JOINTLESS suppresses sympodial identity in inflorescence meristems of tomato

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

The essential role of the hickory StMADS11 subfamily in flower organogenesis and flowering time in Arabidopsis

The StMADS11 subfamily genes play a crucial role in regulating flowering time, flower development, and bud dormancy in plants. These genes exhibit functional differences between annual and perennial woody plants. In hickory (Carya cathayensis Sarg.), the specific roles of these genes in flowering regulation have not been elucidated. In this study, we identified five StMADS11 subfamily genes in the hickory genome, designated as CcSVP-like, CcAGL24-like1, CcAGL24-like2, CcJOINTLESS-like1, and CcJOINTLESS-like2, based on their clustering characteristics. Sequence analyses revealed distinct structural features in this subfamily, including differences in intron length, C domain, and conserved motifs. Transcript analysis indicated high expression levels of these genes in female flower buds, along with a notable seasonal expression pattern. Overexpression studies on Arabidopsis have demonstrated that the StMADS11 subfamily genes lead to various floral organ and pod anomalies. Specifically, overexpression of CcSVP-like resulted in delayed flowering, while overexpression of CcAGL24-like1, CcAGL24-like2, CcJOINTLESS-like1, and CcJOINTLESS-like2 promoted flowering. Protein interaction studies have shown that the StMADS11 subfamily proteins bind to the CcFUL-like protein. Notably, CcFUL-like, CcSVP-like, CcJOINTLESS-like1, and CcJOINTLESS-like2 proteins were able to bind to the CcSOC1-like promoter and suppress its expression. Our findings elucidate the distinct roles of the StMADS11 subfamily genes in flower development and timing, contribute to developing the current understanding of flowering regulation in hickory, and offer a foundation for further studies in perennial woody plants.

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 novel tomato interspecific (Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm

We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.

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.

CRISPR/Cas9-mediated mutations of FANTASTIC FOUR gene family for creating early flowering mutants in tomato

Flowering time is of great agricultural importance and the timing and extent of flowering usually determines yield and availability of flowers, fruits and seeds. Identification of genes determining flowering has important practical applications for tomato breeding. Here we demonstrate the roles of the FANTASTIC FOUR (FAF) gene family in regulating tomato flowering time. In this plant-specific gene family, SlFAF1/2a shows a constitutive expression pattern during the transition of the shoot apical meristem (SAM) from vegetative to reproductive growth and significantly influences flowering time. Overexpressing SlFAF1/2a causes earlier flowering compared with the transformations of other genes in the FAF family. SlFAF1/2c also positively regulates tomato flowering, although to a lesser extent. The other members of the SlFAF gene family, SlFAF1/2b, SlFAF3/4a and SlFAF3/4b, are negative regulators of tomato flowering and faf1/2b, faf3/4a and faf3/4b single mutants all display early flowering. We generated a series of early flowering mutants using the CRISPR/Cas9 editing system, and the faf1/2b faf3/4a faf3/4b triple mutant flowering earliest compared with other mutants. More importantly, these mutants show no adverse effect on yield. Our results have uncovered the role of the FAF gene family in regulating tomato flowering time and generated early flowering germplasms for molecular breeding.

EARLY FLOWERING is a dominant gain-of-function allele of FANTASTIC FOUR 1/2c that promotes early flowering in tomato

Flowering time, an important factor in plant adaptability and genetic improvement, is regulated by various genes in tomato (Solanum lycopersicum). In this study, we characterized a tomato mutant, EARLY FLOWERING (EF), that developed flowers much earlier than its parental control. EF is a dominant gain-of-function allele with a T-DNA inserted 139 bp downstream of the stop codon of FANTASTIC FOUR 1/2c (FAF1/2c). The transcript of SlFAF1/2c was at elevated levels in the EF mutant. Overexpressing SlFAF1/2c in tomato plants phenocopied the early flowering trait of the EF mutant. Knocking out SlFAF1/2c in the EF mutant reverted the early flowering phenotype of the mutant to the normal flowering time of the wild-type tomato plants. SlFAF1/2c promoted the floral transition by shortening the vegetative phase rather than by reducing the number of leaves produced before the emergence of the first inflorescence. The COP9 signalosome subunit 5B (CSN5B) was shown to interact with FAF1/2c, and knocking out CSN5B led to an early flowering phenotype in tomato. Interestingly, FAF1/2c was found to reduce the accumulation of the CSN5B protein by reducing its protein stability. These findings imply that FAF1/2c regulates flowering time in tomato by reducing the accumulation and stability of CSN5B, which influences the expression of SINGLE FLOWER TRUSS (SFT), JOINTLESS (J) and UNIFLORA (UF). Thus, a new allele of SlFAF1/2c was discovered and found to regulate flowering time in tomato.

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.

Natural variation in the promoter of FLOWERING LOCUS T-LIKE 2 in pumpkin (Cucurbita moschata Duch.) is associated with flowering time under short-day conditions

Late flowering is a serious bottleneck in pumpkin (Cucurbita moschata Duch.) agriculture production. Although key genes governing flowering time have been reported in many species, the regulatory network of flowering in pumpkin remains largely obscure, thereby impeding the resolution of industry-wide challenges associated with delayed fruit ripening in pumpkin cultivation. Here, we report an early flowering pumpkin germplasm accession (LXX-4). Using LXX-4 and a late flowering germplasm accession (HYM-9), we constructed an F2 segregation population. A significant difference in FLOWERING LOCUS T-LIKE 2 (FTL2) expression level was identified to be the causal factor of the flowering time trait discrepancy in LXX-4 and HYM-9. Moreover, we have shown that a 21 bp InDel in the FTL2 promoter was the key reason for the waxing and waning of its transcript level. The 21 bp deletion excluded a repressor-AGL19 and recruited activators-BBX7, WRKY40 and SVP to the FTL2 promoter in LXX-4. Together, our data add a useful element to our knowledge which could be used to simplify breeding efforts for early-maturing pumpkin.

