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Transcriptomic and Co-expression Network Analyses on Diverse Wheat Landraces Identifies Candidate Master Regulators of the Response to Early Drought

ABSTRACT: Transcriptomic and Co-expression Network Analyses on Diverse Wheat Landraces Identifies Candidate Master Regulators of the Response to Early Drought

PROVIDER: PRJNA937632 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23584240_1.fastq.gz	Fastqsanger.gz
	SRR23584240_2.fastq.gz	Fastqsanger.gz
	SRR23584241_1.fastq.gz	Fastqsanger.gz
	SRR23584241_2.fastq.gz	Fastqsanger.gz
	SRR23584242_1.fastq.gz	Fastqsanger.gz

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Transcriptomic and co-expression network analyses on diverse wheat landraces identifies candidate master regulators of the response to early drought.

Project description:IntroductionOver four billion people around the world rely on bread wheat (Triticum aestivum L.) as a major constituent of their diet. The changing climate, however, threatens the food security of these people, with periods of intense drought stress already causing widespread wheat yield losses. Much of the research into the wheat drought response has centred on the response to drought events later in development, during anthesis or grain filling. But as the timing of periods of drought stress become increasingly unpredictable, a more complete understanding of the response to drought during early development is also needed.MethodsHere, we utilized the YoGI landrace panel to identify 10,199 genes which were differentially expressed under early drought stress, before weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network and identify hub genes in modules particularly associated with the early drought response.ResultsOf these hub genes, two stood out as novel candidate master regulators of the early drought response - one as an activator (TaDHN4-D1; TraesCS5D02G379200) and the other as a repressor (uncharacterised gene; TraesCS3D02G361500).DiscussionAs well as appearing to coordinate the transcriptional early drought response, we propose that these hub genes may be able to regulate the physiological early drought response due to potential control over the expression of members of gene families well-known for their involvement in the drought response in many plant species, namely dehydrins and aquaporins, as well as other genes seemingly involved in key processes such as, stomatal opening, stomatal closing, stomatal morphogenesis and stress hormone signalling.

| S-EPMC10326901 | biostudies-literature

Transcriptomic and Co-expression Network Analyses on Diverse Wheat Landraces Identifies Candidate Master Regulators of the Response to Early Drought

Project description:More than four billion people rely on bread wheat (Triticum aestivum L.) as a major constituent of their diet. However, the changing climate threatens wheat production, with periods of intense drought stress already causing widespread wheat yield losses. Much of the research into the wheat drought response has centred on the response to drought events later in development, during anthesis or grain filling. But as the timing of periods of drought stress become increasingly unpredictable, a more complete understanding of the response to drought during early development is also needed. Here, we utilized the YoGI landrace panel to identify the key genes regulating processes such as, stomatal opening, stomatal closing, stomatal morphogenesis and stress hormone signalling related to drought stress.

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Mexican maize landraces under drought stress and recovery irrigation

Project description:Transcriptional profiling of three mexican maize landraces under 10, and 17 days stress and recovery irrigation A dye balanced modified loop design was implemented. Two biological replicates (pooling five representative plants) representing each sampling point for each genotype were obtained for purified RNA from 120 randomly chosen seedlings. This experiment involved a total of forty-eight (24 sets) of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across the three landraces. This design allowed us to determine differences in gene expression between the three different landraces under drought stress (10 and 17 days) and at recovery irrigation compared to irrigated controls.

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Identification of Candidate Master Regulators of the Response to Early Heat Stress in Climate-adapted Wheat Landraces via Transcriptomic and Co-expression Network Analyses

Project description:Climate change is not only causing a rise of global temperature but also more variable climates. In major wheat-producing countries, spring temperatures have increased up to 40°C in recent years. Considering the wheat optimal growth temperature of around 20°C, wheat is particularly prone to damage by heat stress. To combat this threat, it is imperative to understand the response of wheat to early heat stress. This research is focus on understanging the transcriptional reprogramming of wheat when exposed to heat stress during the three-leaf stage. Differential expression and weighted gene co-expression network analysis have been used here before and after the stress to to identify candidate master-regulators of this transcriptional response.

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Identification of Candidate Master Regulators of the Response to Early Heat Stress in Climate-adapted Wheat Landraces via Transcriptomic and Co-expression Network Analyses

Project description:Identification of Candidate Master Regulators of the Response to Early Heat Stress in Climate-adapted Wheat Landraces via Transcriptomic and Co-expression Network Analyses

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Co-expression network analysis of diverse wheat landraces reveals markers of early thermotolerance and a candidate master regulator of thermotolerance genes.

Project description:Triticum aestivum L. (bread wheat) is a crop relied upon by billions of people around the world, as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprising 342 accessions that show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110 790 transcripts from the panel and used these data to conduct weighted co-expression network analysis and to identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat-shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belong to the same module, with one (TraesCS4D01G207500.1) being a candidate master-regulator potentially controlling the expression of the other two hub genes, as well as a suite of other HSPs and heat-stress transcription factors (HSFs). In this work, therefore, we identify three validated hub genes, the expression of which can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and HSF expression - presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate-resilient crops.

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P-stalk ribosomes act as master regulators of cytokine-mediated processes

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