Transcriptome Analysis to Explore the Cause of the Formation of Different Inflorescences in Tomato

The number of inflorescence branches is an important agronomic character of tomato. The meristem differentiation and development pattern of tomato inflorescence is complex and its regulation mechanism is very different from those of other model plants. Therefore, in order to explore the cause of tomato inflorescence branching, transcriptome analysis was conducted on two kinds of tomato inflorescences (single racemes and compound inflorescences). According to the transcriptome data analysis, there were many DEGs of tomato inflorescences at early, middle, and late stages. Then, GO and KEGG enrichments of DEGs were performed. DEGs are mainly enriched in metabolic pathways, biohormone signaling, and cell cycle pathways. According to previous studies, DEGs were mainly enriched in metabolic pathways, and FALSIFLORA (FA) and ANANTHA (AN) genes were the most notable of 41 DEGs related to inflorescence branching. This study not only provides a theoretical basis for understanding inflorescence branching, but also provides a new idea for the follow-up study of inflorescence.

The auxin-responsive transcription factor SlDOF9 regulates inflorescence and flower development in tomato

Understanding the mechanisms underlying differentiation of inflorescence and flower meristems is essential towards enlarging our knowledge of reproductive organ formation and to open new prospects for improving yield traits. Here, we show that SlDOF9 is a new modulator of floral differentiation in tomato. CRISPR/Cas9 knockout strategy uncovered the role of SlDOF9 in controlling inflorescence meristem and floral meristem differentiation via the regulation of cell division genes and inflorescence architecture regulator LIN. Tomato dof9-KO lines have more flowers in both determinate and indeterminate cultivars and produce more fruit upon vibration-assisted fertilization. SlDOF9 regulates inflorescence development through an auxin-dependent ARF5-DOF9 module that seems to operate, at least in part, differently in Arabidopsis and tomato. Our findings add a new actor to the complex mechanisms underlying reproductive organ differentiation in flowering plants and provide leads towards addressing the diversity of factors controlling the transition to reproductive organs.

The Halophyte Species Solanum chilense Dun. Maintains Its Reproduction despite Sodium Accumulation in Its Floral Organs

Salinity is a growing global concern that affects the yield of crop species, including tomato (Solanum lycopersicum). Its wild relative Solanum chilense was reported to have halophyte properties. We compared salt resistance of both species during the reproductive phase, with a special focus on sodium localization in the flowers. Plants were exposed to NaCl from the seedling stage. Salinity decreased the number of inflorescences in both species but the number of flowers per inflorescence and sepal length only in S. lycopersicum. External salt supply decreased the stamen length in S. chilense, and it was associated with a decrease in pollen production and an increase in pollen viability. Although the fruit set was not affected by salinity, fruit weight and size decreased in S. lycopersicum. Concentrations and localization of Na, K, Mg, and Ca differed in reproductive structures of both species. Inflorescences and fruits of S. chilense accumulated more Na than S. lycopersicum. Sodium was mainly located in male floral organs of S. chilense but in non-reproductive floral organs in S. lycopersicum. The expression of Na transporter genes differed in flowers of both species. Overall, our results indicated that S. chilense was more salt-resistant than S. lycopersicum during the reproductive phase and that differences could be partly related to dissimilarities in element distribution and transport in flowers.

SISTER OF TM3 activates FRUITFULL1 to regulate inflorescence branching in tomato

Selection for favorable inflorescence architecture to improve yield is one of the crucial targets in crop breeding. Different tomato varieties require distinct inflorescence-branching structures to enhance productivity. While a few important genes for tomato inflorescence-branching development have been identified, the regulatory mechanism underlying inflorescence branching is still unclear. Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. High expression levels of STM3 underlie the highly inflorescence-branching phenotype in ST024. STM3 is expressed in both vegetative and reproductive meristematic tissues and in leaf primordia and leaves, indicative of its function in flowering time and inflorescence-branching development. Transcriptome analysis shows that several floral development-related genes are affected by STM3 mutation. Among them, FRUITFULL1 (FUL1) is downregulated in stm3cr mutants, and its promoter is bound by STM3 by ChIP-qPCR analysis. EMSA and dual-luciferase reporter assays further confirmed that STM3 could directly bind the promoter region to activate FUL1 expression. Mutation of FUL1 could partially restore inflorescence-branching phenotypes caused by high STM3 expression in ST024. Our findings provide insights into the molecular and genetic mechanisms underlying inflorescence development in tomato.

