The SEPALLATA MADS-box protein SLMBP21 forms protein complexes with JOINTLESS and MACROCALYX as a transcription activator for development of the tomato flower abscission zone

JOINTLESS Maintains Inflorescence Meristem Identity in Tomato

JOINTLESS (J) was isolated in tomato (Solanum lycopersicum) from mutants lacking a flower pedicel abscission zone (AZ) and encodes a MADS-box protein of the SHORT VEGETATIVE PHASE/AGAMOUS-LIKE 24 subfamily. The loss of J function also causes the return to leaf initiation in the inflorescences, indicating a pivotal role in inflorescence meristem identity. Here, we compared jointless (j) mutants in different accessions that exhibit either an indeterminate shoot growth, producing regular sympodial segments, or a determinate shoot growth, due to the reduction of sympodial segments and causal mutation of the SELF-PRUNING (SP) gene. We observed that the inflorescence phenotype of j mutants is stronger in indeterminate (SP) accessions such as Ailsa Craig (AC), than in determinate (sp) ones, such as Heinz (Hz). Moreover, RNA-seq analysis revealed that the return to vegetative fate in j mutants is accompanied by expression of SP, which supports conversion of the inflorescence meristem to sympodial shoot meristem in j inflorescences. Other markers of vegetative meristems such as APETALA2c and branching genes such as BRANCHED 1 (BRC1a/b) were differentially expressed in the inflorescences of j(AC) mutant. We also found in the indeterminate AC accession that J represses homeotic genes of B- and C-classes and that its overexpression causes an oversized leafy calyx phenotype and has a dominant negative effect on AZ formation. A model is therefore proposed where J, by repressing shoot fate and influencing reproductive organ formation, acts as a key determinant of inflorescence meristems.

A SEPALLATA MADS-Box Transcription Factor, SlMBP21, Functions as a Negative Regulator of Flower Number and Fruit Yields in Tomato

MADS-box transcription factors act as the crucial regulators in plant organ differentiation. Crop yields are highly influenced by the flower number and fruit growth. However, flower identification is a very complex biological process, which involves many cascade regulations. The molecular mechanisms underlying the genetic regulation of flower identification in cultivated plants, such as tomato, are intricate and require further exploration. In this study, we investigated the vital function of a SEPALLATA (SEP) MADS-box gene, SlMBP21, in tomato sympodial inflorescence meristem (SIM) development for the conversion from SIMs to floral meristems (FMs). SlMBP21 transcripts were primarily accumulated in young inflorescence meristem, flowers, sepals, and abscission zones. The Ailsa Craig (AC++) tomato plants with suppressed SlMBP21 mRNA levels using RNAi exhibited a large increase in flower number and fruit yields in addition to enlarged sepals and inhibited abscission zone development. Scanning electron microscopy (SEM) revealed that the maturation of inflorescence meristems (IMs) was repressed in SlMBP21-RNAi lines. RNA-seq and qRT-PCR analyses showed that numerous genes related to the flower development, plant hormone signal transduction, cell cycle, and cell proliferation et al. were dramatically changed in SlMBP21-RNAi lines. Yeast two-hybrid assay exhibited that SlMBP21 can respectively interact with SlCMB1, SFT, JOINTLESS, and MC, which play key roles in inflorescence meristems or FM development. In summary, our data demonstrate that SlMBP21 functions as a key regulator in SIM development and the conversion from SIMs to FMs, through interacting with other regulatory proteins to control the expression of related genes.

Integrated analysis of the transcriptome and metabolome reveals the molecular mechanism regulating cotton boll abscission under low light intensity

BACKGROUND

Cotton boll shedding is one of the main factors adversely affecting the cotton yield. During the cotton plant growth period, low light conditions can cause cotton bolls to fall off prematurely. In this study, we clarified the regulatory effects of low light intensity on cotton boll abscission by comprehensively analyzing the transcriptome and metabolome.

RESULTS

When the fruiting branch leaves were shaded after pollination, all of the cotton bolls fell off within 5 days. Additionally, H2O2 accumulated during the formation of the abscission zone. Moreover, 10,172 differentially expressed genes (DEGs) and 81 differentially accumulated metabolites (DAMs) were identified. A KEGG pathway enrichment analysis revealed that the identified DEGs and DAMs were associated with plant hormone signal transduction and flavonoid biosynthesis pathways. The results of the transcriptome analysis suggested that the expression of ethylene (ETH) and abscisic acid (ABA) signaling-related genes was induced, which was in contrast to the decrease in the expression of most of the IAA signaling-related genes. A combined transcriptomics and metabolomics analysis revealed that flavonoids may help regulate plant organ abscission. A weighted gene co-expression network analysis detected two gene modules significantly related to abscission. The genes in these modules were mainly related to exosome, flavonoid biosynthesis, ubiquitin-mediated proteolysis, plant hormone signal transduction, photosynthesis, and cytoskeleton proteins. Furthermore, TIP1;1, UGT71C4, KMD3, TRFL6, REV, and FRA1 were identified as the hub genes in these two modules.

CONCLUSIONS

In this study, we elucidated the mechanisms underlying cotton boll abscission induced by shading on the basis of comprehensive transcriptomics and metabolomics analyses of the boll abscission process. The study findings have clarified the molecular basis of cotton boll abscission under low light intensity, and suggested that H2O2, phytohormone, and flavonoid have the potential to affect the shedding process of cotton bolls under low light stress.

Two SEPALLATA MADS-Box Genes, SlMBP21 and SlMADS1, Have Cooperative Functions Required for Sepal Development in Tomato

MADS-box transcription factors have crucial functions in numerous physiological and biochemical processes during plant growth and development. Previous studies have reported that two MADS-box genes, SlMBP21 and SlMADS1, play important regulatory roles in the sepal development of tomato, respectively. However, the functional relationships between these two genes are still unknown. In order to investigate this, we simultaneously studied these two genes in tomato. Phylogenetic analysis showed that they were classified into the same branch of the SEPALLATA (SEP) clade. qRT-PCR displayed that both SlMBP21 and SlMADS1 transcripts are preferentially accumulated in sepals, and are increased with flower development. During sepal development, SlMBP21 is increased but SlMADS1 is decreased. Using the RNAi, tomato plants with reduced SlMBP21 mRNA generated enlarged and fused sepals, while simultaneous inhibition of SlMBP21 and SlMADS1 led to larger (longer and wider) and fused sepals than that in SlMBP21-RNAi lines. qRT-PCR results exhibited that the transcripts of genes relating to sepal development, ethylene, auxin and cell expansion were dramatically changed in SlMBP21-RNAi sepals, especially in SlMBP21-SlMADS1-RNAi sepals. Yeast two-hybrid assay displayed that SlMBP21 can interact with SlMBP21, SlAP2a, TAGL1 and RIN, and SlMADS1 can interact with SlAP2a and RIN, respectively. In conclusion, SlMBP21 and SlMADS1 cooperatively regulate sepal development in tomato by impacting the expression or activities of other related regulators or via interactions with other regulatory proteins.

New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches

The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.

Tomato plant response to heat stress: a focus on candidate genes for yield-related traits

Climate change and global warming represent the main threats for many agricultural crops. Tomato is one of the most extensively grown and consumed horticultural products and can survive in a wide range of climatic conditions. However, high temperatures negatively affect both vegetative growth and reproductive processes, resulting in losses of yield and fruit quality traits. Researchers have employed different parameters to evaluate the heat stress tolerance, including evaluation of leaf- (stomatal conductance, net photosynthetic rate, Fv/Fm), flower- (inflorescence number, flower number, stigma exertion), pollen-related traits (pollen germination and viability, pollen tube growth) and fruit yield per plant. Moreover, several authors have gone even further, trying to understand the plants molecular response mechanisms to this stress. The present review focused on the tomato molecular response to heat stress during the reproductive stage, since the increase of temperatures above the optimum usually occurs late in the growing tomato season. Reproductive-related traits directly affects the final yield and are regulated by several genes such as transcriptional factors, heat shock proteins, genes related to flower, flowering, pollen and fruit set, and epigenetic mechanisms involving DNA methylation, histone modification, chromatin remodelling and non-coding RNAs. We provided a detailed list of these genes and their function under high temperature conditions in defining the final yield with the aim to summarize the recent findings and pose the attention on candidate genes that could prompt on the selection and constitution of new thermotolerant tomato plant genotypes able to face this abiotic challenge.

