Dataset Information

Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar.

ABSTRACT: Salt stress is one of the major adverse environmental factors limiting crop productivity. Considering Iran as one of the bread wheat origins, we sequenced root transcriptome of an Iranian salt tolerant cultivar, Arg, under salt stress to extend our knowledge of the molecular basis of salinity tolerance in Triticum aestivum. RNA sequencing resulted in more than 113 million reads and about 104013 genes were obtained, among which 26171 novel transcripts were identified. A comparison of abundances showed that 5128 genes were differentially expressed due to salt stress. The differentially expressed genes (DEGs) were annotated with Gene Ontology terms, and the key pathways were identified using Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping. The DEGs could be classified into 227 KEGG pathways among which transporters, phenylpropanoid biosynthesis, transcription factors, glycosyltransferases, glutathione metabolism and plant hormone signal transduction represented the most significant pathways. Furthermore, the expression pattern of nine genes involved in salt stress response was compared between the salt tolerant (Arg) and susceptible (Moghan3) cultivars. A panel of novel genes and transcripts is found in this research to be differentially expressed under salinity in Arg cultivar and a model is proposed for salt stress response in this salt tolerant cultivar of wheat employing the DEGs. The achieved results can be beneficial for better understanding and improvement of salt tolerance in wheat.

SUBMITTER: Amirbakhtiar N

PROVIDER: S-EPMC6420002 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar.

Amirbakhtiar Nazanin N Ismaili Ahmad A Ghaffari Mohammad Reza MR Nazarian Firouzabadi Farhad F Shobbar Zahra-Sadat ZS

PloS one 20190315 3

Salt stress is one of the major adverse environmental factors limiting crop productivity. Considering Iran as one of the bread wheat origins, we sequenced root transcriptome of an Iranian salt tolerant cultivar, Arg, under salt stress to extend our knowledge of the molecular basis of salinity tolerance in Triticum aestivum. RNA sequencing resulted in more than 113 million reads and about 104013 genes were obtained, among which 26171 novel transcripts were identified. A comparison of abundances s ...[more]

PMID: 30875373

Similar Datasets

Project description:BACKGROUND:Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3'-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. RESULTS:Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. CONCLUSION:The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.

Project description:BACKGROUND: Wheat seed germination directly affects wheat yield and quality. Although transcriptome and proteome analyses during seed germination have been reported in some crop plant species, dynamic transcriptome characterization during wheat seed germination has not been conducted. We performed the first comprehensive dynamic transcriptome analysis during different seed germination stages of elite Chinese bread wheat cultivar Jimai 20 using the Affymetrix Wheat Genome Array. RESULTS: A total of 61,703 probe sets representing 51,411 transcripts were identified during the five seed germination stages of Jimai 20, of which 2,825 differential expression probe sets corresponding to 2,646 transcripts with different functions were declared by ANOVA and a randomized variance model. The seed germination process included a rapid initial uptake phase (0-12 hours after imbibition [HAI]), a plateau phase (12-24 HAI), and a further water uptake phase (24-48 HAI), corresponding to switches from the degradation of small-molecule sucrose to the metabolism of three major nutrients and to photosynthesis. Hierarchical cluster and MapMan analyses revealed changes in several significant metabolism pathways during seed germination as well as related functional groups. The signal pathway networks constructed with KEGG showed three important genes encoding the phosphofructokinase family protein, with fructose-1, 6-bisphosphatase, and UTP-glucose-1-phosphate uridylyltransferase located at the center, indicating their pivotal roles in the glycolytic pathway, gluconeogenesis, and glycogenesis, respectively. Several significant pathways were selected to establish a metabolic pathway network according to their degree value, which allowed us to find the pathways vital to seed germination. Furthermore, 51 genes involved in transport, signaling pathway, development, lipid metabolism, defense response, nitrogen metabolism, and transcription regulation were analyzed by gene co-expression network with a k-core algorithm to determine which play pivotal roles in germination. Twenty-three meaningful genes were found, and quantitative RT-PCR analysis validated the expression patterns of 12 significant genes. CONCLUSIONS: Wheat seed germination comprises three distinct phases and includes complicated regulation networks involving a large number of genes. These genes belong to many functional groups, and their co-regulations guarantee regular germination. Our results provide new insight into metabolic changes during seed germination and interactions between some significant genes.

Project description:Salinity stress tolerance is a physiologically complex trait that is conferred by the large array of interacting mechanisms. Among these, vacuolar Na(+) sequestration has always been considered as one of the key components differentiating between sensitive and tolerant species and genotypes. However, vacuolar Na(+) sequestration has been rarely considered in the context of the tissue-specific expression and regulation of appropriate transporters contributing to Na(+) removal from the cytosol. In this work, six bread wheat varieties contrasting in their salinity tolerance (three tolerant and three sensitive) were used to understand the essentiality of vacuolar Na(+) sequestration between functionally different root tissues, and link it with the overall salinity stress tolerance in this species. Roots of 4-day old wheat seedlings were treated with 100 mM NaCl for 3 days, and then Na(+) distribution between cytosol and vacuole was quantified by CoroNa Green fluorescent dye imaging. Our major observations were as follows: (1) salinity stress tolerance correlated positively with vacuolar Na(+) sequestration ability in the mature root zone but not in the root apex; (2) contrary to expectations, cytosolic Na(+) levels in root meristem were significantly higher in salt tolerant than sensitive group, while vacuolar Na(+) levels showed an opposite trend. These results are interpreted as meristem cells playing a role of the "salt sensor;" (3) no significant difference in the vacuolar Na(+) sequestration ability was found between sensitive and tolerant groups in either transition or elongation zones; (4) the overall Na(+) accumulation was highest in the elongation zone, suggesting its role in osmotic adjustment and turgor maintenance required to drive root expansion growth. Overall, the reported results suggest high tissue-specificity of Na(+) uptake, signaling, and sequestration in wheat roots. The implications of these findings for plant breeding for salinity stress tolerance are discussed.

Dataset Information

Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar.

Publications

Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets