Open Access Highly Accessed Research article

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit

Viviana Lima-Silva1, Abel Rosado1, Vitor Amorim-Silva2, Antonio Muñoz-Mérida3, Clara Pons4, Aureliano Bombarely5, Oswaldo Trelles3, Rafael Fernández-Muñoz6, Antonio Granell4, Victoriano Valpuesta1 and Miguel Ángel Botella17*

Author Affiliations

1 Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Molecular y Bioquímica, Universidad de Málaga, 29071, Málaga, Spain

2 BioFIG - Center for Biodiversity, Functional & Integrative Genomics, Departamento de Biologia, Universidade do Minho, Campus de Gualtar, Braga, Portugal

3 Computer Architecture Department, University of Malaga, Campus de Teatinos, 29071, Málaga, Spain

4 Instituto de Biología Molecular y Celular de Plantas, Consejo Superior deInvestigaciones Científicas, Universidad Politécnica de Valencia, 46022, Valencia, Spain

5 Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY, 14853, USA

6 Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Est. Exp. La Mayora, Algarrobo-Costa, Málaga, Spain

7 Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain

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BMC Genomics 2012, 13:187  doi:10.1186/1471-2164-13-187

Published: 14 May 2012



L-ascorbic acid (AsA; vitamin C) is essential for all living plants where it functions as the main hydrosoluble antioxidant. It has diverse roles in the regulation of plant cell growth and expansion, photosynthesis, and hormone-regulated processes. AsA is also an essential component of the human diet, being tomato fruit one of the main sources of this vitamin. To identify genes responsible for AsA content in tomato fruit, transcriptomic studies followed by clustering analysis were applied to two groups of fruits with contrasting AsA content. These fruits were identified after AsA profiling of an F8 Recombinant Inbred Line (RIL) population generated from a cross between the domesticated species Solanum lycopersicum and the wild relative Solanum pimpinellifollium.


We found large variability in AsA content within the RIL population with individual RILs with up to 4-fold difference in AsA content. Transcriptomic analysis identified genes whose expression correlated either positively (PVC genes) or negatively (NVC genes) with the AsA content of the fruits. Cluster analysis using SOTA allowed the identification of subsets of co-regulated genes mainly involved in hormones signaling, such as ethylene, ABA, gibberellin and auxin, rather than any of the known AsA biosynthetic genes. Data mining of the corresponding PVC and NVC orthologs in Arabidopis databases identified flagellin and other ROS-producing processes as cues resulting in differential regulation of a high percentage of the genes from both groups of co-regulated genes; more specifically, 26.6% of the orthologous PVC genes, and 15.5% of the orthologous NVC genes were induced and repressed, respectively, under flagellin22 treatment in Arabidopsis thaliana.


Results here reported indicate that the content of AsA in red tomato fruit from our selected RILs are not correlated with the expression of genes involved in its biosynthesis. On the contrary, the data presented here supports that AsA content in tomato fruit co-regulates with genes involved in hormone signaling and they are dependent on the oxidative status of the fruit.