ArticleBMC genomics2016
Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Combining Transcriptome and Hormone-Targeted Metabolome Analyses to Dissect the Regulatory Mechanisms Underlying Wheat Peduncle Elongation.Plants (Basel, Switzerland) · 2025Article
- Genome-wide association analysis of wheat stem traits using 55K microarrays.Frontiers in plant science · 2025Article
- Identification of the Solid Stem Suppressor GeneInternational journal of molecular sciences · 2023Article
- Article
- A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population.PLoS genetics · 2022Article
- QTL Identification for Stem Fiber, Strength and Rot Resistance in a DH Population from an Alien Introgression ofPlants (Basel, Switzerland) · 2022Article
- Fusarium head blight resistance exacerbates nutritional loss of wheat grain at elevated COScientific reports · 2022Article
- Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response.BMC genomics · 2021Article
- Genome-Wide Association Analysis for Stem Cross Section Properties, Height and Heading Date in a Collection of Spanish Durum Wheat Landraces.Plants (Basel, Switzerland) · 2021Article
- Using natural variation to understand plant responses to iron availability.Journal of experimental botany · 2021Article
- Article
- Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events in Triticum.Molecular biology and evolution · 2020Article
- AFrontiers in plant science · 2020Article
- De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway.Scientific reports · 2019Article
- High-Throughput Phenotyping Enabled Genetic Dissection of Crop Lodging in Wheat.Frontiers in plant science · 2019Article
- A wheat caffeic acid 3-O-methyltransferase TaCOMT-3D positively contributes to both resistance to sharp eyespot disease and stem mechanical strength.Scientific reports · 2018Article
- Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels.Plant biotechnology journal · 2018Article
- Dissecting the complex regulation of lodging resistance inMolecular breeding : new strategies in plant improvement · 2018Article
- Variation across a wheat genetic diversity panel for saccharification of hydrothermally pretreated straw.Biotechnology for biofuels · 2017Article
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe current approach to reducing the tendency for wheat grown under high fertilizer conditions to collapse (lodge) under the weight of its grain is based on reducing stem height via the introduction of Rht genes. However, these reduce the yield of straw (itself an important commodity) and introduce other undesirable characteristics. Identification of alternative height-control loci is therefore of key interest. In addition, the improvement of stem mechanical strength provides a further way through which lodging can be reduced.
resultsTo investigate the prospects for genetic alternatives to Rht, we assessed variation for plant height and stem strength properties in a training genetic diversity panel of 100 wheat accessions fixed for Rht. Using mRNAseq data derived from RNA purified from leaves, functional genotypes were developed for the panel comprising 42,066 Single Nucleotide Polymorphism (SNP) markers and 94,060 Gene Expression Markers (GEMs). In the first application in wheat of the recently-developed method of Associative Transcriptomics, we identified associations between trait variation and both SNPs and GEMs. Analysis of marker-trait associations revealed candidates for the causative genes underlying the trait variation, implicating xylan acetylation and the COP9 signalosome as contributing to stem strength and auxin in the control of the observed variation for plant height. Predictive capabilities of key markers for stem strength were validated using a test genetic diversity panel of 30 further wheat accessions.
conclusionsThis work illustrates the power of Associative Transcriptomics for the exploration of complex traits of high agronomic importance in wheat. The careful selection of genotypes included in the analysis, allowed for high resolution mapping of novel trait-controlling loci in this staple crop. The use of Gene Expression markers coupled with the more traditional sequence-based markers, provides the power required to understand the biological context of the marker-trait associations observed. This not only adds to the wealth of knowledge that we strive to accumulate regarding gene function and plant adaptation, but also provides breeders with the information required to make more informed decisions regarding the potential consequences of incorporating the use of particular markers into future breeding programmes.
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