title: Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits.
abstract: Carotenoids represent some of the most important secondary metabolites in the human diet, and tomato (Solanum lycopersicum) is a rich source of these health-promoting compounds. In this work, a novel and fruit-related regulator of pigment accumulation in tomato has been identified by artificial neural network inference analysis and its function validated in transgenic plants. A tomato fruit gene regulatory network was generated using artificial neural network inference analysis and transcription factor gene expression profiles derived from fruits sampled at various points during development and ripening. One of the transcription factor gene expression profiles with a sequence related to an Arabidopsis (Arabidopsis thaliana) ARABIDOPSIS PSEUDO RESPONSE REGULATOR2-LIKE gene (APRR2-Like) was up-regulated at the breaker stage in wild-type tomato fruits and, when overexpressed in transgenic lines, increased plastid number, area, and pigment content, enhancing the levels of chlorophyll in immature unripe fruits and carotenoids in red ripe fruits. Analysis of the transcriptome of transgenic lines overexpressing the tomato APPR2-Like gene revealed up-regulation of several ripening-related genes in the overexpression lines, providing a link between the expression of this tomato gene and the ripening process. A putative ortholog of the tomato APPR2-Like gene in sweet pepper (Capsicum annuum) was associated with pigment accumulation in fruit tissues. We conclude that the function of this gene is conserved across taxa and that it encodes a protein that has an important role in ripening.
authors.affiliation: Division of Plant and Crop Sciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, United Kingdom.
authors.forename: Yu
authors.initials: Y
authors.lastname: Pan
authors.forename: Glyn
authors.initials: G
authors.lastname: Bradley
authors.forename: Kevin
authors.initials: K
authors.lastname: Pyke
authors.forename: Graham
authors.initials: G
authors.lastname: Ball
authors.forename: Chungui
authors.initials: C
authors.lastname: Lu
authors.forename: Rupert
authors.initials: R
authors.lastname: Fray
authors.forename: Alexandra
authors.initials: A
authors.lastname: Marshall
authors.forename: Subhalai
authors.initials: S
authors.lastname: Jayasuta
authors.forename: Charles
authors.initials: C
authors.lastname: Baxter
authors.forename: Rik
authors.initials: R
authors.lastname: van Wijk
authors.forename: Laurie
authors.initials: L
authors.lastname: Boyden
authors.forename: Rebecca
authors.initials: R
authors.lastname: Cade
authors.forename: Natalie H
authors.initials: NH
authors.lastname: Chapman
authors.forename: Paul D
authors.initials: PD
authors.lastname: Fraser
authors.forename: Charlie
authors.initials: C
authors.lastname: Hodgman
authors.forename: Graham B
authors.initials: GB
authors.lastname: Seymour
mesh_terms: D029681:Arabidopsis Proteins / Q000737:chemistry*; D002212:Capsicum / Q000235:genetics*; D002338:Carotenoids / Q000378:metabolism; D005638:Fruit / Q000235:genetics* / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development; D016571:Neural Networks, Computer; D010641:Phenotype; D010858:Pigmentation / Q000235:genetics; D010860:Pigments, Biological / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified; D024505:Tocopherols / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
chemical_list: C416544:APRR2 protein, Arabidopsis; D029681:Arabidopsis Proteins; D010860:Pigments, Biological; D010940:Plant Proteins; D014157:Transcription Factors; D002338:Carotenoids; D024505:Tocopherols