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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2775-2) contains supplementary material, which is available to authorized users.
Highlights
The current approach to reducing the tendency for wheat grown under high fertilizer conditions to collapse under the weight of its grain is based on reducing stem height via the introduction of Rht genes
This work illustrates the power of Associative Transcriptomics for the exploration of even the most complex, environmentally sensitive traits
With careful selection of the genotypes included, we have shown that even a relatively small diversity set can, when coupled with high marker density and low linkage disequilibrium, provide the power required for the discovery of novel and agronomically valuable genetic variation
Summary
The 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. These reduce the yield of straw (itself an important commodity) and introduce other undesirable characteristics. Miller et al BMC Genomics (2016) 17:500 wheat accessions are the GA-insensitive Rht-B1 and RhtD1, which markedly increased the yield potential of wheat following their introduction [2] These genes may not be beneficial under some environmental conditions, and efforts to identify other semi-dwarfing genes with different physiological functions are ongoing. The few mapping studies that have been conducted with this aim have been limited by low marker density and mapping resolution through the utilisation of the traditional biparental cross, QTL analysis approach [3, 4]
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