Genome-Wide Analysis of the MADS-Box Gene Family in Hibiscus syriacus and Their Role in Floral Organ Development

Hibiscus syriacus belongs to the Malvaceae family, and is a plant with medicinal, edible, and greening values. MADS-box transcription factor is a large family of regulatory factors involved in a variety of biological processes in plants. Here, we performed a genome-wide characterization of MADS-box proteins in H. syriacus and investigated gene structure, phylogenetics, cis-acting elements, three-dimensional structure, gene expression, and protein interaction to identify candidate MADS-box genes that mediate petal developmental regulation in H. syriacus. A total of 163 candidate MADS-box genes were found and classified into type I (Mα, Mβ, and Mγ) and type II (MIKC and Mδ). Analysis of cis-acting elements in the promoter region showed that most elements were correlated to plant hormones. The analysis of nine HsMADS expressions of two different H. syriacus cultivars showed that they were differentially expressed between two type flowers. The analysis of protein interaction networks also indicated that MADS proteins played a crucial role in floral organ identification, inflorescence and fruit development, and flowering time. This research is the first to analyze the MADS-box family of H. syriacus and provides an important reference for further study of the biological functions of the MADS-box, especially in flower organ development.

Overexpression of <italic>PvSVP1</italic>, an <italic>SVP</italic>-like gene of bamboo, causes early flowering and abnormal floral organs in <italic>Arabidopsis</italic> and rice

<p indent="0mm">Bamboo is a nontimber woody plant featuring a long vegetative stage and uncertain flowering time. Therefore, the genes belonging to flowering repressors might be essential in regulating the transition from the vegetative to reproductive stage in bamboo. The <italic>Short Vegetative Phase</italic> ( <italic>SVP</italic>) gene plays a pivotal role in floral transition and development. However, little is known about the bamboo <italic>SVP</italic> homologues. In this study, <italic>Phyllostachys violascens</italic> <italic>PvSVP1</italic> is isolated by analysis of the <italic>P</italic>. <italic>edulis</italic> transcriptome database. Phylogenetic analysis shows that <italic>PvSVP1</italic> is closely related to <italic>OsMADS55</italic> (rice <italic>SVP</italic> homolog). <italic>PvSVP1</italic> is ubiquitously expressed in various tissues, predominantly in vegetative tissues. To investigate the function of <italic>PvSVP1</italic>, <italic>PvSVP1</italic> is overexpressed in <italic>Arabidopsis</italic> and rice under the influence of the 35S promoter. Overexpression of <italic>PvSVP1</italic> in <italic>Arabidopsis</italic> causes early flowering and produces abnormal petals and sepals. Quantitative real-time PCR reveals that overexpression in <italic>Arabidopsis</italic> produces an early flowering phenotype by downregulating <italic>FLC</italic> and upregulating <italic>FT</italic> and produces abnormal floral organs by upregulating <italic>AP1</italic>, <italic>AP3</italic> and <italic>PI</italic> expressions. Simultaneously, overexpression of <italic>PvSVP1</italic> in rice alters the expressions of flowering-related genes such as <italic>Hd3a</italic>, <italic>RFT1</italic>, <italic>OsMADS56</italic> and <italic>Ghd7</italic> and promotes flowering under field conditions. In addition, PvSVP1 may be a nuclear protein which interacts with PvVRN1 and PvMADS56 on the yeast two-hybrid and BiFC systems. Our study suggests that <italic>PvSVP1</italic> may play a vital role in flowering time and development by interacting with PvVRN1 and PvMADS56 in the nucleus. Furthermore, this study paves the way toward understanding the complex flowering process of bamboo. </p>.

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).

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.

Interactions between SQUAMOSA and SHORT VEGETATIVE PHASE MADS-box proteins regulate meristem transitions during wheat spike development

Inflorescence architecture is an important determinant of crop productivity. The number of spikelets produced by the wheat inflorescence meristem (IM) before its transition to a terminal spikelet (TS) influences the maximum number of grains per spike. Wheat MADS-box genes VERNALIZATION 1 (VRN1) and FRUITFULL 2 (FUL2) (in the SQUAMOSA-clade) are essential to promote the transition from IM to TS and for spikelet development. Here we show that SQUAMOSA genes contribute to spikelet identity by repressing MADS-box genes VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT2), SHORT VEGETATIVE PHASE 1 (SVP1), and SVP3 in the SVP clade. Constitutive expression of VRT2 resulted in leafy glumes and lemmas, reversion of spikelets to spikes, and downregulation of MADS-box genes involved in floret development, whereas the vrt2 mutant reduced vegetative characteristics in spikelets of squamosa mutants. Interestingly, the vrt2 svp1 mutant showed similar phenotypes to squamosa mutants regarding heading time, plant height, and spikelets per spike, but it exhibited unusual axillary inflorescences in the elongating stem. We propose that SQUAMOSA-SVP interactions are important to promote heading, formation of the TS, and stem elongation during the early reproductive phase, and that downregulation of SVP genes is then necessary for normal spikelet and floral development. Manipulating SVP and SQUAMOSA genes can contribute to engineering spike architectures with improved productivity.

Comparative Genome Analysis of Genes Regulating Compound Inflorescences in Tomato

Inflorescences are the main factor affecting fruit yield. The quantity and quality of inflorescences are closely related to fruit quality and yield. The presence of compound inflorescences in cherry tomatoes is well established, and it has been discovered by chance that compound racemes also exist in tomatoes. To explore the formation of compound inflorescences in tomato, transcriptome sequencing was performed on Moneymaker (MM) and Compound Inflorescence (CI) plants. In-florescences were collected in three periods (early, middle and late) in three replicates, for a total of 18 samples. Data analysis showed that the DEGs were most enriched in metabolic pathways and plant hormone signal transduction pathways. The DEGs were also enriched in the cell cycle pathway, photosynthesis pathway, carbon metabolism pathway and circadian rhythm pathway. We found that the FALSIFLORA (FA), COMPOUND INFLORESCENCE (S) and ANANTHA (AN) genes were involved in compound inflorescence development, not only revealing novel genes but also providing a rich theoretical basis for compound inflorescence development.

Evolution and expression of the MADS-box flowering transition genes AGAMOUS-like 24/SHORT VEGETATIVE PHASE with emphasis in selected Neotropical orchids

In angiosperms the reproductive transition results in the transformation of a vegetative apical meristem (SAM) into an inflorescence meristem (IM), capable of forming floral meristems (FM). Two key players in the flowering transition are AGAMOUS-like 24 (AGL24) and SHORT VEGETATIVE PHASE (SVP). They are eudicot MADS-box paralogs performing opposite roles, as AGL24 positively regulates flowering while SVP represses the reproductive transition in Arabidopsis. We confirm that the Arabidopsis functional reference cannot be readily extrapolated to all eudicots as there are additional duplications of AGL24 in early divergent eudicots and core eudicots with significant sequence variation. In addition, we found that in monocots, two additional independent duplication events have resulted in at least three clades of AGL24/SVP homologs, some only found in Orchidaceae. Protein sequence analyses and comparative evolutionary rates point to higher rates of relaxed negative selection in the Core Eudicot AGL24 B and the Orch SVP-like B clades, in eudicots and monocots respectively. On the other hand, expression data points to plesiomorphic pleiotropic roles of AGL24/SVP genes likely similar to SVP core eudicot genes, and the acquisition of new roles as flowering positive regulators in Core Eudicot AGL24 A genes. Our research presents evidence on the diversification and recruitment of AGL24/SVP homologs in flowering transition in orchids. Although, broad expression of most copies does not allow to determine if they act as flowering repressors or promoters, the restricted expression of some homologs in the SAM suggests putative roles in maintaining the vegetative phase. If so studying in detail the function of AGL24/SVP homologs in orchids is critical to identify putative flowering repressors in a lineage where other canonical repressors remain elusive.

Meristem transitions and plant architecture-learning from domestication for crop breeding

Genetic networks that regulate meristem transitions were recurrent targets of selection during crop domestication and allow fine-tuning of plant architecture for improved crop productivity.

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.

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.

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.

Kiwifruit SVP2 controls developmental and drought-stress pathways

Genome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit. The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy. During kiwifruit development SVP2 has a role in growth inhibition, with high-chill kiwifruit Actinidia deliciosa transgenic lines overexpressing SVP2 showing suppressed bud outgrowth. Transcriptomic analyses of these plants suggests that SVP2 mimics the well-documented abscisic acid (ABA) effect on the plant dehydration response. To corroborate the growth inhibition role of SVP2 in kiwifruit development at the molecular level, we analysed the genome-wide direct targets of SVP2 using chromatin immunoprecipitation followed by high-throughput sequencing in kiwifruit A. chinensis. SVP2 was found to bind to at least 297 target sites in the kiwifruit genome, and potentially modulates 252 genes that function in a range of biological processes, especially those involved in repressing meristem activity and ABA-mediated dehydration pathways. In addition, our ChIP-seq analysis reveals remarkable conservation in mechanism of action between SVP genes of taxonomically distant plant species.

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.

ERAMOSA controls lateral branching in snapdragon

Plant forms display a wide variety of architectures, depending on the number of lateral branches, internode elongation and phyllotaxy. These are in turn determined by the number, the position and the fate of the Axillary Meristems (AMs). Mutants that affect AM determination during the vegetative phase have been isolated in several model plants. Among these genes, the GRAS transcription factor LATERAL SUPPRESSOR (Ls) plays a pivotal role in AM determination during the vegetative phase. Hereby we characterize the phylogenetic orthologue of Ls in Antirrhinum, ERAMOSA (ERA). Our data supported ERA control of AM formation during both the vegetative and the reproductive phase in snapdragon. A phylogenetic analysis combined with an analysis of the synteny of Ls in several species strongly supported the hypothesis that ERA is a phylogenetic orthologue of Ls, although it plays a broader role. During the reproductive phase ERA promotes the establishment of the stem niche at the bract axis but, after the reproductive transition, it is antagonized by the MADS box transcription factor SQUAMOSA (SQUA). Surprisingly double mutant era squa plants display a squa phenotype developing axillary meristems, which can eventually turn into inflorescences or flowers.

Genetic interactions of the unfinished flower development (ufd) mutant support a significant role of the tomato UFD gene in regulating floral organogenesis

Genetic interactions of UFD gene support its specific function during reproductive development of tomato; in this process, UFD could play a pivotal role between inflorescence architecture and flower initiation genes. Tomato (Solanum lycopersicum L.) is a major vegetable crop that also constitutes a model species for the study of plant developmental processes. To gain insight into the control of flowering and floral development, a novel tomato mutant, unfinished flower development (ufd), whose inflorescence and flowers were unable to complete their normal development was characterized using double mutant and gene expression analyses. Genetic interactions of ufd with mutations affecting inflorescence fate (uniflora, jointless and single flower truss) were additive and resulted in double mutants displaying the inflorescence structure of the non-ufd parental mutant and the flower phenotype of the ufd mutant. In addition, ufd mutation promotes an earlier inflorescence meristem termination. Taken together, both results indicated that UFD is not involved in the maintenance of inflorescence meristem identity, although it could participate in the regulatory system that modulates the rate of meristem maturation. Regarding the floral meristem identity, the falsiflora mutation was epistatic to the ufd mutation even though FALSIFLORA was upregulated in ufd inflorescences. In terms of floral organ identity, the ufd mutation was epistatic to macrocalyx, and MACROCALYX expression was differently regulated depending on the inflorescence developmental stage. These results suggest that the UFD gene may play a pivotal role between the genes required for flowering initiation and inflorescence development (such as UNIFLORA, FALSIFLORA, JOINTLESS and SINGLE FLOWER TRUSS) and those required for further floral organ development such as the floral organ identity genes.

Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity

Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (ACS2, COP1, CYC-B, RIN, MSH2, NAC-NOR, PHOT1, PHYA, PHYB and PSY1) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, ACS2 and PHOT1 indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.

Characterization of vegetative inflorescence (mc-vin) mutant provides new insight into the role of MACROCALYX in regulating inflorescence development of tomato

Inflorescence development is a key factor of plant productivity, as it determines flower number. Therefore, understanding the mechanisms that regulate inflorescence architecture is critical for reproductive success and crop yield. In this study, a new mutant, vegetative inflorescence (mc-vin), was isolated from the screening of a tomato (Solanum lycopersicum L.) T-DNA mutant collection. The mc-vin mutant developed inflorescences that reverted to vegetative growth after forming two to three flowers, indicating that the mutated gene is essential for the maintenance of inflorescence meristem identity. The T-DNA was inserted into the promoter region of the MACROCALYX (MC) gene; this result together with complementation test and expression analyses proved that mc-vin is a new knock-out allele of MC. Double combinations between mc-vin and jointless (j) and single flower truss (sft) inflorescence mutants showed that MC has pleiotropic effects on the reproductive phase, and that it interacts with SFT and J to control floral transition and inflorescence fate in tomato. In addition, MC expression was mis-regulated in j and sft mutants whereas J and SFT were significantly up-regulated in the mc-vin mutant. Together, these results provide new evidences about MC function as part of the genetic network regulating the development of tomato inflorescence meristem.

A MADS-box gene NtSVP regulates pedicel elongation by directly suppressing a KNAT1-like KNOX gene NtBPL in tobacco (Nicotiana tabacum L.)

Optimal inflorescence architecture is important for plant reproductive success by affecting the ultimate number of flowers that set fruits and for plant competitiveness when interacting with biotic or abiotic conditions. The pedicel is one of the key contributors to inflorescence architecture diversity. To date, knowledge about the molecular mechanisms of pedicel development is derived from Arabidopsis. Not much is known regarding other plants. Here, an SVP family MADS-box gene, NtSVP, in tobacco (Nicotiana tabacum) that is required for pedicel elongation was identified. It is shown that knockdown of NtSVP by RNA interference (RNAi) caused elongated pedicels, while overexpression resulted in compact inflorescences with much shortened pedicels. Moreover, an Arabidopsis BREVIPEDECELLUS/KNAT1 homologue NtBP-Like (NtBPL) was significantly up-regulated in NtSVP-RNAi plants. Disruption of NtBPL decreased pedicel lengths and shortened cortex cells. Consistent with the presence of a CArG-box at the NtBPL promoter, the direct binding of NtSVP to the NtBPL promoter was demonstrated by yeast one-hybrid assay, electrophoretic mobility shift assay, and dual-luciferase assay, in which NtSVP may act as a repressor of NtBPL. Microarray analysis showed that down-regulation of NtBPL resulted in differential expression of genes associated with a number of hormone biogenesis and signalling genes such as those for auxin and gibberellin. These findings together suggest the function of a MADS-box transcription factor in plant pedicel development, probably via negative regulation of a BP-like class I KNOX gene. The present work thus postulates the conservation and divergence of the molecular regulatory pathways underlying the development of plant inflorescence architecture.

De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission

Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.

Overexpression of SlREV alters the development of the flower pedicel abscission zone and fruit formation in tomato

Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been depicted mainly in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Overexpression of a microRNA166-resistant version of SlREV (35S::REV(Ris)) not only resulted in vegetative abnormalities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at the pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged from the exodermises of the pedicel AZs and that ectopic carpels formed between the first and second whorl of floral buds in 35S::REV(Ris) plants. Transcriptional data suggest that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of the flower pedicel abscission zone, and modulate genes in homeodomain and MADS-box families and hormone pathways during fruit formation. Altogether, these results reveal novel roles of SlREV in tomato flower development and fruit formation.

Florigen and anti-florigen - a systemic mechanism for coordinating growth and termination in flowering plants

Genetic studies in Arabidopsis established FLOWERING LOCUS T (FT) as a key flower-promoting gene in photoperiodic systems. Grafting experiments established unequivocal one-to-one relations between SINGLE FLOWER TRUSS (SFT), a tomato homolog of FT, and the hypothetical florigen, in all flowering plants. Additional studies of SFT and SELF PRUNING (SP, homolog of TFL1), two antagonistic genes regulating the architecture of the sympodial shoot system, have suggested that transition to flowering in the day-neutral and perennial tomato is synonymous with "termination." Dosage manipulation of its endogenous and mobile, graft-transmissible levels demonstrated that florigen regulates termination and transition to flowering in an SP-dependent manner and, by the same token, that high florigen levels induce growth arrest and termination in meristems across the tomato shoot system. It was thus proposed that growth balances, and consequently the patterning of the shoot systems in all plants, are mediated by endogenous, meristem-specific dynamic SFT/SP ratios and that shifts to termination by changing SFT/SP ratios are triggered by the imported florigen, the mobile form of SFT. Florigen is a universal plant growth hormone inherently checked by a complementary antagonistic systemic system. Thus, an examination of the endogenous functions of FT-like genes, or of the systemic roles of the mobile florigen in any plant species, that fails to pay careful attention to the balancing antagonistic systems, or to consider its functions in day-neutral or perennial plants, would be incomplete.

