Transcriptomic and splicing changes underlying tomato responses to combined water and nutrient stress

Tomato is a horticultural crop of high economic and nutritional value.Suboptimal environmental conditions, such as limited water and nutrientavailability, cause severe yield reductions. Thus, selection of genotypesrequiring lower inputs is a goal for the tomato breeding sector. We screened10 tomato varieties exposed to water deficit, low nitrate or a combination ofboth. Biometric, physiological and molecular analyses revealed different stressresponses among genotypes, identifying T270 as severely affected, and T250 astolerant to the stresses applied. Investigation of transcriptome changes causedby combined stress in roots and leaves of these two genotypes yielded a lownumber of differentially expressed genes (DEGs) in T250 compared to T270,suggesting that T250 tailors changes in gene expression to efficiently respondto combined stress. By contrast, the susceptible tomato activatedapproximately one thousand and two thousand genes in leaves and rootsrespectively, indicating a more generalized stress response in this genotype. Inparticular, developmental and stress-related genes were differentiallyexpressed, such as hormone responsive factors and transcription factors.Analysis of differential alternative splicing (DAS) events showed thatcombined stress greatly affects the splicing landscape in both genotypes,highlighting the important role of AS in stress response mechanisms. Inparticular, several stress and growth-related genes as well as transcriptionand splicing factors were differentially spliced in both tissues. Taken together,these results reveal important insights into the transcriptional and posttranscriptionalmechanisms regulating tomato adaptation to growth underreduced water and nitrogen inputs.