title: Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation.
abstract: Solanum lycopersicum (tomato) and its wild relatives harbor genetic diversity that yields heritable variation in fruit chemistry that could be exploited to identify genes regulating their synthesis and accumulation. Carotenoids, for example, are essential in plant and animal nutrition, and are the visual indicators of ripening for many fruits, including tomato. Whereas carotenoid synthesis is well characterized, factors regulating flux through the pathway are poorly understood at the molecular level. To exploit the impact of tomato genetic diversity on carotenoids, Solanum pennellii introgression lines were used as a source of defined natural variation and as a resource for the identification of candidate regulatory genes. Ripe fruits were analyzed for numerous fruit metabolites and transcriptome profiles generated using a 12,000 unigene oligoarray. Correlation analysis between carotenoid content and gene expression profiles revealed 953 carotenoid-correlated genes. To narrow the pool, subnetwork analysis of carotenoid-correlated transcription revealed 38 candidates. One candidate for impact on trans-lycopene and β-carotene accumulation was functionally charaterized, SlERF6, revealing that it indeed influences carotenoid biosynthesis and additional ripening phenotypes. Reduced expression of SlERF6 by RNAi enhanced both carotenoid and ethylene levels during fruit ripening, demonstrating an important role for SlERF6 in ripening, integrating the ethylene and carotenoid synthesis pathways.
authors: Boyce Thompson Institute for Plant Research, Tower Rd., Cornell University campus, Ithaca, NY 14853, USA.
authors: Je Min
authors: JM
authors: Lee
authors: Je-Gun
authors: JG
authors: Joung
authors: Ryan
authors: R
authors: McQuinn
authors: Mi-Young
authors: MY
authors: Chung
authors: Zhangjun
authors: Z
authors: Fei
authors: Denise
authors: D
authors: Tieman
authors: Harry
authors: H
authors: Klee
authors: James
authors: J
authors: Giovannoni
mesh_terms: D000595:Amino Acid Sequence; D002338:Carotenoids / Q000378:metabolism; D016000:Cluster Analysis; D005030:Ethylenes / Q000378:metabolism / Q000494:pharmacology; D005638:Fruit / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D014644:Genetic Variation; D018551:Solanum lycopersicum / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D055442:Metabolome; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000378:metabolism / Q000494:pharmacology; D010940:Plant Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D030821:Plants, Genetically Modified; D034622:RNA Interference; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid
chemical_list: D005030:Ethylenes; D010937:Plant Growth Regulators; D010940:Plant Proteins; D002338:Carotenoids; C036216:ethylene