Inferring the gene network underlying the branching of tomato inflorescence

The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior.

Inflorescence development in tomato: gene functions within a zigzag model

Tomato is a major crop plant and several mutants have been selected for breeding but also for isolating important genes that regulate flowering and sympodial growth. Besides, current research in developmental biology aims at revealing mechanisms that account for diversity in inflorescence architectures. We therefore found timely to review the current knowledge of the genetic control of flowering in tomato and to integrate the emerging network into modeling attempts. We developed a kinetic model of the tomato inflorescence development where each meristem was represented by its "vegetativeness" (V), reflecting its maturation state toward flower initiation. The model followed simple rules: maturation proceeded continuously at the same rate in every meristem (dV); floral transition and floral commitment occurred at threshold levels of V; lateral meristems were initiated with a gain of V (ΔV) relative to the V level of the meristem from which they derived. This last rule created a link between successive meristems and gave to the model its zigzag shape. We next exploited the model to explore the diversity of morphotypes that could be generated by varying dV and ΔV and matched them with existing mutant phenotypes. This approach, focused on the development of the primary inflorescence, allowed us to elaborate on the genetic regulation of the kinetic model of inflorescence development. We propose that the lateral inflorescence meristem fate in tomato is more similar to an immature flower meristem than to the inflorescence meristem of Arabidopsis. In the last part of our paper, we extend our thought to spatial regulators that should be integrated in a next step for unraveling the relationships between the different meristems that participate to sympodial growth.

Meristem maturation and inflorescence architecture--lessons from the Solanaceae

Plant apical meristems (AMs) grow continuously by delicately balancing cells leaving at the periphery to form lateral organs with slowly dividing central domain cells that replenish reservoirs of pluripotent cells. This balance can be modified by signals originating from within and outside the meristem, and their integration results in a gradual maturation process that often culminates with the meristem differentiating into a flower. Accompanying this 'meristem maturation' are changes in spacing and size of lateral organs and in rates at which lateral meristems are released from apical dominance. Modulation of distinct meristem maturation parameters through environmental and genetic changes underlies the remarkable diversity of shoot architectures. Here, we discuss recent studies relating the dynamics of meristem maturation with organization of floral branching systems--inflorescences--in the nightshades. From this context, we suggest general principles on how factors coordinating meristem maturation impact shoot organization more broadly.

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

Organ abscission is a key step in a plant's life cycle and is one of the most important agronomic traits for crops. In tomato, two MADS-box genes, JOINTLESS (J) and MACROCAYLYX (MC), have been shown to be implicated in development of the flower abscission zone (AZ), but the molecular mechanisms underlying this process are not well known. We report here that the SEPALLATA (SEP) MADS-box gene SLMBP21 acts as an additional factor for development of the AZ in tomato. We show that knockdown of SLMBP21 abolishes development of the flower AZ, while overexpression of SLMBP21 produces small cells at the proximal section of the pedicel and the peduncle. Bimolecular fluorescence complementation analysis confirms that SLMBP21 interacts with J and MC, and co-immunoprecipitation assays further demonstrates that these three proteins may form higher-order protein complexes. In situ hybridization shows that SLMBP21, J, and MC transcripts accumulate in distinct regions, but overlap at the AZ vasculature. In addition, transactivation assays in yeast show that, of the three interacting proteins, only SLMBP21 can activate reporter gene transcription. RNA-seq analysis furthermore reveals that loss of function of SLMBP21, J, or MC affects a common subset of meristem activity genes including LeWUS and LATERAL SUPPRESSOR that were specifically expressed in the AZ on the tomato flower pedicel. Since SLMBP21 belongs to the FBP9/23 subclade of the SEP gene family, which is absent in Arabidopsis, the SLMBP21-J-MC complex may represent a distinct mechanism for development of the AZ in plants.

CaHAM is autoregulated and regulates CaSTM expression and is required for shoot apical meristem organization in pepper

The angiosperm shoot apical meristem (SAM) is characterized by tightly organized cell layers and zones. The SAM's organization allows it to maintain its indeterminate nature while producing determinate lateral organs. Alterations in SAM gene expression partly account for the immense diversity in plant architecture. The GRAS protein family gene HAIRY MERISTEM (HAM) is an important regulator of SAM organization in Petunia and Arabidopsis. Here we describe CaHAM loss-of-function pepper mutants characterized by an arrested SAM following the formation of several leaves on the primary stem, complete inhibition of axillary meristem development, an expanded tunica domain and trichome formation on the SAM epidermis. CaHAM is expressed in the periphery of the SAM and in the vasculature of young leaves throughout plant development, reaching its highest level in the reproductive growth stage. Analysis of the effect of CaHAM loss-of-function on its own expression showed that CaHAM is negatively autoregulated. Furthermore, CaHAM negatively regulates the expression level and pattern of pepper SHOOT MERISTEMLESS (CaSTM), which is required to maintain the SAM in an undifferentiated state. We conclude that CaHAM is regulated to achieve adjusted functional levels and has a conserved role in controlling SAM maintenance, organization and axillary meristem formation.

