Wild Crop Relatives: Genomic and Breeding Resources

The ripening of fleshy fruits represents the unique coordination of developmental and biochemical pathways leading to changes in color, texture, aroma, and nutritional quality of mature seed-bearing plant organs. The gaseous plant hormone ethylene plays a key regulatory role in ripening of many fruits, including some representing important contributors of nutrition and fiber to the diets of humans. Examples include banana, apple, pear, most stone fruits, melons, squash, and tomato. Molecular exploration of the role of ethylene in fruit ripening has led to the affirmation that mechanisms of ethylene perception and response defined in the model system Arabidopsis thaliana are largely conserved in fruit crop species, although sometimes with modifications in gene family size and regulation. Positional cloning of genes defined by ripening defect mutations in the model fruit system tomato have recently led to the identification of both novel components of ethylene signal transduction and unique transcription factor functions influencing ripening-related ethylene production. Here we summarize recent developments in the regulation of fruit ripening with an emphasis on the regulation of ethylene synthesis, perception, and response.

Ethylene and Fruit Ripening

Analysis of tomato (Solanum lycopersicum) small RNA data sets revealed the presence of a regulatory cascade affecting disease resistance. The initiators of the cascade are microRNA members of an unusually diverse superfamily in which miR482 and miR2118 are prominent members. Members of this superfamily are variable in sequence and abundance in different species, but all variants target the coding sequence for the P-loop motif in the mRNA sequences for disease resistance proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) motifs. We confirm, using transient expression in Nicotiana benthamiana, that miR482 targets mRNAs for NBS-LRR disease resistance proteins with coiled-coil domains at their N terminus. The targeting causes mRNA decay and production of secondary siRNAs in a manner that depends on RNA-dependent RNA polymerase 6. At least one of these secondary siRNAs targets other mRNAs of a defense-related protein. The miR482-mediated silencing cascade is suppressed in plants infected with viruses or bacteria so that expression of mRNAs with miR482 or secondary siRNA target sequences is increased. We propose that this process allows pathogen-inducible expression of NBS-LRR proteins and that it contributes to a novel layer of defense against pathogen attack.

A MicroRNA Superfamily Regulates Nucleotide Binding Site–Leucine-Rich Repeats and Other mRNAs

Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future?

The transition of fleshy fruit maturation to ripening is regulated by exogenous and endogenous signals that coordinate the transition of the fruit to a final state of attractiveness to seed dispersing organisms. Tomato is a model for biology and genetics regulating specific ripening pathways including ethylene, carotenoids and cell wall metabolism in addition to upstream signaling and transcriptional regulators. Ripening-associated transcription factors described to date including the RIN-MADS, CLEAR NON-RIPENING, TAGL1 and LeHB-1 genes all encode positive regulators of ripening phenomena. Here we describe an APETALA2 transcription factor (SlAP2a) identified through transcriptional profiling of fruit maturation that is induced during, and which negatively regulates, tomato fruit ripening. RNAi repression of SlAP2a results in fruits that over-produce ethylene, ripen early and modify carotenoid accumulation profiles by altering carotenoid pathway flux. These results suggest that SlAP2a functions during normal tomato fruit ripening as a modulator of ripening activity and acts to balance the activities of positive ripening regulators.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2010.04384.x

A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening

The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, The Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the 'International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation'. The goal of this grassroots initiative, launched in November 2003, is to establish a network of information, resources and scientists to ultimately tackle two of the most significant questions in plant biology and agriculture: (1) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (2) How can a deeper understanding of the genetic basis of plant diversity be harnessed to better meet the needs of society in an environmentally friendly and sustainable manner? The Solanaceae and closely related species such as coffee, which are included in the scope of the SOL project, are ideally suited to address both of these questions. The first step of the SOL project is to use an ordered BAC approach to generate a high quality sequence for the euchromatic portions of the tomato as a reference for the Solanaceae. Due to the high level of macro and micro-synteny in the Solanaceae the BAC-by-BAC tomato sequence will form the framework for shotgun sequencing of other species. The starting point for sequencing the genome is BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers from the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These seed BACs will be used as anchors from which to radiate the tiling path using BAC end sequence data. Annotation will be performed according to SOL project guidelines. All the information generated under the SOL umbrella will be made available in a comprehensive website. The information will be interlinked with the ultimate goal that the comparative biology of the Solanaceae-and beyond-achieves a context that will facilitate a systems biology approach.

/pdf/the-tomato-sequencing-project-the-first-cornerstone-of-the-1ckb62dg7q.pdf

The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL)

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The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL)