title: Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato.
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 speciesS. pimpinellifoliumby 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.
authors.affiliation: University of Chinese Academy of Sciences, 19A Yuquan Rd., Beijing 100049, China. gswang@sibs.ac.cn.|National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China. gswang@sibs.ac.cn.
authors.forename: Guixiang
authors.initials: G
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China. lweng@sibs.ac.cn.
authors.forename: Lin
authors.initials: L
authors.lastname: Weng
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China. limeng22387@126.com.
authors.forename: Meng
authors.initials: M
authors.lastname: Li
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China. hanxiao@sibs.ac.cn.
authors.forename: Han
authors.initials: H
authors.lastname: Xiao
mesh_terms: D017398:Alternative Splicing; D004777:Environment; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018551:Solanum lycopersicum / Q000145:classification / Q000235:genetics / Q000254:growth & development*; D010641:Phenotype; D017423:Sequence Analysis, RNA / Q000379:methods*
keywords: RNA sequencing; alternative splicing; phenotypic plasticity; tomato; transcriptome