Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids

Vega, Jose J De; Peel, Ned; Purdy, Sarah; Hawkins, Sarah; Donnison, Iain S.; Dyer, Sarah; Farrar, Kerrie

doi:10.1186/s13068-021-01948-4

Cited by 8 publications

(5 citation statements)

References 52 publications

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“…Upset plots (Fig. S2) were created with UpSetR [93] and GO-terms presented using code adapted from [43, 94]. The sensitivity heatmap was produced using mean normalised CPM values determined by dividing the average CPM at any given timepoint by the mean CPM for each gene across the entire time course under both temperature conditions.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide circadian gating of a cold temperature response in bread wheat

Graham

Paajanen

Edwards

et al. 2022

Preprint

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Circadian rhythms coordinate the responses of organisms to their daily fluctuating environments, by establishing a temporal program of gene expression. This schedules aspects of metabolism, physiology, development and behaviour according to the time of day. Circadian regulation in plants is extremely pervasive, and is important because it underpins both productivity and seasonal reproduction. Circadian regulation extends to control of environmental responses through a regulatory mechanism known as circadian gating, whereby the circadian clock regulates the response to environmental cues such that the magnitude of response varies according to the time of day. Here, we show that there is genome-wide circadian gating of responses to cold temperatures in plants. By using bread wheat as an experimental model, we establish that circadian gating is crucial to the programs of gene expression that underlie the environmental responses of a crop of major socioeconomic importance. Furthermore, we identify that circadian gating of cold temperature responses are distributed unevenly across the three wheat subgenomes, which might reflect the geographical origins of the ancestors of modern wheat.

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Section: Methodsmentioning

confidence: 99%

Genome-wide circadian gating of a cold temperature response in bread wheat

Graham

Paajanen

Edwards

et al. 2022

Preprint

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“…GO-slim terms refer to ontology terms for biological processes unless otherwise specified and were obtained from Ensembl Plants 51 [ 11 ] using the BioMart tool. The bubble plot was plotted using ggplot in R adapting code from [ 113 ].…”

Section: Methodsmentioning

confidence: 99%

Circadian regulation of the transcriptome in a complex polyploid crop

Rees

Rusholme‐Pilcher²,

Bailey³

et al. 2022

PLoS Biol

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The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

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“…GO terms refer to ontology terms for biological processes unless otherwise specified and were obtained from Ensembl Plants 51, using the BioMart tool. Bubble plots were plotted using ggplot in R, adapting code from 30 .…”

Section: Go Term Analysismentioning

confidence: 99%

De novo annotation of the wheat pan-genome reveals complexity and diversity within the hexaploid wheat pan-transcriptome

White,

Lux,

Rusholme-Pilcher

et al. 2024

Preprint

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Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled the genomes of 15 wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome withde novoannotation and differential expression analysis for nine of these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of thesede novoannotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homoeologous genes, but also widespread changes in sub-genome homoeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homoeolog expression and identified tissue-associated cultivar-specific expression profiles. In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.

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Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids

Cited by 8 publications

References 52 publications

Genome-wide circadian gating of a cold temperature response in bread wheat

Genome-wide circadian gating of a cold temperature response in bread wheat

Circadian regulation of the transcriptome in a complex polyploid crop

De novo annotation of the wheat pan-genome reveals complexity and diversity within the hexaploid wheat pan-transcriptome

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