Phytohormones and candidate genes synergistically regulate fruitlet abscission in Areca catechu L

BACKGROUND

The fruit population of most plants is under the control of a process named "physiological drop" to selectively abort some developing fruitlets. However, frequent fruitlet abscission severely restricts the yield of Areca catechu. To reveal the physiological and molecular variations in this process, we detected the variation of phytohormone levels in abscised and non-abscised fruitlets in A. catechu.

RESULTS

The levels of gibberellin acid, jasmonic acid, salicylic acid, abscisic acid and zeatin were elevated, while the indole-3-acetic acid and indole-3-carboxaldehyde levels were declined in the "about-to-abscise" part (AB) of abscission zone (AZ) compared to the "non-abscised" part (CK). Then the differentially expressed genes (DEGs) between AB and CK were screened based on transcriptome data. DEGs involved in phytohormone synthesis, response and transportation were identified as key genes. Genes related to cell wall biosynthesis, degradation, loosening and modification, and critical processes during fruit abscission were identified as role players. In addition, genes encoding transcription factors, such as NAC, ERF, WRKY, MADS and Zinc Finger proteins, showed differentially expressed patterns between AB and CK, were also identified as candidates.

CONCLUSIONS

These results unraveled a phytohormone signaling cross talk and key genes involved in the fruitlet abscission process in A. catechu. This study not only provides a theoretical basis for fruitlet abscission in A. catechu, but also identified many candidate genes or potential molecular markers for further breeding of fruit trees.

Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat

Plant breeding is constrained by trade-offs among different agronomic traits by the pleiotropic nature of many genes. Genes that contribute to two or more favourable traits with no penalty on yield are rarely reported, especially in wheat. Here, we describe the editing of a wheat auxin response factor TaARF12 by using CRISPR/Cas9 that rendered shorter plant height with larger spikes. Changes in plant architecture enhanced grain number per spike up to 14.7% with significantly higher thousand-grain weight and up to 11.1% of yield increase under field trials. Weighted Gene Co-Expression Network Analysis (WGCNA) of spatial-temporal transcriptome profiles revealed two hub genes: RhtL1, a DELLA domain-free Rht-1 paralog, which was up-regulated in peduncle, and TaNGR5, an organ size regulator that was up-regulated in rachis, in taarf12 plants. The up-regulation of RhtL1 in peduncle suggested the repression of GA signalling, whereas up-regulation of TaNGR5 in spike may promote GA response, a working model supported by differential expression patterns of GA biogenesis genes in the two tissues. Thus, TaARF12 complemented plant height reduction with larger spikes that gave higher grain yield. Manipulation of TaARF12 may represent a new strategy in trait pyramiding for yield improvement in wheat.

MaABI5 and MaABF1 transcription factors regulate the expression of MaJOINTLESS during fruit abscission in mulberry (Morus alba L.)

Mulberry holds significant economic value. However, during the ripening stage of its fruit, the phenomenon of abscission, resulting in heavy fruit drop, can severely impact the yield. The formation of off-zone structures is a critical factor in the fruit abscission process, and this process is regulated by multiple transcription factors. One such key gene that plays a significant role in the development of the off-zone in the model plant tomato is JOINTLESS, which promotes the expression of abscission-related genes and regulates the differentiation of abscission zone tissue cells. However, there is a lack of information about fruit abscission mechanism in mulberry. Here, we analyzed the MaJOINTLESS promoter and identified the upstream regulators MaABF1 and MaABI5. These two regulators showed binding with MaJOINTLESS promoter MaABF1 (the ABA Binding Factor/ABA-Responsive Element Binding Proteins) activated the expression of MaJOINTLESS, while MaABI5 (ABSCISIC ACID-INSENSITIVE 5) inhibited the expression of MaJOINTLESS. Finally, the differentially expressed genes (DEGs) were analyzed by transcriptome sequencing to investigate the expression and synergistic relationship of endogenous genes in mulberry during abscission. GO classification and KEGG pathway enrichment analysis showed that most of the DEGs were concentrated in MAPK signaling pathway, flavonoid biosynthesis, citric acid cycle, phytohormone signaling, amino acid biosynthesis, and glycolysis. These results provide a theoretical basis for subsequent in-depth study of physiological fruit abscission in mulberry.

TM3 and STM3 Promote Flowering Together with FUL2 and MBP20, but Act Antagonistically in Inflorescence Branching in Tomato

The moment at which a plant transitions to reproductive development is paramount to its life cycle and is strictly controlled by many genes. The transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) plays a central role in this process in Arabidopsis. However, the role of SOC1 in tomato (Solanum lycopersicum) has been sparsely studied. Here, we investigated the function of four tomato SOC1 homologs in the floral transition and inflorescence development. We thoroughly characterized the SOC1-like clade throughout the Solanaceae and selected four tomato homologs that are dynamically expressed upon the floral transition. We show that of these homologs, TOMATO MADS 3 (TM3) and SISTER OF TM3 (STM3) promote the primary and sympodial transition to flowering, while MADS-BOX PROTEIN 23 (MBP23) and MBP18 hardly contribute to flowering initiation in the indeterminate cultivar Moneyberg. Protein-protein interaction assays and whole-transcriptome analysis during reproductive meristem development revealed that TM3 and STM3 interact and share many targets with FRUITFULL (FUL) homologs, including cytokinin regulators. Furthermore, we observed that mutating TM3/STM3 affects inflorescence development, but counteracts the inflorescence-branching phenotype of ful2 mbp20. Collectively, this indicates that TM3/STM3 promote the floral transition together with FUL2/MBP20, while these transcription factors have opposite functions in inflorescence development.

Antagonistic regulation of target genes by the SISTER OF TM3-JOINTLESS2 complex in tomato inflorescence branching

Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)-SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)-have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.

Transcriptomic and metabolomic analyses reveal molecular mechanisms associated with the natural abscission of blue honeysuckle (Lonicera caerulea L.) ripe fruits

Blue honeysuckle (Lonicera caerulea L.) is rich in phenolic compounds and has an extremely high nutritional value. Fruit abscission in the ripe period significantly impacts production and economic benefits. However, the mechanism associated with the abscission of blue honeysuckle fruit remains largely unknown. The easy-abscission cultivar 'HSY' and the hard-abscission cultivar 'Berel' were selected as plant materials. Anatomical changes of the 'HSY' fruit abscission zone (FAZ) during the abscission mainly included cell expansion, detachment, and collapse. Active changes in cell wall-degrading enzyme activity between 39 days postanthesis (DPA) and 55 DPA in 'HSY' FAZ, but not in 'Berel', suggest a critical role for cell-wall-degrading enzymes in regulating abscission. Transcriptome and metabolome analyses revealed that the genes and metabolites responding to abscission mainly act on pathways such as plant hormone signal transduction, starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis. The regulatory pathways of fruit abscission are mainly summarized into two parts: phytohormone synthesis and signal transduction, FAZ cell wall metabolism. In this study, 46 key genes related to plant hormone response, 45 key genes involved in FAZ cell wall metabolism, and 73 transcription factors were screened. Quantitative real-time PCR (qRT-PCR) assessed the expression pattern of 12 selected candidate genes, demonstrating the accuracy of the transcriptome data and elucidating the expression patterns of key candidate genes during growth and development. This study will provide an essential resource for understanding the molecular regulatory mechanism of fruit abscission in the blue honeysuckle.

Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (Juglans sigillata Dode)

Iron walnut (Juglans sigillata Dode) is a native species in southwestern China that exhibits variation in both fruit morphology and shell thickness. However, the underlying molecular processes controlling hardened endocarp development in walnut has not yet been reported. Here, we generated transcriptional profiles of iron walnut endocarp at three developmental stages using “Dapao”, the most common commercial variety. Using pairwise comparisons between these three stages, a total of 8555 non-redundant differentially expressed genes (DEGs) were identified, and more than one-half of the total DEGs exhibited significant differential expression in stage I as compared with stage II or stage III, suggesting that the first stage may ultimately determine the final characteristics of the mature walnut shell. Furthermore, in the clustering analysis of the above DEGs, 3682, 2349, and 2388 genes exhibited the highest expression in stages I, II, and III, respectively. GO enrichment analysis demonstrated that the major transcriptional variation among the three developmental stages was caused by differences in cell growth, plant hormones, metabolic process, and phenylpropanoid metabolism. Namely, using the tissue-specific expression analysis and a gene co-expression network, we identified MADS-box transcription factor JsiFBP2 and bHLH transcription factor JsibHLH94 as candidate regulators of endocarp formation in the early stage, and JsiNAC56 and JsiMYB78 might play key roles in regulating the lignification process of endocarp in the late stage. This study provides useful information for further research to dissect the molecular mechanisms governing the shell formation and development of iron walnut.

Genome-Wide Analysis of the Mads-Box Transcription Factor Family in Solanum melongena

The MADS-box transcription factors are known to be involved in several aspects of plant growth and development, especially in floral organ specification. However, little is known in eggplant. Here, 120 eggplant MADS-box genes were identified and categorized into type II (MIKCC and MIKC*) and type I (Mα, Mβ, and Mγ) subfamilies based on phylogenetic relationships. The exon number in type II SmMADS-box genes was greater than that in type I SmMADS-box genes, and the K-box domain was unique to type II MADS-box TFs. Gene duplication analysis revealed that segmental duplications were the sole contributor to the expansion of type II genes. Cis-elements of MYB binding sites related to flavonoid biosynthesis were identified in three SmMADS-box promoters. Flower tissue-specific expression profiles showed that 46, 44, 38, and 40 MADS-box genes were expressed in the stamens, stigmas, petals, and pedicels, respectively. In the flowers of SmMYB113-overexpression transgenic plants, the expression levels of 3 SmMADS-box genes were co-regulated in different tissues with the same pattern. Correlation and protein interaction predictive analysis revealed six SmMADS-box genes that might be involved in the SmMYB113-regulated anthocyanin biosynthesis pathway. This study will aid future studies aimed at functionally characterizing important members of the MADS-box gene family.

Genome-Wide Identification of the DOF Gene Family Involved in Fruitlet Abscission in Areca catechu L

Fruitlet abscission frequently occurs in Areca catechu L. and causes considerable production loss. However, the inducement mechanism of fruitlet abscission remains mysterious. In this study, we observed that the cell architecture in the abscission zone (AZ) was distinct with surrounding tissues, and varied obviously before and after abscission. Transcriptome analysis of the “about-to-abscise” and “non-abscised” AZs were performed in A. catechu, and the genes encoding the plant-specific DOF (DNA-binding with one finger) transcription factors showed a uniform up-regulation in AZ, suggesting a role of the DOF transcription in A. catechu fruitlet abscission. In total, 36 members of the DOF gene family distributed in 13 chromosomes were identified from the A. catechu genome. The 36 AcDOF genes were classified into nine subgroups based on phylogenic analysis. Six of them showed an AZ-specific expression pattern, and their expression levels varied according to the abscission process. In total, nine types of phytohormone response cis-elements and five types of abiotic stress related cis-elements were identified in the promoter regions of the AcDOF genes. In addition, histochemical staining showed that lignin accumulation of vascular bundles in AZ was significantly lower than that in pedicel and mesocarp, indicating the specific characteristics of the cell architecture in AZ. Our data suggests that the DOF transcription factors might play a role in fruitlet abscission regulation in A. catechu.

Functional characterization of the Serine acetyltransferase family genes uncovers the diversification and conservation of cysteine biosynthesis in tomato

Sulfur-containing compounds are essential for plant development and environmental adaptation, and closely related to the flavor and nutrition of the agricultural products. Cysteine, the first organic sulfur-containing molecule generated in plants, is the precursor for most of these active substances. Serine acetyltransferase (SERAT) catalyzes the rate-limiting step of its formation. However, despite their importance, systematic analyses of these enzymes in individual species, especially in economically important crops, are still limited. Here, The SERAT members (SlSERATs, four in total) were identified and characterized in tomato. Phylogenetically, the four SlSERAT proteins were classified into three subgroups with distinct genomic structures and subcellular localizations. On the function, it was interesting to find that SlSERAT3;1, possessed a high ability to catalyze the formation of OAS, even though it contained a long C-terminus. However, it retained the essential C-terminal Ile, which seems to be a characteristic feature of SERAT3 subfamily members in Solanaceae. Besides, SlSERAT1;1 and SlSERAT2;2 also had high activity levels and their catalyzing abilities were significantly improved by the addition of an OAS-(thiol)-lyase protein. At the transcriptional level, the four SlSERAT genes had distinct expression patterns during tomato plant development. Under abiotic stress conditions, the chloroplast-localized SlSERATs were the main responders, and the SlSERATs adopted different strategies to cope with osmotic, ion toxicity and other stresses. Finally, analyses in the loss-of-function and overexpression lines of SlSERAT1;1 suggested that function redundancy existed in the tomato SERAT members, and the tomato SERAT member was ideal target for S-assimilation manipulating in molecular breeding.

A MADS-box transcription factor, SlMADS1, interacts with SlMACROCALYX to regulate tomato sepal growth

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.

Eco-biochemical responses, phytoremediation potential and molecular genetic analysis of Alhagi maurorum grown in metal-contaminated soils

BACKGROUND

Alhagi maurorum Medik. (camelthorn) is a dominant desert plant indigenous in various habitats, including the Western Desert of Egypt. The plant is especially prevalent in and around economic iron ore deposits. Nutrient and heavy metal levels in A. maurorum tissues and soil samples were assessed to identify associations between heavy metal levels in plants and soil. The objective was to evaluate this species as an indicator of heavy metal pollution. Photosynthetic pigments, protein, proline, alkaloids, flavonoids, 2,2-diphenyl-1-picrylhydrazylscavenging, reduced glutathione, malondialdehyde, antioxidant enzymes, and stress-related gene expression were assessed to determine their functional roles in metal stress adaptation in ultra- and molecular structure. Additionally, the molecular genetic variation in A. maurorum samples was assessed using co-dominant sequence-related amplified polymorphism (SRAP) and inter simple sequence repeats (ISSR).

RESULTS

A substantial difference in enzymatic and non-enzymatic antioxidants of A. maurorum was observed in samples collected from three sites. A. maurorum is suited to the climate in mineralized regions. Morphologically, the stem shows spines, narrow leaves, and a reduced shoot system. Anatomically, modifications included a cuticle coating on leaves and stems, sunken stomata, a compact epidermis, and a thick cortex. Significant anatomical-physiological differences were observed with varying heavy metal soil content, antioxidative enzyme activities increased as a tolerance strategy, and glutathione levels decreased in response to heavy metal toxicity. Heavy metal accumulation also affected the expression of stress-related genes. The highest levels of expression of GST, G6PDH, 6PGD, nitrate reductase 1, and sulfate transporter genes were found in plants collected from site A1. However, auxin-induced protein exhibited its highest expression in plants collected from A2. Six SRAP combinations yielded 25 scoreable markers with a polymorphism rate of 64%, and 5 ISSR markers produced 11 bands with a polymorphism rate of 36.36% for three A. maurorum genotypes. The ME1xEM7 primer combinations provided the most polymorphic information content and resolving power, making it the most useful primer for differentiating A. maurorum genotypes. SRAP markers exhibited a higher diversity index (0.24) than ISSR markers (0.16).

