Dataset Information

Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local.

ABSTRACT: Kharchia Local wheat variety is an Indian salt tolerant land race known for its tolerance to salinity. However, there is a lack of detailed information regarding molecular mechanism imparting tolerance to high salinity in this bread wheat. In the present study, differential root transcriptome analysis identifying salt stress responsive gene networks and functional annotation under salt stress in Kharchia Local was performed. A total of 453,882 reads were obtained after quality filtering, using Roche 454-GS FLX Titanium sequencing technology. From these reads 22,241 ESTs were generated out of which, 17,911 unigenes were obtained. A total of 14,898 unigenes were annotated against nr protein database. Seventy seven transcription factors families in 826 unigenes and 11,002 SSRs in 6,939 unigenes were identified. Kyoto Encyclopedia of Genes and Genomes database identified 310 metabolic pathways. The expression pattern of few selected genes was compared during the time course of salt stress treatment between salt-tolerant (Kharchia Local) and susceptible (HD2687). The transcriptome data is the first report, which offers an insight into the mechanisms and genes involved in salt tolerance. This information can be used to improve salt tolerance in elite wheat cultivars and to develop tolerant germplasm for other cereal crops.

SUBMITTER: Goyal E

PROVIDER: S-EPMC4904219 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local.

Goyal Etika E Amit Singh K SK Singh Ravi S RS Mahato Ajay K AK Chand Suresh S Kanika Kumar K

Scientific reports 20160613

Kharchia Local wheat variety is an Indian salt tolerant land race known for its tolerance to salinity. However, there is a lack of detailed information regarding molecular mechanism imparting tolerance to high salinity in this bread wheat. In the present study, differential root transcriptome analysis identifying salt stress responsive gene networks and functional annotation under salt stress in Kharchia Local was performed. A total of 453,882 reads were obtained after quality filtering, using R ...[more]

PMID: 27293111

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Project description:Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.

Project description:Salinity is one of the most important problems that adversely affect crops growth, productivity and quality worldwide. Salt Overly Sensitive 1 (SOS1) gene family plays vital roles in plant response to salt stress. Herein, we report the identification of the SOS family in wheat and the exploration of the expression profiles of SOSs under salt stress. Complete genome sequences of T. aestivum were downloaded from Ensembl plant database. Conservation and divergence of TaSOS1 family were conducted by using phylogenetic tree, gene structure and synteny distribution analysis. Expression profiles of TaSOS1s were obtained based on transcriptome and qRT-PCR analysis. Totally, 119 TaSOS1 proteins in wheat were identified at the genome-wide level and classified into three groups. Six motifs were conserved in TaSOS1 gene family. Moreover, 25 TaSOS1 genes had three copies distributing in three sub-genomes (A, B and D). A total of 32, 28 and 29 TaSOS1 genes were located on the sub-genomes A, B and D, respectively. Moreover, there were 19, 12, 6, 7, 28, 5 and 12 genes located on the three homologous of chromosomes 1, 2, 3, 4, 5, 6 and 7, respectively. Two genes were mapped to unattributed scaffolds. The duplication events analysis indicated that tandem repeats contributed to the expansion of the SOS1 family in wheat. Collinearity analysis demonstrated that segmental duplications play an important role in the expansion of SOS1 members. Chromosome 7, 5, 3, and 2 showed collinear relationship. Tissue specific expression pattern analysis revealed that 41 TaSOS1 genes expressed in various tissues, such as root, shoot, leaf, spike and grain. Transcriptomic analysis revealed that 28 and 26 genes were up- and down-regulated under salinity stress, respectively, of which 18 genes were further confirmed by RT-qPCR. The plants with high expression level of these genes displayed higher tolerance to salinity stress, stronger root system, higher Fv/Fm value and water potential. The results could be helpful for further elucidating the molecular mechanism of TaSOS1 related to salt tolerance in wheat and provide a toolkit for improving the salinity tolerance of wheat.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-01009-y.

Dataset Information

Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local.

Publications

Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local.

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