Starch deficiency in tomato causes transcriptional reprogramming that modulates fruit development, metabolism, and stress responses.

Tomato (Solanum lycopersicum) fruit store carbon as starch during early development and mobilize it at the onset of ripening. Starch accumulation has been suggested to buffer fluctuations in carbon supply to the fruit under abiotic stress, and contribute to sugar levels in ripe fruit. However, the role of starch accumulation and metabolism during fruit development is still unclear. Here we show that the tomato mutant adpressa (adp) harbors a mutation in a gene encoding the small subunit of ADP-glucose pyrophosphorylase that abolishes starch synthesis. The disruption of starch biosynthesis causes major transcriptional and metabolic remodeling in adp fruit but only minor effects on fruit size and ripening. Changes in gene expression and metabolite profiles indicate that the lack of carbon flow into starch increases levels of soluble sugars during fruit growth, triggers a readjustment of central carbohydrate and lipid metabolism, and activates growth and stress protection pathways. Accordingly, adp fruits are remarkably resistant to blossom-end rot, a common physiological disorder induced by environmental stress. Our results provide insights into the effects of perturbations of carbohydrate metabolism on tomato fruit development, with potential implications for the enhancement of protective mechanisms against abiotic stress in fleshy fruit.

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development.

Fruit formation and early development involve a range of physiological and morphological transformations of the various constituent tissues of the ovary. These developmental changes vary considerably according to tissue type, but molecular analyses at an organ-wide level inevitably obscure many tissue-specific phenomena. We used laser-capture microdissection coupled to high-throughput RNA sequencing to analyze the transcriptome of ovaries and fruit tissues of the wild tomato species Solanum pimpinellifolium. This laser-capture microdissection-high-throughput RNA sequencing approach allowed quantitative global profiling of gene expression at previously unobtainable levels of spatial resolution, revealing numerous contrasting transcriptome profiles and uncovering rare and cell type-specific transcripts. Coexpressed gene clusters linked specific tissues and stages to major transcriptional changes underlying the ovary-to-fruit transition and provided evidence of regulatory modules related to cell division, photosynthesis, and auxin transport in internal fruit tissues, together with parallel specialization of the pericarp transcriptome in stress responses and secondary metabolism. Analysis of transcription factor expression and regulatory motifs indicated putative gene regulatory modules that may regulate the development of different tissues and hormonal processes. Major alterations in the expression of hormone metabolic and signaling components illustrate the complex hormonal control underpinning fruit formation, with intricate spatiotemporal variations suggesting separate regulatory programs.

Mechanisms regulating auxin action during fruit development.

Auxin controls many aspects of fruit development, including fruit set and growth, ripening and abscission. However, the mechanisms by which auxin regulates these processes are still poorly understood. While it is generally agreed that precise spatial and temporal control of auxin distribution and signaling are required for fruit development, the dynamics of auxin biosynthesis and the mechanisms for its transport to different fruit tissues are mostly unknown. Despite major advances in elucidating many aspects of auxin biology in vegetative tissues, until recently, the nature and importance of auxin metabolism, transport and signaling during fruit ontogeny remained obscure. In this review, we summarize recent research that has started to elucidate the molecular mechanisms by which auxin is produced and transported in the fruit and to unravel the complexity of auxin signaling during fruit development. We also discuss recent approaches used to reveal the genes and regulatory networks that mediate cell and tissue-specific control of auxin levels in the developing fruit.

Evaluating auxin distribution in tomato (Solanum lycopersicum) through an analysis of the PIN and AUX/LAX gene families.

The temporal and spatial control of auxin distribution has a key role in the regulation of plant growth and development, and much has been learnt about the mechanisms that influence auxin pools and gradients in vegetative tissues, particularly in Arabidopsis. For example polar auxin transport, mediated by PIN and AUX/LAX proteins, is central to the control of auxin distribution. In contrast, very little information is known about the dynamics of auxin distribution and the molecular basis of its transport within and between fruit tissues, despite the fact that auxin regulates many aspects of fruit development, which include fruit formation, expansion, ripening and abscission. In addition, functional information regarding the key regulators of auxin fluxes during both vegetative and reproductive development in species other than Arabidopsis is scarce. To address these issues, we have investigated the spatiotemporal distribution of auxin during tomato (Solanum lycopersicum) fruit development and the function of the PIN and AUX/LAX gene families. Differential concentrations of auxin become apparent during early fruit growth, with auxin levels being higher in internal tissues than in the fruit pericarp and the pattern of auxin accumulation depended on polar transport. Ten tomato PIN (SlPIN1 to 10) and five AUX/LAX (SlLAX1 to 5) genes were identified and found to display heterogeneous expression patterns, with tissue and developmental-stage specificity. RNAi-mediated co-silencing of SlPIN4 and SlPIN3 did not affect fruit development, which suggested functional redundancy of PIN proteins, but did lead to a vegetative phenotype, and revealed a role for these genes in the regulation of tomato shoot architecture.

N-glycan production in the endoplasmic reticulum of plants.

N-glycosylation is a complex process that encompasses the biosynthesis and modification of sugar moieties in the endoplasmic reticulum (ER) and Golgi. The ER-localized steps of N-glycan production in plants have received relatively little attention, despite their emerging roles in stress responses. Here, we integrate information on the molecular components underlying the three stages of N-glycan production: lipid-linked oligosaccharide synthesis, co-translational oligosaccharyl-transfer and quality control of the folded glycoprotein in the ER. The relative importance of each step for N-glycosylation and plant performance is evaluated on the basis of studies with inhibitors and mutant phenotypes. Finally, we highlight the increasing evidence for crosstalk between N-glycan production and defence responses in plants and discuss the practical implications for pathogen resistance.

EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture.

The root system is essential for the growth and development of plants. In addition to anchoring the plant in the ground, it is the site of uptake of water and minerals from the soil. Plant root systems show an astonishing plasticity in their architecture, which allows for optimal exploitation of diverse soil structures and conditions. The signalling pathways that enable plants to sense and respond to changes in soil conditions, in particular nutrient supply, are a topic of intensive research, and root system architecture (RSA) is an important and obvious phenotypic output. At present, the quantitative description of RSA is labour intensive and time consuming, even using the currently available software, and the lack of a fast RSA measuring tool hampers forward and quantitative genetics studies. Here, we describe EZ-Rhizo: a Windows-integrated and semi-automated computer program designed to detect and quantify multiple RSA parameters from plants growing on a solid support medium. The method is non-invasive, enabling the user to follow RSA development over time. We have successfully applied EZ-Rhizo to evaluate natural variation in RSA across 23 Arabidopsis thaliana accessions, and have identified new RSA determinants as a basis for future quantitative trait locus (QTL) analysis.