Transcriptome analysis of tomato flower pedicel tissues reveals abscission zone-specific modulation of key meristem activity genes

Tomato flower abscises at the anatomically distinct abscission zone that separates the pedicel into basal and apical portions. During abscission, cell separation occurs only at the abscission zone indicating distinctive molecular regulation in its cells. We conducted a transcriptome analysis of tomato pedicel tissues during ethylene promoted abscission. We found that the abscission zone was the most active site with the largest set of differentially expressed genes when compared with basal and apical portions. Gene Ontology analyses revealed enriched transcription regulation and hydrolase activities in the abscission zone. We also demonstrate coordinated responses of hormone and cell wall related genes. Besides, a number of ESTs representing homologs of key Arabidopsis shoot apical meristem activity genes were found to be preferentially expressed in the abscission zone, including WUSCHEL (WUS), KNAT6, LATERAL ORGAN BOUNDARIES DOMAIN PROTEIN 1(LBD1), and BELL-like homeodomain protein 1 (BLH1), as well as tomato axillary meristem genes BLIND (Bl) and LATERAL SUPPRESSOR (Ls). More interestingly, the homologs of WUS and the potential functional partner OVATE FAMILIY PROTEIN (OFP) were subsequently down regulated during abscission while Bl and AGL12 were continuously and specifically induced in the abscission zone. The expression patterns of meristem activity genes corroborate the idea that cells of the abscission zone confer meristem-like nature and coincide with the course of abscission and post-abscission cell differentiation. Our data therefore propose a possible regulatory scheme in tomato involving meristem genes that may be required not only for the abscission zone development, but also for abscission.

Divergences of MPF2-like MADS-domain proteins have an association with the evolution of the inflated calyx syndrome within Solanaceae

The inflated calyx syndrome (ICS) is a post-floral novelty within Solanaceae. Previous work has shown that MPF2-like MADS-box genes have been recruited for the development and evolution of ICS through heterotopic expression from vegetative to floral organs. ICS seems to be a plesiomorphic trait in Physaleae, but it has been secondarily lost in some lineages during evolution. We hypothesized that molecular and functional divergences of MPF2-like proteins might play a role in the loss of ICS. In this study we analyzed the phylogeny, selection and various functions of MPF2-like proteins with respect to the evolution of ICS. Directional selection of MPF2-like orthologs toward evolution of ICS was detected. While auto-activation capacity between proteins varies in yeast, MPF2-like interaction with floral MADS-domain proteins is robustly detected, hence substantiating their integration into the floral developmental programs. Dimerization with A- (MPF3) and E-function (PFSEP1/3) proteins seems to be essential for ICS development within Solanaceae. Moreover, the occurrence of the enlarged sepals, reminiscent of ICS, and MPF2-like interactions with these specific partners were observed in transgenic Arabidopsis. The interaction spectrum relevant to ICS seems to be plesiomorphic, reinforcing the plesiomorphy of this trait. The inability of some MPF2-like to interact with either the A-function or any of the E-function partners characterized is correlated with the loss of ICS in the lineages that showed a MPF2-like expression in the calyx. Our findings suggest that, after recruitment of MPF2-like genes for floral development, diversification in their coding region due to directional selection leads to a modification of the MADS-domain protein interacting spectrum, which might serve as a constraint for the evolution of ICS within Solanaceae.

CaJOINTLESS is a MADS-box gene involved in suppression of vegetative growth in all shoot meristems in pepper

In aiming to decipher the genetic control of shoot architecture in pepper (Capsicum spp.), the allelic late-flowering mutants E-252 and E-2537 were identified. These mutants exhibit multiple pleiotropic effects on the organization of the sympodial shoot. Genetic mapping and sequence analysis indicated that the mutants are disrupted at CaJOINTLESS, the orthologue of the MADS-box genes JOINTLESS and SVP in tomato and Arabidopsis, respectively. Late flowering of the primary and sympodial shoots of Cajointless indicates that the gene functions as a suppressor of vegetative growth in all shoot meristems. While CaJOINTLESS and JOINTLESS have partially conserved functions, the effect on flowering time and on sympodial development in pepper, as well as the epistasis over FASCICULATE, the homologue of the major determinant of sympodial development SELF-PRUNING, is stronger than in tomato. Furthermore, the solitary terminal flower of pepper is converted into a structure composed of flowers and leaves in the mutant lines. This conversion supports the hypothesis that the solitary flowers of pepper have a cryptic inflorescence identity that is suppressed by CaJOINTLESS. Formation of solitary flowers in wild-type pepper is suggested to result from precocious maturation of the inflorescence meristem.

Repression of floral meristem fate is crucial in shaping tomato inflorescence

Tomato is an important crop and hence there is a great interest in understanding the genetic basis of its flowering. Several genes have been identified by mutations and we constructed a set of novel double mutants to understand how these genes interact to shape the inflorescence. It was previously suggested that the branching of the tomato inflorescence depends on the gradual transition from inflorescence meristem (IM) to flower meristem (FM): the extension of this time window allows IM to branch, as seen in the compound inflorescence (s) and falsiflora (fa) mutants that are impaired in FM maturation. We report here that JOINTLESS (J), which encodes a MADS-box protein of the same clade than SHORT VEGETATIVE PHASE (SVP) and AGAMOUS LIKE 24 (AGL24) in Arabidopsis, interferes with this timing and delays FM maturation, therefore promoting IM fate. This was inferred from the fact that j mutation suppresses the high branching inflorescence phenotype of s and fa mutants and was further supported by the expression pattern of J, which is expressed more strongly in IM than in FM. Most interestingly, FA - the orthologue of the Arabidopsis LEAFY (LFY) gene - shows the complementary expression pattern and is more active in FM than in IM. Loss of J function causes premature termination of flower formation in the inflorescence and its reversion to a vegetative program. This phenotype is enhanced in the absence of systemic florigenic protein, encoded by the SINGLE FLOWER TRUSS (SFT) gene, the tomato orthologue of FLOWERING LOCUS T (FT). These results suggest that the formation of an inflorescence in tomato requires the interaction of J and a target of SFT in the meristem, for repressing FA activity and FM fate in the IM.

