Abstract
Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops.
Highlights
IntroductionPlants have to cope with changing environments during their life cycles
As sessile organisms, plants have to cope with changing environments during their life cycles
The genetic and molecular basis underlying the differences in inflorescence plasticity among different tomato accessions remains to be unraveled, we hypothesize that transcriptional and/or posttranscriptional regulation on particular pathways might associate with this phenotypic plasticity because as mentioned above, environments impose significant impact on transcriptome dynamics
Summary
Plants have to cope with changing environments during their life cycles. A survey on AS patterns by computational analysis of expressed sequence tags (EST), mRNA and short reads from public available RNA-seq data has revealed that depending on species, 39.1%–70.4% of the genes with introns produced more than one splice variant in the nine plant species investigated [23]. The genetic and molecular basis underlying the differences in inflorescence plasticity among different tomato accessions remains to be unraveled, we hypothesize that transcriptional and/or posttranscriptional regulation on particular pathways might associate with this phenotypic plasticity because as mentioned above, environments impose significant impact on transcriptome dynamics. We assessed, by RNA-seq, genome-wide gene expression of tomato seedlings and alternative splicing of pre-mRNA in response to distinct growth environments.
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