Transcriptome analysis provides insights into the stress response in cultivated peanut (Arachis hypogaea L) subjected to drought-stress (original) (raw)
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Identification of drought-responsive transcripts in peanut (Arachis hypogaea L
2001
We have used a reverse transcriptase polymerase chain reaction procedure (differential display) to identify cDNAs corresponding to transcripts affected by water stress in peanuts ( Arachis hypogaea L.). Using this method, we have identified several mRNA transcripts that are up-or down-regulated following water stress. With 21 primer combinations, a total of 1235 differential display products were observed in irrigated samples, compared to 950 differential display products in stressed samples. These products demonstrated qualitative and quantitative differences in the gene expression. The differentially expressed transcripts were collectively named PTRD (Peanut Transcripts Responsive to Drought). We have identified a total of 43 PTRD, which were significantly altered due to water stress. Slot blot analysis of 16 PTRD indicated that 12 were completely suppressed due to prolonged drought, two were down-regulated, and two were up-regulated under drought stress conditions. The 12 completely suppressed transcripts were studied further by RNA dot-blot analysis to compare their expression in drought tolerant and susceptible line , which underwent three *Corresponding author weeks of water stress. PTRD-1, -10, and -16 expressed for longer period in tolerant line compared to the susceptible lines and can be used as molecular markers for screening peanut lines for drought tolerance.
Molecular Genetics and Genomics, 2009
Peanut, found to be relatively drought tolerant crop, has been the choice of study to characterize the genes expressed under gradual water deWcit stress. Nearly 700 genes were identiWed to be enriched in subtractive cDNA library from gradual process of drought stress adaptation. Further, expression of the drought inducible genes related to various signaling components and gene sets involved in protecting cellular function has been described based on dot blot experiments. Fifty genes (25 regulators and 25 functional related genes) selected based on dot blot experiments were tested for their stress responsiveness using northern blot analysis and conWrmed their nature of diVerential regulation under diVerent Weld capacity of drought stress treatments. ESTs generated from this subtracted cDNA library oVered a rich source of stress-related genes including signaling components. Additional 50% uncharacterized sequences are noteworthy. Insights gained from this study would provide the foundation for further studies to understand the question of how peanut plants are able to adapt to naturally occurring harsh drought conditions. At present functional validation cannot be deemed in peanut, hence as a proof of concept seven orthologues of drought induced genes of peanut have been silenced in heterologous N. benthamiana system, using virus induced gene silencing method. These results point out the functional importance for HSP70 gene and key regulators such as Jumonji in drought stress response.
Plant Molecular Biology Reporter, 2015
Peanut (Arachis hypogaea L.) is an important legume cultivated mostly in drought-prone areas where its productivity can be limited by water scarcity. The development of more drought-tolerant varieties is, therefore, a priority for peanut breeding programs worldwide. In contrast to cultivated peanut, wild relatives have a broader genetic diversity and constitute a rich source of resistance/tolerance alleles to biotic and abiotic stresses. The present study takes advantage of this diversity to identify drought-responsive genes by analyzing the expression profile of two wild species, Arachis duranensis and Arachis magna (AA and BB genomes, respectively), in response to progressive water deficit in soil. Data analysis from leaves and roots of A. duranensis (454 sequencing) and A. magna (suppression subtractive hybridization (SSH)) stressed and control complementary DNA (cDNA) libraries revealed several differentially expressed genes in silico, and 44 of them were selected for further validation by quantitative RT-PCR (qRT-PCR). This allowed the identification of drought-responsive candidate genes, such as Expansin, Nitrilase, NAC, and bZIP transcription factors, displaying significant levels of differential expression during stress imposition in both species. This is the first report on identification of differentially expressed genes under drought stress and recovery in wild Arachis species. The generated transcriptome data, Accession numbers for the GenBank sequence database: JZ390113 to JZ390862
Identification and annotation of abiotic stress responsive candidate genes in peanut ESTs
2012
Peanut (Arachis hypogaea L.) ranks fifth among the world oil crops and is widely grown in India and neighbouring countries. Due to its large and unknown genome size, studies on genomics and genetic modification of peanut are still scanty as compared to other model crops like Arabidopsis, rice, cotton and soybean. Because of its favourable cultivation in semi-arid regions, study on abiotic stress responsive genes and its regulation in peanut is very much important. Therefore, we aim to identify and annotate the abiotic stress responsive candidate genes in peanut ESTs. Expression data of drought stress responsive corresponding genes and EST sequences were screened from dot blot experiments shown as heat maps and supplementary tables, respectively as reported by Govind et al. (2009). Some of the screened genes having no information about their ESTs in above mentioned supplementary tables were retrieved from NCBI. A phylogenetic analysis was performed to find a group of utmost similar ESTs for each selected gene. Individual EST of the said group were further searched in peanut ESTs (1,78,490 whole EST sequences) using stand alone BLAST. For the prediction as well as annotation of abiotic stress responsive selected genes, various tools (like Vec-Screen, Repeat Masker, EST-Trimmer, DNA Baser, WISE2 and I-TASSER) were used. Here we report the predicted result of Contigs, domain as well as 3D structure for HSP 17.3KDa protein, DnaJ protein and Type 2 Metallothionein protein.