Fruit weight is controlled by Cell Size Regulator encoding a novel protein that is expressed in maturing tomato fruits

Increases in fruit weight of cultivated vegetables and fruits accompanied the domestication of these crops. Here we report on the positional cloning of a quantitative trait locus (QTL) controlling fruit weight in tomato. The derived allele of Cell Size Regulator (CSR-D) increases fruit weight predominantly through enlargement of the pericarp areas. The expanded pericarp tissues result from increased mesocarp cell size and not from increased number of cell layers. The effect of CSR on fruit weight and cell size is found across different genetic backgrounds implying a consistent impact of the locus on the trait. In fruits, CSR expression is undetectable early in development from floral meristems to the rapid cell proliferation stage after anthesis. Expression is low but detectable in growing fruit tissues and in or around vascular bundles coinciding with the cell enlargement stage of the fruit maturation process. CSR encodes an uncharacterized protein whose clade has expanded in the Solanaceae family. The mutant allele is predicted to encode a shorter protein due to a 1.4 kb deletion resulting in a 194 amino-acid truncation. Co-expression analyses and GO term enrichment analyses suggest association of CSR with cell differentiation in fruit tissues and vascular bundles. The derived allele arose in Solanum lycopersicum var cerasiforme and appears completely fixed in many cultivated tomato’s market classes. This finding suggests that the selection of this allele was critical to the full domestication of tomato from its intermediate ancestors.

Starting about 10,000 years ago, during the Neolithic period, human societies began the transformation from a hunting and gathering-dependent lifestyle to an agrarian lifestyle. This transformation was accompanied by plant and animal domestication. Tomato shows a huge increase in fruit weight that has arisen as a consequence of its domestication. We identified a gene that encodes a poorly characterized protein that controls fruit weight in tomato. The mutation that led to the increase in fruit weight arose early during the cultivation of tomato and is now incorporated in all large tomato varieties. The gene regulates cell size in the fruit and is called Cell Size Regulator. The increases in cell size are proposed to relate to cellular maturation that accompanies fruit growth.

The control of tomato fruit elongation orchestrated by sun, ovate and fs8.1 in a wild relative of tomato

Within the cultivated tomato germplasm, sun, ovate and fs8.1 are the three predominant QTLs controlling fruit elongation. Although SUN and OVATE have been cloned, their role in plant growth and development are not well understood. To compare and contrast the effects of the three QTLs in a homogeneous background, we developed near isogenic lines (NILs) in the wild species Solanum pimpinellifolium LA1589 background. We carried out detailed morphological characterization of reproductive and vegetative organs in the single, double and triple NILs and determined the epistatic interactions of the three loci affecting fruit shape. The phenotypic evaluations demonstrated that the three loci regulate unique aspects of ovary and fruit elongation and in different temporal manners. The strongest effect on organ shape was caused by sun. In addition to fruit shape, sun also affected leaf and sepal elongation and stem thickness. The synergistic interaction between sun and ovate or fs8.1 suggested that the pathways involving SUN, OVATE and the gene(s) underlying fs8.1 may converge at a common node. The results of an extensive profiling analysis suggested that the degree of fruit elongation was not related to the accumulation of any of the classical hormones.

Capsicum annuum S (CaS) promotes reproductive transition and is required for flower formation in pepper (Capsicum annuum)

The genetic control of the transition to flowering has mainly been studied in model species, while few data are available in crop species such as pepper (Capsicum spp.). To elucidate the genetic control of the transition to flowering in pepper, mutants that lack flowers were isolated and characterized. Genetic mapping and sequencing allowed the identification of the gene disrupted in the mutants. Double mutants and expression analyses were used to characterize the relationships between the mutated gene and other genes controlling the transition to flowering and flower differentiation. The mutants were characterized by a delay in the initiation of sympodial growth, a delay in the termination of sympodial meristems and complete inhibition of flower formation. Capsicum annuum S (CaS), the pepper (Capsicum annuum) ortholog of tomato (Solanum lycopersicum) COMPOUND INFLORESCENCE and petunia (Petunia hybrida) EVERGREEN, was found to govern the mutant phenotype. CaS is required for the activity of the flower meristem identity gene Ca-ANANTHA and does not affect the expression of CaLEAFY. CaS is epistatic over other genes controlling the transition to flowering with respect to flower formation. Comparative homologous mutants in the Solanaceae indicate that CaS has uniquely evolved to have a critical role in flower formation, while its role in meristem maturation is conserved in pepper, tomato and petunia.

