Gene expression analysis of Solanum lycopersicum and Solanum habrochaites under drought conditions

Mishra, Upama; Rai, Anurag; Kumar, Rajesh; Singh, Mahesh Kumar; Pandey, Harsh

doi:10.1016/j.gdata.2016.04.001

Cited by 12 publications

(11 citation statements)

References 6 publications

(6 reference statements)

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“…The L12 experiment correspond to drought stress considering samples of leaves from four-week-old S. lycopersicum and S. habrochaites , previously non-irrigated for 14 days. Finally, the L13 experiment corresponded to a heat stress assay considering samples of leaves from four-week-old S. lycopersicum and S. habrochaites treated at 40 °C [47]. The profiles are relative to the control without stress.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The RabGAP Gene Family in Tomato (Solanum lycopersicum) and Wild Relatives: Identification, Interaction Networks, and Transcriptional Analysis during Plant Development and in Response to Salt Stress

Madrid-Espinoza

Salinas-Cornejo

Ruíz-Lara

2019

Genes

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RabGTPase activating proteins (RabGAP) are responsible for directing the deactivation of vesicular trafficking master regulators associated to plant development, the RabGTPase proteins. Recently, RabGAPs were identified in Arabidopsis and rice, but studies were not yet reported in tomato. Herein, we identified 24 RabGAP-encoding genes in cultivated tomato (Solanum lycopersicum) and its wild relative genomes (Solanum pimpinellifolium and Solanum pennellii). We analyzed them based on their exon-intron structures, conserved protein motifs, putative subcellular localizations, phylogenetic and gene duplications analyses, interaction networks, and gene expression patterns in tomato. Phylogenetic relationship analysis also indicated that RabGAP family is classified into seven subclasses, of which subclasses I and II are plant-exclusive. Furthermore, segmental duplication events and positive evolutionary forces are associated with the maintenance of the number and function of their members. On the other hand, the protein–protein interaction networks on tomato suggested that members of subclasses I, II, and III could be associated to endocytic traffic routes. In addition, the qRT-PCR experiments in S. lycopersicum and Solanum chilense exposed to a salt stress treatment validated the differential expression patterns of 20 RabGAP genes in different tissues, development stages, and stress conditions obtained through extensive microarray-based analyses. This work suggests the critical role of RabGAP family in the context of intracellular vesicular trafficking in tomato, particularly under conditions of abiotic stress. It also contributes to the breeding programs associated with the development of crops tolerant to salt stress.

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Section: Methodsmentioning

confidence: 99%

“…Heat stress: S. lycopersicum versus S. habrochaites (GEO accession GSE22304). RNA extraction from leaves of four-week-old plants treated at 40 °C [47]. All values are detailed in Table S7.…”

Section: Figurementioning

confidence: 99%

The RabGAP Gene Family in Tomato (Solanum lycopersicum) and Wild Relatives: Identification, Interaction Networks, and Transcriptional Analysis during Plant Development and in Response to Salt Stress

Madrid-Espinoza

Salinas-Cornejo

Ruíz-Lara

2019

Genes

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“…In addition to genetic studies conducted at the DNA level, efforts have also been made in candidate gene discovery through RNA deep sequencing ( Chang et al , 2016 ; Garg et al , 2016 ; Shankar et al , 2016 ) and microarray analysis ( Mishra et al , 2016 ). For example, whole-genome transcriptome-profiling studies have identified a large number of transcripts encoding members of various gene families reported to play an important role in abiotic stress tolerance, including AP2/EREBP , bLHL , MYB , and auxin-related families ( Chang et al , 2016 ; Garg et al , 2016 ).…”

Section: Rapid Progress In Molecular Physiology and Genomics Applied mentioning

confidence: 99%

Improving crop performance under drought – cross-fertilization of disciplines

Tardieu

Varshney

Tuberosa

2017

Journal of Experimental Botany

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“…Most of the recent tomato cultivars are drought-sensitive at all stages of plant development; the stage of seed germination and early seedling growth are the most sensitive (Mishra, Rai, Kumar, Singh, & Pandey, 2016). Genetic variability among the modern cultivated tomato is limited owing to natural and artificial selection during domestication and evolution (Steinhauser et al, 2011), which makes tomato wild relatives a good source of drought tolerance genes.…”

Section: Introductionmentioning

confidence: 99%

Multi-trait selection of tomato introgression lines under drought-induced conditions at germination and seedling stages

et al. 2022

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To be considered drought-tolerant, a tomato cultivar is required to present some level of tolerance at all developmental stages of plant growth. Since drought tolerance is a stage-specific phenomenon, genotype assessment must be performed separately at all developmental stages. In this study, we used a multi-trait index based on factor analysis and genotype-ideotype distance (FAI-BLUP index) to properly rank 49 tomato genotypes according to their tolerance to drought stress conditions at germination and seedling stages. Seeds of 47 introgression lines, which cultivar M82 is considered drought-sensitive, and the Solanum pennellii wild accession LA 716, which is considered drought-tolerant, were subjected to a control condition, where seeds were soaked in distilled water, and a drought condition, where seeds were soaked in a polyethylene glycol (PEG) solution (-0.3 MPa). Drought stress, induced by PEG, had a significant impact on all nine germination and growth performance-related traits; there was a reduction in shoot length (SL), total length (TL), initial germination percentage (IGP), final germination percentage (FGP), germination velocity index (GVI), and germination rate (GR). In contrast, the root-to-shoot ratio (R/S) and time to reach 50% germination (T50) increased under drought stress. Root length (RL) was less affected by drought, and in some genotypes, it was even increased. As expected, LA 716 ranked closest to the drought tolerance ideotype. IL 1-4-18, IL 2-3, IL 1-2, IL 9-2, and IL 10-1 were the most drought-tolerant at the germination stage. These results will serve as guidance for breeders who are aiming at developing drought-resistant tomato cultivars.

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Gene expression analysis of Solanum lycopersicum and Solanum habrochaites under drought conditions

Cited by 12 publications

References 6 publications

The RabGAP Gene Family in Tomato (Solanum lycopersicum) and Wild Relatives: Identification, Interaction Networks, and Transcriptional Analysis during Plant Development and in Response to Salt Stress

The RabGAP Gene Family in Tomato (Solanum lycopersicum) and Wild Relatives: Identification, Interaction Networks, and Transcriptional Analysis during Plant Development and in Response to Salt Stress

Improving crop performance under drought – cross-fertilization of disciplines

Multi-trait selection of tomato introgression lines under drought-induced conditions at germination and seedling stages

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