CONCLUSIONS

A. maurorum displayed adaptive characteristics for heavy metal sequestration from mining site soils and is proposed as a strong candidate for phytoremediation.

Hydrogen sulfide inhibits the abscission of tomato pedicel through reconstruction of a basipetal auxin gradient

Abscission is an important developmental process and an essential agricultural trait. Auxin and ethylene are two phytohormones with important roles in the complex, but still elusive signaling network of abscission. Here, we found that hydrogen sulfide (H₂S), a newly identified gasotransmitter, inhibits the initiation of tomato pedicel abscission. The underlying mechanism was explored through transcriptome profile analysis in various pedicel tissues with or without H₂S treatment in the early abscission stage. The data suggested that H₂S strongly influences the global transcription of pedicel tissues, exerts differential expression regulation along the pedicel, and markedly influences both the auxin and ethylene signaling pathways. Computational analysis revealed that H₂S reconstructs a basipetal auxin gradient along the pedicel at 4 h after treatment; this finding was further substantiated by the GUS-staining results of DR5::GUS pedicels. The inhibitory effect of H₂S to the ethylene signaling pathway might be an indirect action. Moreover, the subtilisin-like proteinase family members involved in the release of peptide signal molecules are critical components of the abscission signaling network downstream of auxin and ethylene.

FRUITFULL-like genes regulate flowering time and inflorescence architecture in tomato

The timing of flowering and the inflorescence architecture are critical for the reproductive success of tomato (Solanum lycopersicum), but the gene regulatory networks underlying these traits have not been fully explored. Here, we show that the tomato FRUITFULL-like (FUL-like) genes FUL2 and MADS-BOX PROTEIN 20 (MBP20) promote the vegetative-to-reproductive transition and repress inflorescence branching by inducing floral meristem (FM) maturation. FUL1 fulfils a less prominent role and appears to depend on FUL2 and MBP20 for its upregulation in the inflorescence- and floral meristems. MBP10, the fourth tomato FUL-like gene, has probably lost its function. The tomato FUL-like proteins cannot homodimerize in in vitro assays, but heterodimerize with various other MADS-domain proteins, potentially forming distinct complexes in the transition meristem and FM. Transcriptome analysis of the primary shoot meristems revealed various interesting downstream targets, including four repressors of cytokinin signaling that are upregulated during the floral transition in ful1 ful2 mbp10 mbp20 mutants. FUL2 and MBP20 can also bind in vitro to the upstream regions of these genes, thereby probably directly stimulating cell division in the meristem upon the transition to flowering. The control of inflorescence branching does not occur via the cytokinin oxidase/dehydrogenases (CKXs) but may be regulated by repression of transcription factors such as TOMATO MADS-box gene 3 (TM3) and APETALA 2b (AP2b).

SEPALLATA--like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs

BACKGROUND

The architecture of inflorescence and the development of floral organs can influence the yield of seeds and have a significant impact on plant propagation. E-class floral homeotic MADS-box genes exhibit important roles in regulation of floral transition and differentiation of floral organs. Woad (Isatis indigotica) possesses unique inflorescence, floral organs and fruit. However, very little research has been carried out to determine the function of MADS-box genes in this medicinal cruciferous plant species.

RESULTS

SEPALLATA orthologs in I. indigotica were cloned by degenerate PCR. The sequence possessing the highest identity with SEP2 and SEP4 of Arabidopsis were named as IiSEP2 and IiSEP4, respectively. Constitutive expression of IiSEP2 in Columbia (Col-0) ecotype of Arabidopsis led to early flowering, and the number of the flowers and the lateral branches was reduced, indicating an alteration in architecture of the inflorescences. Moreover, the number of the floral organs was declined, the sepals were turned into carpelloid tissues bearing stigmatic papillae and ovules, and secondary flower could be produced in apetalous terminal flowers. In 35S::IiSEP4-GFP transgenic Arabidopsis plants in Landsberg erecta (Ler) genetic background, the number of the floral organs was decreased, sepals were converted into curly carpelloid structures, accompanied by generation of ovules. Simultaneously, the size of petals, stamens and siliques was diminished. In 35S::IiSEP4-GFP transgenic plants of apetalous ap1 cal double mutant in Ler genetic background, the cauliflower phenotype was attenuated significantly, and the petal formation could be rescued. Occasionally, chimeric organs composed of petaloid and sepaloid tissues, or petaloid and stamineous tissues, were produced in IiSEP4 transgenic plants of apl cal double mutant. It suggested that overexpression of IiSEP4 could restore the capacity in petal differentiation. Silencing of IiSEP4 by Virus-Induced Gene Silencing (VIGS) can delay the flowering time, and reduce the number and size of the floral organs in woad flowers.

CONCLUSION

All the results showed that SEPALLATA-like genes could influence the architecture of the inflorescence and the determinacy of the floral meristems, and was also related to development of the floral organs.

Silencing of SlMYB55 affects plant flowering and enhances tolerance to drought and salt stress in tomato

The transcription factors of the MYB family are involved in plant growth and development and responses to biotic and abiotic stresses. Here, we isolated the R2R3-MYB transcription factor gene SlMYB55 and found that it is responsive to abscisic acid (ABA), drought, and salt stress. Notably, the expression levels of multiple stress-related and inflorescence and flowering time-related genes were changed in SlMYB55-RNAi plants compared to wild-type plants. Transient tobacco expression experiments indicated that SlMYB55 directly targets the WUS and 4CL genes to regulate the development of inflorescence and flavonoid biosynthesis. Yeast two-hybrid experiments showed that the SlMYB55 protein interacts with the MADS-box family protein MBP21. Based on these results, we concluded that SlMYB55 affects the biosynthesis of ABA, regulates drought and salt responses through ABA-mediated signal transduction pathways, and directly or indirectly affects the expression of genes related to drought and salt response, flowering time, sepal size and inflorescence, thereby regulating stress tolerance and flower development. In summary, this study identified essential roles for SlMYB55 in regulating drought and salt tolerance and flower development.

Thidiazuron Promotes Leaf Abscission by Regulating the Crosstalk Complexities between Ethylene, Auxin, and Cytokinin in Cotton

Thidiazuron (TDZ) is widely used as a defoliant to induce leaf abscission in cotton. However, the underlying molecular mechanism is still unclear. In this study, RNA-seq and enzyme-linked immunosorbent assays (ELISA) were performed to reveal the dynamic transcriptome profiling and the change of endogenous phytohormones upon TDZ treatment in leaf, petiole, and abscission zone (AZ). We found that TDZ induced the gene expression of ethylene biosynthesis and signal, and promoted ethylene accumulation earlier in leaf than that in AZ. While TDZ down-regulated indole-3-acetic acid (IAA) biosynthesis genes mainly in leaf and IAA signal and transport genes. Furthermore, the IAA content reduced more sharply in the leaf than that in AZ to change the auxin gradient for abscission. TDZ suppressed CTK biosynthesis genes and induced CTK metabolic genes to reduce the IPA accumulation for the reduction of ethylene sensitivity. Furthermore, TDZ regulated the gene expression of abscisic acid (ABA) biosynthesis and signal and induced ABA accumulation between 12-48 h, which could up-regulate ABA response factor genes and inhibit IAA transporter genes. Our data suggest that TDZ orchestrates metabolism and signal of ethylene, auxin, and cytokinin, and also the transport of auxin in leaf, petiole, and AZ, to control leaf abscission.

