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RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

Emilie Villar123, Christophe Klopp4, Céline Noirot4, Evandro Novaes56, Matias Kirst5, Christophe Plomion27 and Jean-Marc Gion12*

Author Affiliations

1 CIRAD, UMR AGAP, Campus de Baillarguet TA 10C, F-34398 Montpellier Cedex 5, France

2 INRA, UMR1202 BIOGECO, F-33610 Cestas, France

3 CRDPI, BP1291, Pointe Noire, République du Congo

4 Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France

5 School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA

6 Universidade Federal de Goiás, Caixa Postal 131, CEP 74690-900, Goiânia, Brazil

7 Université de Bordeaux, UMR1202 BIOGECO, F-33610 Cestas, France

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BMC Genomics 2011, 12:538  doi:10.1186/1471-2164-12-538

Published: 2 November 2011



In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantations, water availability is a key factor limiting productivity. However, the molecular mechanisms underlying the adaptation of eucalyptus to water shortage remain unclear. In this study, we compared the molecular responses of two commercial eucalyptus hybrids during the dry season. Both hybrids differ in productivity when grown under water deficit.


Pyrosequencing of RNA extracted from shoot apices provided extensive transcriptome coverage - a catalog of 129,993 unigenes (49,748 contigs and 80,245 singletons) was generated from 398 million base pairs, or 1.14 million reads. The pyrosequencing data enriched considerably existing Eucalyptus EST collections, adding 36,985 unigenes not previously represented. Digital analysis of read abundance in 14,460 contigs identified 1,280 that were differentially expressed between the two genotypes, 155 contigs showing differential expression between treatments (irrigated vs. non irrigated conditions during the dry season), and 274 contigs with significant genotype-by-treatment interaction. The more productive genotype displayed a larger set of genes responding to water stress. Moreover, stress signal transduction seemed to involve different pathways in the two genotypes, suggesting that water shortage induces distinct cellular stress cascades. Similarly, the response of functional proteins also varied widely between genotypes: the most productive genotype decreased expression of genes related to photosystem, transport and secondary metabolism, whereas genes related to primary metabolism and cell organisation were over-expressed.


For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance of biomass growth during the dry season. Its strategy may involve a decrease of photosynthetic activity during the dry season associated with resources reallocation through major changes in the expression of primary metabolism associated genes. Further efforts will be needed to assess the adaptive nature of the genes highlighted in this study.