Changes in the transcript and protein profiles of Quercus ilex seedlings in response to drought stress

Quercus ilex is the dominant tree species in natural forest ecosystems across the Mediterranean Basin and in the agrosilvopastoral system dehesa, which has a high ecological and economical significance. As in other forestry species, survival in Q. ilex is threatened by long periods of drought. This paper reports the transcriptome and proteome profiles of 6-month-old seedlings subjected to severe drought conditions. Drought was imposed by water withholding in seedlings grown in perlite for 28 days. Seedling leaves were collected when leaf fluorescence had decreased by 20% and 45% relative to well-watered seedlings. The transcriptome and proteome were analyzed by using Illumina and shotgun platforms. The quality and confidence of the mRNA and protein identifications and quantifications were assessed, obtaining 25,169 transcripts and 3312 proteins. Variable transcripts and proteins were analyzed by Venn diagram, Pearson's correlation, GO enrichment, KEGG pathways, multivariate analysis and interaction networks. Despite the poor correlation between mRNA and protein, both platforms gave a complementary view of the changes in the abundance of several gene products under drought conditions and indicated that gene expression regulation and translation to phenotype is quite complex and genespecific. As a general tendency, while transcripts and proteins of the metabolism were down-accumulated, those of stress related were up-accumulated. Out of the variable dataset, four gene products (viz., FtSH6, CLPB1, CLPB3, and HSP22) were up-accumulated at both omics levels at the two surveyed times, being the first work where they are described in drought response in forest species. These chaperones and proteases could be considered as potential drought tolerance markers to be used in the selection of elite, resilient genotypes, and in breeding programs.

Automated summary

This study investigated the response of Quercus ilex seedlings to drought conditions through transcriptome and proteome analysis, revealing complex and gene-specific mechanisms in gene expression regulation and translation to phenotype under drought stress. While transcripts and proteins related to metabolism were down-regulated, those related to stress response showed an up-regulation trend. Additionally, certain chaperones and proteases were identified as potential drought tolerance markers for elite genotype selection and breeding programs.