Reflections on the Triptych of Meristems That Build Flowering Branches in Tomato

Branching is an important component determining crop yield. In tomato, the sympodial pattern of shoot and inflorescence branching is initiated at floral transition and involves the precise regulation of three very close meristems: (i) the shoot apical meristem (SAM) that undergoes the first transition to flower meristem (FM) fate, (ii) the inflorescence sympodial meristem (SIM) that emerges on its flank and remains transiently indeterminate to continue flower initiation, and (iii) the shoot sympodial meristem (SYM), which is initiated at the axil of the youngest leaf primordium and takes over shoot growth before forming itself the next inflorescence. The proper fate of each type of meristems involves the spatiotemporal regulation of FM genes, since they all eventually terminate in a flower, but also the transient repression of other fates since conversions are observed in different mutants. In this paper, we summarize the current knowledge about the genetic determinants of meristem fate in tomato and share the reflections that led us to identify sepal and flower abscission zone initiation as a critical stage of FM development that affects the branching of the inflorescence.

Firming up your tomato: a natural promoter variation in a MADS-box gene is causing all-flesh tomatoes

This article comments on: Liu L, Zhang K, Bai JR, Lu J, Lu X, Hu J, Pan C, He S, Yuan J, Zhang Y, Zhang M, Guo Y, Wang X, Huang Z, Du Y, Cheng F, Li J. 2022. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. Journal of Experimental Botany 73, 123–138.

The wheat AGL6-like MADS-box gene is a master regulator for floral organ identity and a target for spikelet meristem development manipulation

The AGAMOUS-LIKE6 (AGL6)-like genes are ancient MADS-box genes and are functionally studied in a few model plants. The knowledge of these genes in wheat remains limited. Here, by studying a 'double homoeolog mutant' of the AGL6 gene in tetraploid wheat, we showed that AGL6 was required for the development of all four whorls of floral organs with dosage-dependent effect on floret fertility. Yeast two-hybrid analyses detected interactions of AGL6 with all classes of MADS-box proteins in the ABCDE model for floral organ development. AGL6 was found to interact with several additional proteins, including the G protein β and γ (DEP1) subunits. Analysis of the DEP1-B mutant showed a significant reduction in spikelet number per spike in tetraploid wheat, while overexpression of AGL6 in common wheat increased the spikelet number per spike and hence the grain number per spike. RNA-seq analysis identified the regulation of several meristem activity genes by AGL6, such as FUL2 and TaMADS55. Our work therefore extensively updated the wheat ABCDE model and proposed an alternative approach to improve wheat grain yield by manipulating the AGL6 gene.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15,309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production.

Cross-talk between transcriptome, phytohormone and HD-ZIP gene family analysis illuminates the molecular mechanism underlying fruitlet abscission in sweet cherry (Prunus avium L)

BACKGROUND

The shedding of premature sweet cherry (Prunus avium L) fruitlet has significantly impacted production, which in turn has a consequential effect on economic benefits.

RESULT

To better understand the molecular mechanism of sweet cherry fruitlet abscission, pollen viability and structure had been observed from the pollination trees. Subsequently, the morphological characters of the shedding fruitlet, the plant hormone titers of dropping carpopodium, the transcriptome of the abscising carpopodium, as well as the HD-ZIP gene family were investigated. These findings showed that the pollens giving rise to heavy fruitlet abscission were malformed in structure, and their viability was lower than the average level. The abscising fruitlet and carpopodium were characterized in red color, and embryos of abscising fruitlet were aborted, which was highly ascribed to the low pollen viability and malformation. Transcriptome analysis showed 6462 were significantly differentially expressed, of which 2456 genes were up-regulated and 4006 down-regulated in the abscising carpopodium. Among these genes, the auxin biosynthesis and signal transduction genes (α-Trp, AUX1), were down-regulated, while the 1-aminocyclopropane-1-carboxylate oxidase gene (ACO) affected in ethylene biosynthesis, was up-regulated in abscising carpopodium. About genes related to cell wall remodeling (CEL, PAL, PG EXP, XTH), were up-regulated in carpopodium abscission, which reflecting the key roles in regulating the abscission process. The results of transcriptome analysis considerably conformed with those of proteome analysis as documented previously. In comparison with those of the retention fruitlet, the auxin contents in abscising carpopodium were significantly low, which presumably increased the ethylene sensitivity of the abscission zone, conversely, the abscisic acid (ABA) accumulation was considerably higher in abscising carpopodium. Furthermore, the ratio of (TZ + IAA + GA3) / ABA also obviously lower in abscising carpopodium. Besides, the HD-ZIP gene family analysis showed that PavHB16 and PavHB18 were up-regulated in abscising organs.

CONCLUSION

Our findings combine morphology, cytology and transcriptional regulation to reveal the molecular mechanism of sweet cherry fruitlet abscission. It provides a new perspective for further study of plant organ shedding.

Tomato SlBL4 plays an important role in fruit pedicel organogenesis and abscission

Abscission, a cell separation process, is an important trait that influences grain and fruit yield. We previously reported that BEL1-LIKE HOMEODOMAIN 4 (SlBL4) is involved in chloroplast development and cell wall metabolism in tomato fruit. In the present study, we showed that silencing SlBL4 resulted in the enlargement and pre-abscission of the tomato (Solanum lycopersicum cv. Micro-TOM) fruit pedicel. The anatomic analysis showed the presence of more epidermal cell layers and no obvious abscission zone (AZ) in the SlBL4 RNAi lines compared with the wild-type plants. RNA-seq analysis indicated that the regulation of abscission by SlBL4 was associated with the altered abundance of genes related to key meristems, auxin transporters, signaling components, and cell wall metabolism. Furthermore, SlBL4 positively affected the auxin concentration in the abscission zone. A dual-luciferase reporter assay revealed that SlBL4 activated the transcription of the JOINTLESS, OVATE, PIN1, and LAX3 genes. We reported a novel function of SlBL4, which plays key roles in fruit pedicel organogenesis and abscission in tomatoes.

Multifunctional evolution of B and AGL6 MADS box genes in orchids

We previously found that B and AGL6 proteins form L (OAP3-2/OAGL6-2/OPI) and SP (OAP3-1/OAGL6-1/OPI) complexes to determine lip/sepal/petal identities in orchids. Here, we show that the functional L' (OAP3-1/OAGL6-2/OPI) and SP' (OAP3-2/OAGL6-1/OPI) complexes likely exist and AP3/PI/AGL6 genes have acquired additional functions during evolution. We demonstrate that the presumed L' complex changes the structure of the lower lateral sepals and helps the lips fit properly in the center of the flower. In addition, we find that OAP3-1/OAGL6-1/OPI in SP along with presumed SP' complexes regulate anthocyanin accumulation and pigmentation, whereas presumed L' along with OAP3-2/OAGL6-2/OPI in L complexes promotes red spot formation in the perianth. Furthermore, the B functional proteins OAP3-1/OPI and OAGL6-1 in the SP complex could function separately to suppress sepal/petal senescence and promote pedicel abscission, respectively. These findings expand the current knowledge behind the multifunctional evolution of the B and AGL6 genes in plants.

Functional characterization of PETIOLULE-LIKE PULVINUS (PLP) gene in abscission zone development in Medicago truncatula and its application to genetic improvement of alfalfa

Alfalfa (Medicago sativa L.) is one of the most important forage crops throughout the world. Maximizing leaf retention during the haymaking process is critical for achieving superior hay quality and maintaining biomass yield. Leaf abscission process affects leaf retention. Previous studies have largely focused on the molecular mechanisms of floral organ, pedicel and seed abscission but scarcely touched on leaf and petiole abscission. This study focuses on leaf and petiole abscission in the model legume Medicago truncatula and its closely related commercial species alfalfa. By analysing the petiolule-like pulvinus (plp) mutant in M. truncatula at phenotypic level (breakstrength and shaking assays), microscopic level (scanning electron microscopy and cross-sectional analyses) and molecular level (expression level and expression pattern analyses), we discovered that the loss of function of PLP leads to an absence of abscission zone (AZ) formation and PLP plays an important role in leaflet and petiole AZ differentiation. Microarray analysis indicated that PLP affects abscission process through modulating genes involved in hormonal homeostasis, cell wall remodelling and degradation. Detailed analyses led us to propose a functional model of PLP in regulating leaflet and petiole abscission. Furthermore, we cloned the PLP gene (MsPLP) from alfalfa and produced RNAi transgenic alfalfa plants to down-regulate the endogenous MsPLP. Down-regulation of MsPLP results in altered pulvinus structure with increased leaflet breakstrength, thus offering a new approach to decrease leaf loss during alfalfa haymaking process.

Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition

MADS box genes are class of transcription factors involved in various physiological and developmental processes in plants. To understand their role in floral transition-related pathways, a genome-wide identification was done in Cajanus cajan, identifying 102 members which were classified into two different groups based on their gene structure. The status of all these genes was further analyzed in three wild species i.e. C. scarabaeoides, C. platycarpus and C. cajanifolius which revealed absence of 31-34 MADS box genes in them hinting towards their role in domestication and evolution. We could locate only a single copy of both FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) genes, while three paralogs of SUPPRESSOR OF ACTIVATION OF CONSTANS 1 (SOC1) were found in C. cajan genome. One of those SOC1 paralogs i.e. CcMADS1.5 was found to be missing in all three wild relatives, also forming separate clade in phylogeny. This SOC1 gene was also lacking the characteristic MADS box domain in it. Expression profiling of major MADS box genes involved in flowering was done in different tissues viz shoot apical meristem, vegetative leaf, reproductive meristem, and reproductive bud. Gene-based time tree of FLC and SOC1 gene dictates their divergence from Arabidopsis before 71 and 23 million year ago (mya), respectively. This study provides valuable insights into the functional characteristics, expression pattern, and evolution of MADS box proteins in grain legumes with emphasis on C. cajan, which may help in further characterizing these genes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02605-7.

First approach to pod dehiscence in faba bean: genetic and histological analyses

Pod dehiscence causes important yield losses in cultivated crops and therefore has been a key trait strongly selected against in crop domestication. In spite of the growing knowledge on the genetic basis of dehiscence in different crops, no information is available so far for faba bean. Here we conduct the first comprehensive study for faba bean pod dehiscence by combining, linkage mapping, comparative genomics, QTL analysis and histological examination of mature pods. Mapping of dehiscence-related genes revealed conservation of syntenic blocks among different legumes. Three QTLs were identified in faba bean chromosomes II, IV and VI, although none of them was stable across years. Histological analysis supports the convergent phenotypic evolution previously reported in cereals and related legume species but revealed a more complex pattern in faba bean. Contrary to common bean and soybean, the faba bean dehiscence zone appears to show functional equivalence to that described in crucifers. The lignified wall fiber layer, which is absent in the paucijuga primitive line Vf27, or less lignified and vacuolated in other dehiscent lines, appears to act as the major force triggering pod dehiscence in this species. While our findings, provide new insight into the mechanisms underlying faba bean dehiscence, full understanding of the molecular bases will require further studies combining precise phenotyping with genomic analysis.

Comparative Transcriptomic Analysis of the Development of Sepal Morphology in Tomato (Solanum Lycopersicum L.)

Sepal is an important component of the tomato flower and fruit that typically protects the flower in bud and functions as a support for petals and fruits. Moreover, sepal appearance influences the commercial property of tomato nowadays. However, the phenotype information and development mechanism of the natural variation of sepal morphology in the tomato is still largely unexplored. To study the developmental mechanism and to determine key genes related to downward sepal in the tomato, we compared the transcriptomes of sepals between downward sepal (dsp) mutation and the wild-type by RNA sequencing and found that the differentially expressed genes were dominantly related to cell expansion, auxin, gibberellins and cytokinin. dsp mutation affected cell size and auxin, and gibberellins and cytokinin contents in sepals. The results showed that cell enlargement or abnormal cell expansion in the adaxial part of sepals in dsp. As reported, auxin, gibberellins and cytokinin were important factors for cell expansion. Hence, dsp mutation regulated cell expansion to control sepal morphology, and auxin, gibberellins and cytokinin may mediate this process. One ARF gene and nine SAUR genes were dramatically upregulated in the sepal of the dsp mutant, whereas seven AUX/IAA genes were significantly downregulated in the sepal of dsp mutant. Further bioinformatic analyses implied that seven AUX/IAA genes might function as negative regulators, while one ARF gene and nine SAUR genes might serve as positive regulators of auxin signal transduction, thereby contributing to cell expansion in dsp sepal. Thus, our data suggest that 17 auxin-responsive genes are involved in downward sepal formation in the tomato. This study provides valuable information for dissecting the molecular mechanism of sepal morphology control in the tomato.

Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains

The herbaceous peony (Paeonia lactiflora Pall.) is a perennial flowering plant of the Paeoniaceae species that is widely cultivated for medical and ornamental uses. The monoterpene glucoside paeoniflorin and its derivatives are the active compounds of the P. lactiflora roots. However, the gene regulation pathways associated with monoterpene and paeoniflorin biosynthesis in P. lactiflora are still unclear. Here, we selected three genotypes of P. lactiflora with distinct morphologic features and chemical compositions that were a result of long-term reproductive isolation. We performed an RNA-sequencing experiment to profile the transcriptome changes of the shoots and roots. Using de novo assembly analysis, we identified 36,264 unigenes, including 521 genes responsible for encoding transcription factors. We also identified 28,925 unigenes that were differentially expressed in different organs and/or genotypes. Pathway enrichment analysis showed that the P. lactiflora unigenes were significantly overrepresented in several secondary metabolite biosynthesis pathways. We identified and profiled 33 genes responsible for encoding the enzymescontrolling the major catalytic reactions in the terpenoid backbone and in monoterpenoid biosynthesis. Our study identified the candidate genes in the terpenoid biosynthesis pathways, providing useful information for metabolic engineering of P. lactiflora intended for pharmaceutical uses and facilitating the development of strategies to improve marker-assist P. lactiflora in the future.

Validation of MADS-box genes from apple fruit pedicels during early fruit abscission by transcriptome analysis and real-time PCR

BACKGROUND

Fruit abscission in an isolated region called abscission zone (AZ) is regulated by several genes including JOINTLESS, MACROCALYX and SEPALLATA, MADS-box genes, in tomato.

OBJECTIVE

The surviving central pedicels and the abscised lateral pedicels were examined in fruit clusters in order to investigate apple MADS-box genes from fruit pedicels of self-abscising apple 'Saika' during early fruit abscission.

METHODS

After performing RNA-Seq, transcription profiling was conducted on the MADS-box genes from apple central and lateral pedicels. The JOINTLESS homolog of apple (MdJOINTLESS) was amplified using degenerate primers annealing to a highly conserved domain based on the orthologous genes of various crops, including JOINTLESS gene of tomato. The expression pattern of MdJOINTLESS was investigated in central and lateral pedicles by real-time PCR.

RESULTS

Some homologs were found which similar to JOINTLESS, MACROCALYX and SEPALLATA of tomato MADS-box genes from transcriptome analysis and RACE. Using phylogenetic analyses with the MADS-box gene family, MdJOINTLESS was classified into the SHORT VEGETATIVE PHASE (SVP) clade that included Arabidopsis and other crops. The expression level of MdJOINTLESS in central pedicel was more than twice as high as that of lateral pedicel.

CONCLUSION

In the current study, we could find apple homologs of JOINTLESS, MACROCALYX, SEPALLATA, which were known to regulate pedicel AZ development in tomato. Furthermore, MdJOINTLESS might contribute to auxin gradation, influencing hierarchical ranking of auxin transport between fruit pedicels of self-abscising apple.

