Transcriptome Analyses of Near Isogenic Lines Reveal Putative Drought Tolerance Controlling Genes in Wheat

Nouraei, Sina; Mia, Sultan; Liu, Hui; Turner, Neil C.; Yan, Guijun

doi:10.3389/fpls.2022.857829

Cited by 14 publications

(16 citation statements)

References 93 publications

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“…These genes are related with other 106 biological processes, being the most represented protein folding (16%) and transcription regulation (8%), 41 cellular components with nucleus and integral component membrane being associated with a greater number of genes (14% each), and 105 molecular functions, being the most represented ATP binding (12.6%), protein binding (8.7%), and unfolded protein binding (7.3%). These classes of DEGs where also recently associated with wheat tolerance to drought during grain filling stage (Nouraei et al, 2022). Regarding unfolded protein binding, as expected, a great number of genes encode heat shock proteins (Hsp) and heat shock factors (Hsf).…”

Section: Functional Annotation and Gene Ontology Mapping Of High Temp...mentioning

confidence: 58%

Grain Transcriptome Dynamics Induced by Heat in Commercial and Traditional Bread Wheat Genotypes

2022

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High temperature (HT) events have negative impact on wheat grains yield and quality. Transcriptome profiles of wheat developing grains of commercial genotypes (Antequera and Bancal) and landraces (Ardito and Magueija) submitted to heatwave-like treatments during grain filling were evaluated. Landraces showed significantly more differentially expressed genes (DEGs) and presented more similar responses than commercial genotypes. DEGs were more associated with transcription and RNA and protein synthesis in Antequera and with metabolism alterations in Bancal and landraces. Landraces upregulated genes encoding proteins already described as HT responsive, like heat shock proteins and cupins. Apart from the genes encoding HSP, two other genes were upregulated in all genotypes, one encoding for Adenylate kinase, essential for the cellular homeostasis, and the other for ferritin, recently related with increased tolerance to several abiotic stress in Arabidopsis. Moreover, a NAC transcription factor involved in plant development, known to be a negative regulator of starch synthesis and grain yield, was found to be upregulated in both commercial varieties and downregulated in Magueija landrace. The detected diversity of molecular processes involved in heat response of commercial and traditional genotypes contribute to understand the importance of genetic diversity and relevant pathways to cope with these extreme events.

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Section: Functional Annotation and Gene Ontology Mapping Of High Temp...mentioning

confidence: 58%

Grain Transcriptome Dynamics Induced by Heat in Commercial and Traditional Bread Wheat Genotypes

2022

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“…Mia et al (2019) employed heterogeneous inbred family analysis coupled with an immature embryo culturebased fast generation technique to develop NILs from a cross between C306 and Dharwar Dry. In a previous study, we discovered six candidate genes at the qDSI.4B.1 locus by transcriptomic (RNA-seq) analysis of grains from two pairs of NILs under control and DS conditions (Nouraei et al, 2022). However, because post-transcriptional modification plays a crucial role in regulating gene expression, the transcriptome examination alone is not sufficient to decipher the complex trait of drought tolerance (Pan et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Proteomic analysis of near‐isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance

et al. 2023

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Drought is a major constraint for wheat production that is receiving increased attention due to global climate change. This study conducted isobaric tags for relative and absolute quantitation proteomic analysis on near‐isogenic lines to shed light on the underlying mechanism of qDSI.4B.1 quantitative trait loci (QTL) on the short arm of chromosome 4B conferring drought tolerance in wheat. Comparing tolerant with susceptible isolines, 41 differentially expressed proteins were identified to be responsible for drought tolerance with a p‐value of < 0.05 and fold change >1.3 or <0.7. These proteins were mainly enriched in hydrogen peroxide metabolic activity, reactive oxygen species metabolic activity, photosynthetic activity, intracellular protein transport, cellular macromolecule localization, and response to oxidative stress. Prediction of protein interactions and pathways analysis revealed the interaction between transcription, translation, protein export, photosynthesis, and carbohydrate metabolism as the most important pathways responsible for drought tolerance. The five proteins, including 30S ribosomal protein S15, SRP54 domain‐containing protein, auxin‐repressed protein, serine hydroxymethyltransferase, and an uncharacterized protein with encoding genes on 4BS, were suggested as candidate proteins responsible for drought tolerance in qDSI.4B.1 QTL. The gene coding SRP54 protein was also one of the differentially expressed genes in our previous transcriptomic study.

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“…Additionally, RNA-seq enables the identification of candidate genes and expression analysis through quantified mRNA sequencing, along with microarray technology in RNA analysis research [ 30 ]. Moreover, gene of interest (GOI) searches and gene expression analysis are being actively used in the study of abiotic stresses, such as drought, heat, salinity, cold damage, and moisture stress [ 31 , 32 , 33 , 34 , 35 ]. The identification of DEGs (differentially expressed genes) though RNA-seq under different stress conditions may provide evidence for an understanding of the genetic effect and metabolic mechanism of wheat.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and Proteome Co-Profiling Offers an Understanding of Pre-Harvest Sprouting (PHS) Molecular Mechanisms in Wheat (Triticum aestivum)

Park

Jung²,

Bang³

et al. 2022

Plants

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While wheat (Triticum aestivum L.) is a widely grown and enjoyed crop, the diverse and complex global situation and climate are exacerbating the instability of its supply. In particular, pre-harvest sprouting (PHS) is one of the major abiotic stresses that frequently occurs due to irregular climate conditions, causing serious damage to wheat and its quality. In this study, transcriptomic analysis with RNA-seq and proteomic analysis with LC-MS/MS were performed in PHS-treated spikes from two wheat cultivars presenting PHS sensitivity and tolerance, respectively. A total of 13,154 differentially expressed genes (DEGs) and 706 differentially expressed proteins (DEPs) were identified in four comparison groups between the susceptible/tolerant cultivars. Gene function and correlation analysis were performed to determine the co-profiled genes and proteins affected by PHS treatment. In the functional annotation of each comparative group, similar functions were confirmed in each cultivar under PHS treatment; however, in Keumgang PHS+7 (K7) vs. Woori PHS+7 (W7), functional annotations presented clear differences in the ”spliceosome” and ”proteasome” pathways. In addition, our results indicate that alternative splicing and ubiquitin–proteasome support the regulation of germination and seed dormancy. This study provides an advanced understanding of the functions involved in transcription and translation related to PHS mechanisms, thus enabling specific proposals for the further analysis of germination and seed dormancy mechanisms and pathways in wheat.

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Transcriptome Analyses of Near Isogenic Lines Reveal Putative Drought Tolerance Controlling Genes in Wheat

Cited by 14 publications

References 93 publications

Grain Transcriptome Dynamics Induced by Heat in Commercial and Traditional Bread Wheat Genotypes

Grain Transcriptome Dynamics Induced by Heat in Commercial and Traditional Bread Wheat Genotypes

Proteomic analysis of near‐isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance

Transcriptome and Proteome Co-Profiling Offers an Understanding of Pre-Harvest Sprouting (PHS) Molecular Mechanisms in Wheat (Triticum aestivum)

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