Flower development in garlic: the ups and downs of gaLFY expression

The lack of sexual processes prohibits genetic studies and conventional breeding in commercial cultivars of garlic. Recent restoration of garlic flowering ability by environmental manipulations has opened new avenues for physiological and genetic studies. The LEAFY homologue gaLFY has been shown to be involved in the floral development, while two alternatively spliced gaLFY transcripts are expressed in flowering genotypes. In the present work, quantitative real-time PCR and two techniques of RNA in situ hybridization were employed to analyze spatiotemporal expression patterns of the gaLFY during consequent stages of the garlic reproductive process. Temporal accumulation of gaLFY is strongly associated with reproductive organs, significantly increased during florogenesis and gametogenesis, and is down-regulated in the vegetative meristems and topsets in the inflorescence. The two alternative transcripts of the gene show different expression patterns: a high level of the long gaLFY transcript coincided only with floral transition, while further up-regulation of this gene in the reproductive organs is associated mainly with the short gaLFY transcript. It is concluded that gaLFY is involved at different stages of the sexual reproduction of garlic. These new insights broaden our basic understanding of flower biology of garlic and help to establish conventional and molecular breeding systems for this important crop.

Constitutive co-suppression of the GA 20-oxidase1 gene in tomato leads to severe defects in vegetative and reproductive development

To dissect the role of gibberellins in tomato development, we have constitutively down-regulated the gene GA 20-oxidase1 (GA20ox1). Plants co-suppressed for GA20ox1 (referred to as CO-6 plants) showed vegetative defects typical of GA deficiency such as darker and mis-shaped leaves and dwarfism. CO-6 plants flowered as the controls, although their flowers had subtle defects in the pedicel and in organ insertion. Analysis of male development revealed defects before, during and after meiosis, and a final pollen viability of 22%. The development of female organs and gametes appeared normal. Pollination experiments indicated that the pollen produced by CO-6 plants was able to fertilize control ovaries, but the analysis of the progeny showed that the construct was not transmitted. Ovaries of CO-6 plants showed high fruit set and normal fruit development when pollinated with control pollen. However these fruits were completely seedless due to a stenospermocarpic behaviour that was evidenced by callose layering in the endothelium between 7 and 15 days after pollination. We conclude that GA20ox1 in tomato exerts specific developmental roles that are not redundantly shared with other members of this gene family. For reproductive male development, silencing of this gene is detrimental for pollen production and either gametophytically lethal or severely hampering seed germination. In the pistil, the co-suppression construct does not affect the progamic phase, nor fruit set and growth, but it interferes with seed development after fertilization leading to seed abortion.

Flowering response of the uniflora:blind:self-pruning and jointless:uniflora:self-pruning tomato (Solanum lycopersicum) triple mutants

Tomato (Solanum lycopersicum) is a day-neutral plant with a sympodial growth habit. Triple mutants were produced in order to investigate the genetic interactions in the flowering regulation of this species in the initial and sympodial segments. The jointless:uniflora:self-pruning and uniflora:blind:self-pruning triple mutants were produced by crossing the jointless:uniflora and uniflora:blind double mutants with the uniflora:self-pruning double mutant. The phenotype of the triple mutants was characterized and the expression of the affected genes was studied in the uniflora (uf) mutant through semi-quantitative reverse transcriptase polymerase chain reaction (PCR). The triple mutants produced solitary flowers, as their uf parent, instead of inflorescences. They were both late flowering in the initial segment with a flowering time intermediate between their parental double mutants. The flowering time of the sympodial segments was delayed in the jointless:uniflora:self-pruning triple mutant while the uniflora:blind:self-pruning triple mutant did not initiate sympodial segments. The expression of the studied genes was not markedly affected by the uf mutation. These results suggest that floral transition of the primary shoot and of sympodial segments is regulated differently in tomato. The UNIFLORA (UF) gene acts upstream of the other investigated genes in controlling reproductive structure and flowering time of the initial segment although their expression does not seem to be affected by the uf mutation. In the sympodial segments, the self-pruning determinate phenotype is strengthened by the blind mutation and suppressed by the jointless mutation.

The MADS-domain protein MPF1 of Physalis floridana controls plant architecture, seed development and flowering time

Floral and vegetative development of plants is dependent on the combinatorial action of MADS-domain transcription factors. Members of the STMADS11 subclade, such as MPF1 of Physalis, are abundantly expressed in leaves as well as in floral organs, but their function is not yet clear. Our studies with transgenic Arabidopsis that over-express MPF1 suggest that MPF1 interacts with SOC1 to determine flowering time. However, MPF1 RNAi-mediated knockdown Physalis plants revealed a complex phenotype with changes in flowering time, plant architecture and seed size. Flowering of these plants was delayed by about 20% as compared to wild type. Expression of PFLFY is upregulated in the MPF1 RNAi lines, while PFFT and MPF3 genes are strongly repressed. MPF1 interacts with a subset of MADS-domain factors, namely with PFSOC1 in planta, and with PFSEP3 and PFFUL in yeast, supporting a regulatory role for this protein in flowering. The average size of seeds produced by the transgenic MPF1 RNAi plants is increased almost twofold. The height of these plants is also increased about twofold, but most axillary buds are stunted when compared to controls. Taken together, this suggests that members of the STMADS11 subclade act as positive regulators of flowering but have diverse functions in plant growth.

Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach

BACKGROUND

Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach. These genes are not expressed in the peach mutant evergrowing, which fails to cease growth and enter dormancy under dormancy-inducing conditions. We analyzed the phylogenetic relationships among and the rates and patterns of molecular evolution within DAM genes in the phylogenetic context of the MADS-box gene family.

RESULTS

The peach DAM genes grouped with the SVP/StMADS11 lineage of type II MIKCC MADS-box genes. Phylogenetic analyses suggest that the peach SVP/StMADS11-like gene family, which contains significantly more members than annual model plants, expanded through serial tandem gene duplication. We found evidence of strong purifying selection acting to constrain functional divergence among the peach DAM genes and only a single codon, located in the C-terminal region, under significant positive selection.