Genome-Wide Analysis of the MADS-Box Transcription Factor Family in Solanum lycopersicum

MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit development and ripening, remains obscure. To gain insight into the MADS-box genes in tomato, 131 tomato MADS-box genes were identified. These genes could be divided into five groups (Mα, Mβ, Mγ, Mδ, and MIKC) and were found to be located on all 12 chromosomes. We further analyzed the phylogenetic relationships among Arabidopsis and tomato, as well as the protein motif structure and exon–intron organization, to better understand the tomato MADS-box gene family. Additionally, owing to the role of MADS-box genes in floral organ identification and fruit development, the constitutive expression patterns of MADS-box genes at different stages in tomato development were identified. We analyzed 15 tomato MADS-box genes involved in floral organ identification and five tomato MADS-box genes related to fruit development by qRT-PCR. Collectively, our study provides a comprehensive and systematic analysis of the tomato MADS-box genes and would be valuable for the further functional characterization of some important members of the MADS-box gene family.

Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the huanglongbing-associated fruit abscission

Citrus greening disease or huanglongbing (HLB) is associated with excessive pre-harvest fruit drop. To understand the mechanisms of the HLB-associated fruit abscission, transcriptomes were analyzed by RNA sequencing of calyx abscission zones (AZ-C) of dropped "Hamlin" oranges from HLB-diseased trees upon shaking the trees (Dd), retained oranges on diseased trees (Rd), dropped oranges from healthy shaken trees (Dh), and retained oranges on healthy trees (Rh). Cluster analysis of transcripts indicated that Dd had the largest distances from all other groups. Comparisons of transcriptomes revealed 1047, 1599, 813, and 764 differentially expressed genes (DEGs) between Dd/Rd, Dd/Dh, Dh/Rh, and Rd/Rh. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated hormone signaling, defense response, and secondary metabolism were involved in HLB-associated fruit abscission. Ethylene (ET) and jasmonic acid (JA) synthesis/signaling-related genes were upregulated in Dd, while other phytohormone-related genes were generally downregulated. In addition, genes related to JA/ET-activated defense response were upregulated in Dd as well. Consistent with the phytohormone gene expression data, increased levels (p < 0.05) of ET and JA, and a decreased level (p < 0.05) of abscisic acid were found in Dd compared with Rd, Dh or Rh. Lasiodiploidia theobromae level in Dd AZ-C was higher than the other fruit types, confirmed by qPCR, indicating AZ-C secondary fungal infection of HLB fruit may exacerbate their abscission. This information will help formulate effective strategies to control HLB-related abscission.

Phenotypic and genetic characterization of tomato mutants provides new insights into leaf development and its relationship to agronomic traits

BACKGROUND

Tomato mutants altered in leaf morphology are usually identified in the greenhouse, which demands considerable time and space and can only be performed in adequate periods. For a faster but equally reliable scrutiny method we addressed the screening in vitro of 971 T-DNA lines. Leaf development was evaluated in vitro in seedlings and shoot-derived axenic plants. New mutants were characterized in the greenhouse to establish the relationship between in vitro and in vivo leaf morphology, and to shed light on possible links between leaf development and agronomic traits, a promising field in which much remains to be discovered.

RESULTS

Following the screening in vitro of tomato T-DNA lines, putative mutants altered in leaf morphology were evaluated in the greenhouse. The comparison of results in both conditions indicated a general phenotypic correspondence, showing that in vitro culture is a reliable system for finding mutants altered in leaf development. Apart from providing homogeneous conditions, the main advantage of screening in vitro lies in the enormous time and space saving. Studies on the association between phenotype and nptII gene expression showed co-segregation in two lines (P > 99%). The use of an enhancer trap also allowed identifying gain-of-function mutants through reporter expression analysis. These studies suggested that genes altered in three other mutants were T-DNA tagged. New mutants putatively altered in brassinosteroid synthesis or perception, mutations determining multiple pleiotropic effects, lines affected in organ curvature, and the first tomato mutant with helical growth were discovered. Results also revealed new possible links between leaf development and agronomic traits, such as axillary branching, flower abscission, fruit development and fruit cracking. Furthermore, we found that the gene tagged in mutant 2635-MM encodes a Sterol 3-beta-glucosyltransferase. Expression analysis suggested that abnormal leaf development might be due to the lack-off-function of this gene.

CONCLUSION

In vitro culture is a quick, efficient and reliable tool for identifying tomato mutants altered in leaf morphology. The characterization of new mutants in vivo revealed new links between leaf development and some agronomic traits. Moreover, the possible implication of a gene encoding a Sterol 3-beta-glucosyltransferase in tomato leaf development is reported.

An AGAMOUS MADS-box protein, SlMBP3, regulates the speed of placenta liquefaction and controls seed formation in tomato

AGAMOUS (AG) MADS-box transcription factors have been shown to play crucial roles in floral organ and fruit development in angiosperms. Here, we isolated a tomato (Solanum lycopersicum) AG MADS-box gene SlMBP3 and found that it is preferentially expressed in flowers and during early fruit developmental stages in the wild-type (WT), and in the Nr (never ripe) and rin (ripening inhibitor) mutants. Its transcripts are notably accumulated in the pistils; transcripts abundance decrease during seed and placental development, increasing again during flower development. SlMBP3-RNAi tomato plants displayed fleshy placenta without locular gel and extremely malformed seeds with no seed coat, while SlMBP3-overexpressing plants exhibited advanced liquefaction of the placenta and larger seeds. Enzymatic activities related to cell wall modification, and the contents of cell wall components and pigments were dramatically altered in the placentas of SlMBP3-RNAi compared with the WT. Alterations in these physiological features were also observed in the placentas of SlMBP3-overexpressing plants. The lignin content of mature seeds in SlMBP3-RNAi lines was markedly lower than that in the WT. RNA-seq and qRT-PCR analyses revealed that genes involved in seed development and the biosynthesis of enzymes related to cell wall modification, namely gibberellin, indole-3-acetic acid, and abscisic acid were down-regulated in the SlMBP3-RNAi lines. Taking together, our results demonstrate that SlMBP3 is involved in the regulation of placenta and seed development in tomato.

Characterization of the O-acetylserine(thiol)lyase gene family in Solanum lycopersicum L

This research demonstrated the conservation and diversification of the functions of the O-acetylserine-(thiol) lyase gene family genes in Solanum lycopersicum L. Cysteine is the first sulfur-containing organic molecule generated by plants and is the precursor of many important biomolecules and defense compounds. Cysteine and its derivatives are also essential in various redox signaling-related processes. O-acetylserine(thiol)lyase (OASTL) proteins catalyze the last step of cysteine biosynthesis. Previously, researches focused mainly on OASTL proteins which were the most abundant or possessed the authentic OASTL activity, whereas few studies have ever given a comprehensive view of the functions of all the OASTL members in one specific species. Here, we characterized 8 genes belonging to the OASTL gene family from tomato genome (SlOAS2 to SlOAS9), including the sequence analyses, subcellular localization, enzymatic activity assays, expression patterns, as well as the interaction property with SATs. Apart from SlOAS3, all the other genes encoded OASTL-like proteins. Tomato OASTLs were differentially expressed during the development of tomato plants, and their encoded proteins had diverse compartmental distributions and functions. SlOAS5 and SlOAS6 catalyzed the biogenesis of cysteine in chloroplasts and in the cytosol, respectively, and this was in consistent with their interaction abilities with SlSATs. SlOAS4 catalyzed the generation of hydrogen sulfide, similar to its Arabidopsis ortholog, DES1. SlOAS2 also functioned as an L-cysteine desulfhydrase, but its expression pattern was very different from that of SlOAS4. Additionally, SlOAS8 might be a β-cyanoalanine synthase in mitochondria, and the S-sulfocysteine synthase activity appeared lost in tomato plants. SlOAS7 exhibited a transactivational ability in yeast; while the subcellular localization of SlOAS9 was in the peroxisome and correlated with the process of leaf senescence, indicating that these two genes might have novel roles.

