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Genome-wide analysis of stress-responsive genes and alternative splice variants in Arabidopsis roots under osmotic stresses

ABSTRACT: The shoots and roots of a plant respond differently to osmotic stress, as they have distinct functions and anatomical structures. Under conditions of high solute concentration, such as in saline soils or drought, water uptake by the roots is reduced, resulting in cellular dehydration. In this study, we performed transcriptional profiling of roots of Arabidopsis under osmotic stress conditions such as high salinity and drought using mRNA-Seq for the assessment of gene expression changes in roots of Arabidopsis. mRNA-Seq analysis showed that many differentially expressed genes showed differential expressions under both salt stress and drought stress conditions in roots and were distinct from aerial parts. We confirmed 68 transcription factor genes which is involved in osmotic stress signal transduction in roots and are connected tightly. Interestingly, well-known ABA-dependent and/or -independent osmotic stress-responsive genes were less increased in roots, indicating that osmotic stress response in roots might be regulated by stress pathways other than well-known pathways. We identified 26 osmotic stress-responsive genes, which have alternative splicing variant isoforms, showed distinct expression in roots under osmotic stress conditions from the mRNA-Seq analysis. Quantitative RT-PCR confirmed that alternative splicing variants, such as ANNAT4, MAGL6, TRM19, and CAD9, have differential expressions in roots under osmotic stress conditions, indicating that alternative splicing is an important regulatory mechanism in osmotic stress response in roots. Taken together, our study suggest that many transcription factor families are involved in osmotic stress response in roots and tightly connected each other. In addition, alternative splicing and function of alternative splicing variant isoforms are also important in osmotic stress response in roots. To understand the alternative splicing mechanism in roots, further study is necessary.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE229217 | GEO | 2023/12/08

REPOSITORIES: GEO

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Project description:Since the roots of grapevine rootstocks have a direct contact with drying soil and has an important role in abiotic stimuli, any plasticity on the architecture of the rootstocks would enable grapevine varieties to a better respond to drought stress. However, genomics evidences behind the physiological responses of rootstocks under prolonged drought stress are poorly documented in the literature. In the current study, eight widely used hybrid grapevine rootstocks in viticulture were firstly grafted with sultana seedless and subjected to drought stress to test their physiological and biochemical responses. The results of experiment indicated that the roots of V.rupestris X V.berlandieri (110 R, 1103P, 140 Ru) rootstocks possessed much higher water content as well as non-structural carbohydrate and nitrogen concentrations compared to V.riparia X V.berlandieri (SO4, 5BB, 420A, 8B) and V.vinifera X V.berlandieri (41B) hybrids under drought. V.rupestris X V.berlandieri hybrids were also performed much higher root elongation performance under drought compared to other rootstock hybrids. Three rootstock varieties (110R, 5BB and 41B) having different pedigrees and root architectural responses to drought were also investigated at transcriptome level to find out gene regulation network behind differential physiological responses to drought. Transcriptome analysis revealed 2795, 1196 and 1612 differentially expressed transcripts for the roots of 110R, 5BB and 41B, respectively. The highest expression increases in 110R compared to other rootstocks were recorded for the transcripts functional in carbohydrate (SWEET14, CWINV) and nitrate/peptide (NRT1/ PTR FAMILY) transportation as well as osmoregulation (dehydrins, osmotins, LEAs and proline-glycine rich proteins) during drought. Higher induction of these genes in the roots of tolerant 110R genotype indicated importance of efficient uptake of carbohydrate and nitrogen source released from canopy under drought and preservation of water with osmotic regulation on the root elongation and drought tolerance of grapevines. Expression increases in several other pathogenesis related proteins, regulation of cell wall modification enzymes and activity of several secondary metabolites have been also associated to altered root architecture and drought tolerance in the grapevine rootstocks for the first time with the current study.

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Genome-wide analysis of stress-responsive genes and alternative splice variants in Arabidopsis roots under osmotic stresses

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