RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat

Iquebal, Mir Asif; Sharma, Pradeep; Jasrotia, Rahul Singh; Jaiswal, Sarika; Kaur, Amandeep; Saroha, Monika; Angadi, U. B.; Sheoran, Sonia; Singh, Rajender; Singh, Gyanendra; Rai, Anil; Tiwari, Ruchi; Kumar, Dinesh

doi:10.1038/s41598-019-49915-2

Cited by 67 publications

(39 citation statements)

References 140 publications

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“…Further, a direct role of ABA-dependent WRKY transcription factors was evident from their up-regulation in response to drought stress. The role of WRKY as a regulator of reactive oxygen species and antioxidant accumulation, cellular membrane stability, and altered osmotic adjustment was suggested [59,62,66]. We found, that the important mechanisms of drought sensing by roots were also regulated by hormones.…”

Section: Discussionmentioning

confidence: 61%

“…Similar to MYB TFs, abundant NAC TFs were up-regulated in drought-exposed roots. They can regulate development of thicker roots with enlarged stele, cortex, and epidermis, control a higher number of cells in stele and aerenchyma tissues, and induce lateral roots development and greater root biomass [64][65][66]. In our meta-analysis of multiple transcriptomes, NAC expression was not limited to the root; although, some of the NACs were found specifically or preferentially in this organ.…”

Section: Discussionmentioning

confidence: 75%

“…The predominant role was attributed to abscisic acid (ABA), ethylene, auxins, and cytokinins. They are key regulators of complex heat-drought stress genetic networks in wheat [59,61,62,66]. ABA is important for early response to drought stress, but its high content in roots is not beneficial under prolonged and severe stress.…”

Section: Discussionmentioning

confidence: 99%

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Variation Among Spring Wheat (Triticum aestivum L.) Genotypes in Response to the Drought Stress. II—Root System Structure

Grzesiak

Hordyńska

Maksymowicz

et al. 2019

Plants

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(1) Background: The study analyzed wheat morphological traits to assess the role of roots structure in the tolerance of drought and to recognize the mechanisms of root structure adjustment to dry soil environment. (2) Methods: Root-box and root-basket methods were applied to maintain an intact root system for analysis. (3) Results: Phenotypic differences among six genotypes with variable drought susceptibility index were found. Under drought, the resistant genotypes lowered their shoot-to-root ratio. Dry matter, number, length, and diameter of nodal and lateral roots were higher in drought-tolerant genotypes than in sensitive ones. The differences in the surface area of the roots were greater in the upper parts of the root system (in the soil layer between 0 and 15 cm) and resulted from the growth of roots of the tolerant plant at an angle of 0–30° and 30–60°. (4) Conclusions: Regulation of root bending in a more downward direction can be important but is not a priority in avoiding drought effects by tolerant plants. If this trait is reduced and accompanied by restricted root development in the upper part of the soil, it becomes a critical factor promoting plant sensitivity to water-limiting conditions.

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Section: Discussionmentioning

confidence: 61%

Section: Discussionmentioning

confidence: 75%

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Variation Among Spring Wheat (Triticum aestivum L.) Genotypes in Response to the Drought Stress. II—Root System Structure

Grzesiak

Hordyńska

Maksymowicz

et al. 2019

Plants

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“…RNAseq analysis of wheat root tissue under drought stress led to the identification of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers (28807 SSRs, 276369 and 130653) variants in two contrasting genotypes. Further analysis revealed the drought‐responsive QTLs on chromosome 3B in wheat roots possess 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels; Iquebal et al , 2019). Similarly, transcriptome analysis of wheat root tissue revealed up regulation of auxin receptor (AFB2) and ABA‐responsive transcription factors (MYB78, WRKY18 and GBF3) under drought stress (Dalal et al , 2018).…”

Section: Transcriptomics: From Microarrays To Next‐generation Sequencmentioning

confidence: 99%

PANOMICS meets germplasm

Weckwerth

Ghatak

Bellaire

et al. 2020

Plant Biotechnology Journal

108

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Summary Genotyping‐by‐sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post‐transcriptional, translational, post‐translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment‐dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost‐effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment‐dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker‐dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large‐scale functional validation of trait‐specific precision breeding.

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“…In recent years, high-throughput sequencing technologies have been widely used in plant research, and their e ciency has dramatically improved [8][9][10][11]. In this study, gene expression in 10-day-old wheat seedlings cultured in the presence or absence of AC was compared through transcriptome sequencing.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of activated charcoal-induced growth promotion of wheat seedlings in tissue culture

Dong

Wang

et al. 2020

Preprint

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Background: Activated charcoal (AC) is highly adsorbent and is often used to promote seedling growth in plant tissue culture; however, the underlying molecular mechanism remains unclear. In this study, root and leaf tissues of 10-day-old seedlings grown via immature embryo culture in the presence or absence of AC in the culture medium were subjected to global transcriptome analysis by RNA sequencing to provide insights into the effects of AC on seedling growth. Results: In total, we identified 18,555 differentially expressed genes (DEGs). Of these, 11,182 were detected in the roots and 7,373 in the leaves. In seedlings grown in the presence of AC, 9,460 DEGs were upregulated and 7,483 DEGs were downregulated in the presence of AC as compared to the control. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed 254 DEG-enriched pathways, 226 of which were common between roots and leaves. Further analysis of the major metabolic pathways revealed that AC stimulated the expression of nine genes in the phenylpropanoid biosynthesis pathway, including PLA, CYP73A, COMT, CYP84A, and 4CL , the protein products of which promote cell differentiation and seedling growth. Further, AC upregulated genes involved in plant hormone signaling related to stress resistance and disease resistance, including EIN3, BZR1, JAR1, JAZ , and PR1 , and downregulated genes related to plant growth inhibition, including BKI1, ARR-B , DELLA , and ABF . Conclusions: Growth medium containing AC promotes seedling growth by increasing the expression of certain genes in the phenylpropanoid biosynthesis pathway, which are related to cell differentiation and seedling growth, as well as genes involved in plant hormone signaling, which is related to resistance.

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RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat

Cited by 67 publications

References 140 publications

Variation Among Spring Wheat (Triticum aestivum L.) Genotypes in Response to the Drought Stress. II—Root System Structure

Variation Among Spring Wheat (Triticum aestivum L.) Genotypes in Response to the Drought Stress. II—Root System Structure

PANOMICS meets germplasm

Transcriptome analysis of activated charcoal-induced growth promotion of wheat seedlings in tissue culture

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