Suppression of a tomato SEPALLATA MADS-box gene, SlCMB1, generates altered inflorescence architecture and enlarged sepals

The SEPALLATA (SEP) MADS-box transcription factors play essential roles in reproductive growth, especially in floral organ differentiation. Here, SlCMB1, a tomato SEP MADS-box gene, was isolated. SlCMB1 is noticeably expressed in inflorescences and flowers. Its transcript levels were higher in sepals than in other floral organs and decreased during sepal development. Tomato plants with reduced SlCMB1 mRNA levels displayed longer, branched and indeterminate inflorescences that exhibited a transition from reproductive to vegetative growth and enlarged and abnormally fused sepals. The transcript levels of genes known to regulate the development of inflorescence architecture and sepal size in tomato were dramatically changed. In addition, the expression levels of cell elongation-related and gibberellin biosynthetic genes also showed significant differences between the transgenic lines and the wild type, and the GA content of the peduncle in the transgenic lines was higher than that in the wild type. Yeast two-hybrid assay showed that SlCMB1 could interact individually with MC, J, AP2a and SlMBP21. Overall, our results indicate that SlCMB1 is an important regulator involved in the development of inflorescence architecture and sepal size in tomato plants.

TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

BACKGROUND

MADS-box genes are key regulators of plant reproductive development and members of most lineages of this gene family have been extensively studied. However, the function and diversification of the ancient TM8 lineage remains elusive to date. The available data suggest a possible function in flower development in tomato and fast evolution through numerous gene loss events in flowering plants.

RESULTS

We show the broad conservation of TM8 within angiosperms and find that in contrast to other MADS-box gene lineages, no gene duplicates have been retained after major whole genome duplication events. Through knock-down of NbTM8 by virus induced gene silencing in Nicotiana benthamiana, we show that NbTM8 represses miR172 together with another MADS-box gene, SHORT VEGETATIVE PHASE (NbSVP). In the closely related species Petunia hybrida, PhTM8 is not expressed under the conditions we investigated and consistent with this, a knock-out mutant did not show a phenotype. Finally, we generated transgenic tomato plants in which TM8 was silenced or ectopically expressed, but these plants did not display a clear phenotype. Therefore, no clear function could be confirmed for Solanum lycopersium.

CONCLUSIONS

While the presence of TM8 is generally conserved, it remains difficult to propose a general function in angiosperms. Based on all the available data to date, supplemented with our own results, TM8 function seems to have diversified quickly throughout angiosperms and acts as repressor of miR172 in Nicotiana benthamiana, together with NbSVP.

Aquatic plants for phytostabilization of cadmium and zinc in hydroponic experiments

Cadmium (Cd) may be toxic to aquatic plants even at modest concentrations, and excessive quantities of zinc (Zn) decrease plant performance. The Cd and Zn phytoremediation potential of several aquatic plant species (Thalia geniculate, Cyperus alternifolius, Canna indica, Eichhornia crassipes, Pistia stratiotes) and one grass species (Vetiveria zizanioides) was evaluated in hydroponic experiments. Vetiveria zizanioides, E. crassipes, and P. stratiotes experienced reduced growth performance in the presence of Cd as determined from biomass production, survival rate, and crown root number (CN); however, they accumulated high quantities of metals in their tissues, particularly in roots. Root accumulation is considered a key characteristic of so-called excluder species. In this study, only E. crassipes and P. stratiotes had bioconcentration factors and translocation factors (> 1000 and < 1, respectively) suitable for high phytostabilization of Cd. Furthermore, V. zizanioides and P. stratiotes showed the highest percent metal uptake from solution and removal capacity for Zn (~70% and ~2 mg d^-1 g^-1, respectively). Emergent aquatic species (particularly C. alternifolius and T. geniculate) adapted and lived well in Cd- and Zn-contaminated solution and took up high quantities of Cd and Zn in roots, and are therefore considered strong excluders. Beneficial uses of such species in contaminated wetlands include stabilizing toxic metals and limiting erosion. Plant tissue can be applied to other uses, including as a biomass fuel. In field situations, the candidate species may work best when grown together, since each plant genotype possesses a different potential to control Cd and Zn.

MADS-box genes and crop domestication: the jack of all traits

MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.

A tomato MADS-box protein, SlCMB1, regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening

The MADS-box transcription factors play essential roles in many physiological and biochemical processes of plants, especially in fruit ripening. Here, a tomato MADS-box gene, SlCMB1, was isolated. SlCMB1 expression declined with the fruit ripening from immature green to B + 7 (7 days after Breaker) fruits in the wild type (WT) and was lower in Nr and rin mutants fruits. Tomato plants with reduced SlCMB1 mRNA displayed delayed fruit ripening, reduced ethylene production and carotenoid accumulation. The ethylene production in SlCMB1-RNAi fruits decreased by approximately 50% as compared to WT. The transcripts of ethylene biosynthesis genes (ACS2, ACS4, ACO1 and ACO3), ethylene-responsive genes (E4, E8 and ERF1) and fruit ripening-related genes (RIN, TAGL1, FUL1, FUL2, LoxC and PE) were inhibited in SlCMB1-RNAi fruits. The carotenoid accumulation was decreased and two carotenoid synthesis-related genes (PSY1 and PDS) were down-regulated while three lycopene cyclase genes (CYCB, LCYB and LCYE) were up-regulated in transgenic fruits. Furthermore, yeast two-hybrid assay showed that SlCMB1 could interact with SlMADS-RIN, SlMADS1, SlAP2a and TAGL1, respectively. Collectively, these results indicate that SlCMB1 is a new component to the current model of regulatory network that regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening.

Suppression of SlMBP15 Inhibits Plant Vegetative Growth and Delays Fruit Ripening in Tomato

MADS-box genes have been demonstrated to participate in a number of processes in tomato development, especially fruit ripening. In this study, we reported a novel MADS-box gene, SlMBP15, which is implicated in fruit ripening. Based on statistical analysis, the ripening time of SlMBP15-silenced tomato was delayed by 2-4 days compared with that of the wild-type (WT). The accumulation of carotenoids and biosynthesis of ethylene in fruits were decreased in SlMBP15-silenced tomato. Genes related to carotenoid and ethylene biosynthesis were greatly repressed. SlMBP15 can interact with RIN, a MADS-box regulator affecting the carotenoid accumulation and ethylene biosynthesis in tomato. In addition, SlMBP15-silenced tomato produced dark green leaves, and its plant height was reduced. The gibberellin (GA) content of transgenic plants was lower than that of the WT and GA biosynthesis genes were repressed. These results demonstrated that SlMBP15 not only positively regulated tomato fruit ripening but also affected the morphogenesis of the vegetative organs.

The MADS-Box Gene SlMBP21 Regulates Sepal Size Mediated by Ethylene and Auxin in Tomato

Normal organ size is achieved by successful co-ordination of cell proliferation and cell expansion, which are modulated by multiple factors such as ethylene and auxin. In our work, SlMBP21-RNAi (RNA interference) tomato exhibited longer sepals and improved fruit set. Histological analysis indicated that longer sepals were attributed to cell expansion. To explore how SlMBP21 regulates sepal size, we compared the transcriptomes of sepals between SlMBP21-RNAi and the wild type by RNA sequencing and found that the differentially expressed genes were dominantly related to cell expansion, ethylene and auxin, and photosynthesis. Down-regulation of SlMBP21 affected ethylene production and the free IAA and IAA-Val intensity in sepals. Hormone treatment further indicated that SlMBP21 was involved in the ethylene and auxin pathways. As reported, ethylene and auxin were important factors for cell expansion. Hence, SlMBP21 negatively regulated cell expansion to control sepal size, and ethylene and auxin may mediate this process. Additionally, the contents of Chl and the activity of ribulose-1, 5-bisphosphate carboxylase/oxygenase, the key photosynthetic enzyme, were both increased in SlMBP21-RNAi sepals, which indicated that photosynthesis might be enhanced in transgenic longer sepals. Therefore, the longer sepal, with better protection and enhanced photosynthesis, may contribute to improve fruit set. Altogether, these results suggested that SlMBP21 was a novel factor involved in organ size control. Moreover, our study provided potential application value for improving fruit set.