CONCLUSION

Because all DAM genes are expressed in peach and are subjected to strong purifying selection we suggest that the duplicated genes have been maintained by subfunctionalization and/or neofunctionalization. In addition, this pattern of selection suggests that the DAM genes are important for peach growth and development.

Characterization and structural analysis of wild type and a non-abscission mutant at the development funiculus (Def) locus in Pisum sativum L

BACKGROUND

In pea seeds (Pisum sativum L.), the Def locus defines an abscission event where the seed separates from the funicle through the intervening hilum region at maturity. A spontaneous mutation at this locus results in the seed failing to abscise from the funicle as occurs in wild type peas. In this work, structural differences between wild type peas that developed a distinct abscission zone (AZ) between the funicle and the seed coat and non-abscission def mutant were characterized.

RESULTS

A clear abscission event was observed in wild type pea seeds that were associated with a distinct double palisade layers at the junction between the seed coat and funicle. Generally, mature seeds fully developed an AZ, which was not present in young wild type seeds. The AZ was formed exactly below the counter palisade layer. In contrast, the palisade layers at the junction of the seed coat and funicle were completely absent in the def mutant pea seeds and the cells in this region were seen to be extensions of surrounding parenchymatous cells.

CONCLUSION

The Def wild type developed a distinct AZ associated with palisade layer and counterpalisade layer at the junction of the seed coat and funicle while the def mutant pea seed showed non-abscission and an absence of the double palisade layers in the same region. We conclude that the presence of the double palisade layer in the hilum of the wild type pea seeds plays an important structural role in AZ formation by delimiting the specific region between the seed coat and the funicle and may play a structural role in the AZ formation and subsequent detachment of the seed from the funicle.

PnMADS1, encoding an StMADS11-clade protein, acts as a repressor of flowering in Pharbitis nil

We previously isolated PnMADS1, a MADS-box transcription factor and member of the functionally diverse StMADS11 clade of the MADS-box family, from Pharbitis nil, which is a typical SD plant. However, its precise function remained unclear. To investigate the biological role of PnMADS1, and especially its involvement in flowering, we constructed transgenic P. nil plants that overexpresses or underexpresses PnMADS1. PnMADS1-RNAi transformants had an increased number of flower buds, whereas overexpression of PnMADS1 led to a decrease in the number of flower buds, although both transgenic plants maintained the photoperiodic responses of flowering. These results suggest that PnMADS1 negatively regulates floral evocation from the vegetative phase to the reproductive phase but it has no essential role in floral induction by photoperiodic signals. Results of yeast two-hybrid experiments revealed that PnMADS1 can interact with itself, suggesting that this protein functions in floral evocation as a homodimer. PnMADS1 also interacts with PnSAH3, an AP1-clade protein, suggesting that PnMADS1 has a functional role in flower formation as a heterodimer with other MADS-box protein(s).

Rice SVP-group MADS-box proteins, OsMADS22 and OsMADS55, are negative regulators of brassinosteroid responses

Most short vegetative phase (SVP)-group MADS-box genes control meristem identity and flowering time. Among the three SVP-group genes in rice, OsMADS47 has been reported as a negative regulator of brassinosteroid (BR) responses. Here, we investigated the functional roles of two close homologs, OsMADS22 and OsMADS55, by generating single, double and triple RNAi lines and overexpression lines. Analyses of the plants showed that their roles in regulating meristem identity are well conserved; however, the involvement of these genes in determining flowering time has diversified. Most importantly, OsMADS55 works as a major negative regulator of BR responses, and OsMADS22 functions to support OsMADS55. Whereas single OsMADS55 RNAi plants display weak BR responses in the lamina joint (LJ), OsMADS22-OsMADS55 double and OsMADS22-OsMADS47-OsMADS55 triple RNAi plants manifest dramatic BR responses with regard to LJ inclination, coleoptile elongation and senescence. Stem elongation is also notably reduced in the double and triple RNAi plants, probably because of BR oversensitivity. Expression analyses indicate the diversified roles in age-dependent BR responses. Altogether, our study demonstrates that all three rice SVP-group genes work as negative regulators of BR responses, but that their spatial and temporal roles are diversified.

The rice StMADS11-like genes OsMADS22 and OsMADS47 cause floral reversions in Arabidopsis without complementing the svp and agl24 mutants

During floral induction and flower development plants undergo delicate phase changes which are under tight molecular control. MADS-box transcription factors have been shown to play pivotal roles during these transition phases. SHORT VEGETATIVE PHASE (SVP) and AGAMOUS LIKE 24 (AGL24) are important regulators both during the transition to flowering and during flower development. During vegetative growth they exert opposite roles on floral transition, acting as repressor and promoter of flowering, respectively. Later during flower development they act redundantly as negative regulators of AG expression. In rice, the orthologues of SVP and AGL24 are OsMADS22, OsMADS47, and OsMADS55 and these three genes are involved in the negative regulation of brassinosteroid responses. In order to understand whether these rice genes have maintained the ability to function as regulators of flowering time in Arabidopsis, complementation tests were performed by expressing OsMADS22 and OsMADS47 in the svp and agl24 mutants. The results show that the rice genes are not able to complement the flowering-time phenotype of the Arabidopsis mutants, indicating that they are biologically inactive in Arabidopsis. Nevertheless, they cause floral reversions, which mimic the SVP and AGL24 floral overexpressor phenotypes. Yeast two-hybrid analysis suggests that these floral phenotypes are probably the consequence of protein interactions between OsMADS22 and OsMADS47 and other MADS-box proteins which interfere with the formation of complexes required for normal flower development.