Authorea
Drought stress at germination stage is an important environmental stress limiting crop yield. Hence, our study investigated comparative root transcriptome profiles of four contrasting soybean genotypes viz., drought-tolerant (PI342618B/DTP & A214/DTL) and drought-sensitive (NN86-4/DSP & A195/DSL) under drought stress using RNA-Seq approach. Total of 4850 and 6272 differentially expressed genes (DEGs) were identified in tolerant (DTP & DTL) and sensitive (DSP & DSL) genotypes, respectively. Principle component analysis (PCA) and correlation analysis revealed higher correlation of DTP with DTL. Both gene ontology (GO) and MapMan analyses showed drought response was enriched in the DEGs associated with water and auxin transport, cell wall/membrane, antioxidant activity, catalytic activity, secondary metabolism, signaling and transcription factor (TF) activities. Out of 981 DEGs screened from above terms, only 547 showed consistent opposite expression between contrasting genotypes. Twenty-eight DEGs of 547 were located on Chr.08 rich in QTLs and "Hotspot regions" associated with drought stress, and eight of them showed non-synonymous SNP polymorphism. Hence, ten genes (including above eight genes plus two hub genes) were predicated as possible candidates regulating drought tolerance, which needs further functional validation. Overall, the transcriptome profiling provided in-depth understanding about the genetic mechanism and candidate genes underlying drought tolerance in soybean.
Plant Molecular Biology Reporter, 2019
Chickpea (Cicer arietinum L.) is a pulse crop valued for its high protein content, grown in semi-arid tropics and Mediterranean regions. Its yield remains affected by biotic and abiotic stresses with drought alone being responsible for up to 50% annual loss of yield. Transcriptome analysis of a sensitive and a tolerant cultivar of chickpea has been done earlier to unravel the molecular basis for drought and salinity stress responses. In the present study, we performed transcriptome analysis of two drought-tolerant genotypes, BG-362 and P-256, under polyethylene glycol-simulated drought stress to decipher the genes and pathways that are commonly regulated in these genotypes. RNA-Seq using Illumina platform generated 152 million high-quality reads. Referenceguided assembly of genome yielded a total of 37,943 transcripts representing 22,701 genes. Among the 1624 genes that were observed to be differentially expressed under drought, 97 genes were common in both the genotypes. These included the upregulated genes, such as probable mannitol dehydrogenase, serine hydroxymethyltransferase 4-like, 17.5 kDa class I heat shock protein-like, cytochrome P450 81E8-like, and galactinol-sucrose galactosyltransferase-like, and downregulated genes, such as probable xyloglucan endotransglucosylase/hydrolase protein 23, abscisic acid 8′-hydroxylase 1-like, Calmodulin-like protein 11, and proline dehydrogenase 2 mitochondrial-like genes. A major finding was the involvement of transcription factors, including AP2-EREBP, bHLH, bZIP, C3H, MYB, NAC, WRKY, and MADS. The present study is the first comparative analysis of RNA-Seq data for two drought-tolerant chickpea genotypes. These findings would help in improving drought tolerance across chickpea genotypes.
Isolation and characterization of drought responsive genes from rice (Oryza sativa L.)
2008
Background: Peanut (Arachis hypogaea L.) is an important economic and oilseed crop. Long-term rainless conditions and seasonal droughts can limit peanut yields and were conducive to preharvest aflatoxin contamination. To elucidate the molecular mechanisms by which peanut responds and adapts to water limited conditions, we isolated and characterized several drought-induced genes from peanut roots using a suppression subtractive hybridization (SSH) technique. Results: RNA was extracted from peanut roots subjected to a water stress treatment (45% field capacity) and from control plants (75% field capacity), and used to generate an SSH cDNA library. A total of 111 non-redundant sequences were obtained, with 80 unique transcripts showing homology to known genes and 31 clones with no similarity to either hypothetical or known proteins. GO and KEGG analyses of these differentially expressed ESTs indicated that drought-related responses in peanut could mainly be attributed to genes involved in cellular structure and metabolism. In addition, we examined the expression patterns of seven differentially expressed candidate genes using real-time reverse transcription-PCR (qRT-PCR) and confirmed that all were up-regulated in roots in response to drought stress, but to differing extents. Conclusions: We successfully constructed an SSH cDNA library in peanut roots and identified several drought-related genes. Our results serve as a foundation for future studies into the elucidation of the drought stress response mechanisms of peanut.
Jayant & Sarangi Biochemical and molecular responses of peanut varieties to drought stress
The research was performed to study the effect of water deficit on Biochemical and Molecular response of two varieties (JL-24, a drought susceptible variety and K-1375, a drought tolerant variety) of Peanut (Arachis hypogea L.) plants. Findings showed that the drought stress results into decrease in total RNA content whereas activities of antioxidant enzymes such as Superoxide Dismutase, Catalase, and Glutathione Reductase increased. It has been also found that, the lethal effect of drought stress in JL-24 variety is more prominent than the K-1375 variety, whereas the capability to develop tolerance in K-1375 is found to be more efficient than JL-24.
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
BMC Genomics, 2012
Background: Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.