What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape

Domestication of fruit and vegetables resulted in a huge diversity of shapes and sizes of the produce. Selections that took place over thousands of years of alleles that increased fruit weight and altered shape for specific culinary uses provide a wealth of resources to study the molecular bases of this diversity. Tomato (Solanum lycopersicum) evolved from a wild ancestor (S. pimpinellifolium) bearing small and round edible fruit. Molecular genetic studies led to the identification of two genes selected for fruit weight: FW2.2 encoding a member of the Cell Number Regulator family; and FW3.2 encoding a P450 enzyme and the ortholog of KLUH. Four genes were identified that were selected for fruit shape: SUN encoding a member of the IQD family of calmodulin-binding proteins leading to fruit elongation; OVATE encoding a member of the OVATE family proteins involved in transcriptional repression leading to fruit elongation; LC encoding most likely the ortholog of WUSCHEL controlling meristem size and locule number; FAS encoding a member in the YABBY family controlling locule number leading to flat or oxheart shape. For this article, we will provide an overview of the putative function of the known genes, when during floral and fruit development they are hypothesized to act and their potential importance in regulating morphological diversity in other fruit and vegetable crops.

Inflorescence development in petunia: through the maze of botanical terminology

Flowering plants have developed many ways to arrange their flowers. A flower-bearing branch or system of branches is called an inflorescence. The number of flowers that an inflorescence contains ranges from a single flower to endless flower-clusters. Over the past centuries, botanists have classified inflorescences based on their morphology, which has led to an unfortunate maze of complex botanical terminology. With the rise of molecular developmental biology, research has become increasingly focused on how inflorescences develop, rather than on their morphology. It is the decisions taken by groups of stem cells at the growing tips of shoots, called meristems, on when and where to produce a flower or a shoot that specify the course of inflorescence development. Modelling is a helpful aid to follow the consequences of these decisions for inflorescence development. The so-called transient model can produce the broad inflorescence types: cyme, raceme, and panicle, into which most inflorescences found in nature can be classified. The analysis of several inflorescence branching mutants has led to a solid understanding of cymose inflorescence development in petunia (Petunia hybrida). The cyme of petunia is a distinct body plan compared with the well-studied racemes of Arabidopsis and Antirrhinum, which provides an excellent opportunity to study evolutionary developmental biology (evo-devo) related questions. However, thus far, limited use has been made of this opportunity, which may, at least in part, be due to researchers getting lost in the terminology. Some general issues are discussed here, while focusing on inflorescence development in petunia.

The key role of morphology in modelling inflorescence architecture

Emerging evidence suggests that certain key genes control the branching patterns of flower-bearing axes (i.e. inflorescences) in angiosperms. However, the terminology surrounding inflorescence architecture is heavily typological and suffers from radically divergent definitions of terms that together reduce the value of some recent predictive models. We attempt to resolve the paradox of conflicting definitions of the same terms and clarify the assumptions surrounding this complex subject. We argue in favour of uniform terminology and against over-simplification. The valid conceptual platforms for modelling should be clearly defined and should adequately reflect observed structural diversity.

Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape

BACKGROUND

Universally accepted landmark stages are necessary to highlight key events in plant reproductive development and to facilitate comparisons among species. Domestication and selection of tomato resulted in many varieties that differ in fruit shape and size. This diversity is useful to unravel underlying molecular and developmental mechanisms that control organ morphology and patterning. The tomato fruit shape gene SUN controls fruit elongation. The most dramatic effect of SUN on fruit shape occurs after pollination and fertilization although a detailed investigation into the timing of the fruit shape change as well as gene expression profiles during critical developmental stages has not been conducted.

RESULTS

We provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new floral and fruit landmarks to present a framework for tomato developmental studies. In addition, gene expression profiles of three key stages in floral and fruit development are presented, namely floral buds 10 days before anthesis (floral landmark 7), anthesis-stage flowers (floral landmark 10 and fruit landmark 1), and 5 days post anthesis fruit (fruit landmark 3). To demonstrate the utility of the landmarks, we characterize the tomato shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post-anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. The expression profiles of the NILs that differ at sun show that only 34 genes were differentially expressed and most of them at a less than 2-fold difference.

CONCLUSION

The landmarks for flower and fruit development in tomato were outlined and integrated with the effect of SUN on fruit shape. Although we did not identify many genes differentially expressed in the NILs that differ at the sun locus, higher or lower transcript levels for many genes involved in phytohormone biosynthesis or signaling as well as organ identity and patterning of tomato fruit were found between developmental time points.