinolide (EBL) at 20% and 1 μmol L^- 1, respectively. The positive effect of MRW on AR formation was blocked by brassinoazole (Brz, a synthetic inhibitor of EBL), indicating that BRs might be involved in MRW-regulated AR formation. MRW promoted EBL accumulation during rooting by up-regulating the content of campestanol (CN), cathasterone (CT), and castasterone (CS) and the activity of Steroid 5α-reductase (DET2), 22α-hydroxylase (DWF4), and BR-6-oxidase (BR6ox), indicating that CH₄ could induce endogenous brassinolide (BR) production during rooting. Further results showed that MRW and EBL significantly down-regulated the content of cellulose, hemicellulose and lignin during rooting and significantly up-regulated the hydrolase activity, i.e. cmcase, xylanase and laccase. In addition, MRW and EBL also significantly promoted the activity of two major cell wall relaxing factors, xyloglucan endotransglucosylase/hydrolase (XTH) and peroxidase, which in turn promoted AR formation. While, Brz inhibited the role of MRW on these substances.

CONCLUSIONS

BR might be involved in CH₄-promoted AR formation by increasing cell wall relaxation.

Identification of quantitative trait loci (QTL) and meta-QTL analysis for kernel size-related traits in wheat (Triticum aestivum L.)

BACKGROUND

Kernel size-related traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR) and kernel thickness (KT), are critical determinants for wheat kernel weight and yield and highly governed by a type of quantitative genetic basis. Genome-wide identification of major and stable quantitative trait loci (QTLs) and functional genes are urgently required for genetic improvement in wheat kernel yield. A hexaploid wheat population consisting of 120 recombinant inbred lines was developed to identify QTLs for kernel size-related traits under different water environments. The meta-analysis and transcriptome evaluation were further integrated to identify major genomic regions and putative candidate genes.

RESULTS

The analysis of variance (ANOVA) revealed more significant genotypic effects for kernel size-related traits, indicating the moderate to high heritability of 0.61-0.89. Thirty-two QTLs for kernel size-related traits were identified, explaining 3.06%-14.2% of the phenotypic variation. Eleven stable QTLs were detected in more than three water environments. The 1103 original QTLs from the 34 previous studies and the present study were employed for the MQTL analysis and refined into 58 MQTLs. The average confidence interval of the MQTLs was 3.26-fold less than that of the original QTLs. The 1864 putative candidate genes were mined within the regions of 12 core MQTLs, where 70 candidate genes were highly expressed in spikes and kernels by comprehensive analysis of wheat transcriptome data. They were involved in various metabolic pathways, such as carbon fixation in photosynthetic organisms, carbon metabolism, mRNA surveillance pathway, RNA transport and biosynthesis of secondary metabolites.

CONCLUSIONS

Major genomic regions and putative candidate genes for kernel size-related traits in wheat have been revealed by an integrative strategy with QTL linkage mapping, meta-analysis and transcriptomic assessment. The findings provide a novel insight into understanding the genetic determinants of kernel size-related traits and will be useful for the marker-assisted selection of high yield in wheat breeding.

Genome-wide identification of SHMT family genes in cucumber (Cucumis sativus L.) and functional analyses of CsSHMTs in response to hormones and abiotic stresses

Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate-dependent enzyme that plays crucial roles in the photorespiration and one-carbon metabolism of plants. In the present research, we conducted a systematic analysis of the SHMT gene family in cucumber (Cucumis sativus L). Results show that a total of 6 SHMT members were identified from the cucumber genome database. CsSHMT1 and CsSHMT2 participate in a fragment duplication event, indicating that CsSHMTs may complete the expansion of family members through fragment duplication. Gene structure analysis found that the number of exons of CsSHMTs ranges from 4 to 15. Members with the same number of exons are classified into the same class in the phylogenetic analysis. Each class reflects its subcellular distribution. Expression and function analysis reveals that CsSHMTs express in a variety of plant tissues, indicating that SHMT gene expression pattern is not organ-specific. qRT-PCR analysis found that CsSHMT3 and CsSHMT5 positively respond to abscisic acid (ABA), and CsSHMT2-6 are induced by indole-3-acetic acid (IAA) and methyl jasmonate (MeJA). Abiotic stress analysis shows that CsSHMT3 is significantly induced by drought and salt stress. These results may provide useful information for further function and evolution analysis of cucumber SHMT genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03378-x.