Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency.

Optimising plant nitrogen (N) usage and inhibiting N leaching loss in the soil-crop system is crucial to maintaining crop yield and reducing environmental pollution. This study aimed at identifying quantitative trait loci (QTLs) and differentially expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related contrasting traits in tomato varieties. We characterised a genetic diversity core-collection (CC) and a multi-parental advanced generation intercross (MAGIC) tomato population grown in greenhouse under two nitrogen levels and assessed several N-related traits and mapped QTLs. Transcriptome response under the two N conditions was also investigated through RNA sequencing of fruit and leaves in four parents of the MAGIC population. Significant differences in response to N input reduction were observed at the phenotypic level for biomass and N-related traits. Twenty-seven (27) QTLs were detected for three target traits (Leaf N content, leaf Nitrogen Balance Index and petiole NO3- content), ten and six at low and high N condition, respectively; while 19 QTLs were identified for plasticity traits. At the transcriptome level, 4,752 and 2,405 DEGs were detected between the two N conditions in leaves and fruits, respectively, among which 3,628 (50.6%) in leaves and 1,717 (71.4%) in fruit were genotype specific. When considering all the genotypes, 1,677 DEGs were shared between organs or tissues. Finally, we integrated DEGs and QTLs analyses to identify the most promising candidate genes. The results highlighted a complex genetic architecture of N homeostasis in tomato and novel putative genes useful for breeding tomato varieties requiring less N input.

Sublethal cadmium intoxication in Arabidopsis thaliana impacts translation at multiple levels.

To study the impact of translational regulation during heavy metal poisoning, Arabidopsis thaliana cell cultures were submitted to sublethal cadmium stress. At the concentration used, cadmium had a minimal impact on the growth of the culture but induced an accumulation of high molecular weight polysomes without de novo production of new ribosomes together with a reduction of protein synthesis. In addition, cadmium stress induces phosphorylation of eukaryotic initiation factor 2α by GCN2 and, in planta, gcn2 mutants are more sensitive to cadmium stress, suggesting a role for this translational regulation mechanism in the response to cadmium stress. Microarray analysis of total and polysomal RNAs in control and cadmium-treated cells reveals a large class of genes for which a variation in total RNA abundance is not linked to a variation in polysomal loading, suggesting that transcription and translation are uncoupled and that these genes are not recruited at the initiation step of translation.