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Miller C.N.,John Innes Center | Harper A.L.,John Innes Center | Harper A.L.,University of York | Trick M.,John Innes Center | And 4 more authors.
BMC Genomics | Year: 2016

Background: 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. 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. Results: To 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. Conclusions: This 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. © 2016 The Author(s). Source


Boys E.F.,Rothamsted Research | Boys E.F.,University of Nottingham | Roques S.E.,Rothamsted Research | West J.S.,Rothamsted Research | And 6 more authors.
Plant Pathology | Year: 2012

The phenotype of the R gene-mediated resistance derived from oilseed rape (Brassica napus) cv. Imola against the light leaf spot plant pathogen, Pyrenopeziza brassicae, was characterized. Using a doubled haploid B. napus mapping population that segregated for resistance against P. brassicae, development of visual symptoms was characterized and symptomless growth was followed using quantitative PCR and scanning electron microscopy on leaves of resistant/susceptible lines inoculated with suspensions of P. brassicae conidia. Initially, in controlled-environment experiments, growth of P. brassicae was unaffected; then from 8days post-inoculation (dpi) some epidermal cells collapsed ('black flecking') in green living tissue of cv. Imola and from 13 to 36dpi there was no increase in the amount of P. brassicae DNA and no asexual sporulation (acervuli/pustules). By contrast, during this period there was a 300-fold increase in P. brassicae DNA and extensive asexual sporulation in leaves of the susceptible cv. Apex. However, when leaf tissue senesced, the amount of P. brassicae DNA increased rapidly in the resistant but not in the susceptible cultivar and sexual sporulation (apothecia) was abundant on senescent tissues of both. These results were consistent with observations from both controlled condition and field experiments with lines from the mapping population that segregated for this resistance. Analysis of results of both controlled-environment and field experiments suggested that the resistance was mediated by a single R gene located on chromosome A1. © 2011 The Authors. Plant Pathology © 2011 BSPP. Source


Harper A.L.,John Innes Center | Trick M.,John Innes Center | Higgins J.,John Innes Center | Higgins J.,Genome Analysis Center | And 7 more authors.
Nature Biotechnology | Year: 2012

Association genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. But most crops are polyploid, making it difficult to identify the required markers and to assemble a genome sequence to order those markers. To circumvent this difficulty, we developed associative transcriptomics, which uses transcriptome sequencing to identify and score molecular markers representing variation in both gene sequences and gene expression, and correlate this with trait variation. Applying the method in the recently formed tetraploid crop Brassica napus, we identified genomic deletions that underlie two quantitative trait loci for glucosinolate content of seeds. The deleted regions contained orthologs of the transcription factor HAG1 (At5g61420), which controls aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. This approach facilitates the application of association genetics in a broad range of crops, even those with complex genomes. © 2012 Nature America, Inc. All rights reserved. Source


Looseley M.E.,James Hutton Institute | Newton A.C.,James Hutton Institute | Atkins S.D.,Rothamsted Research | Fitt B.D.L.,Rothamsted Research | And 7 more authors.
Euphytica | Year: 2012

The genetic basis of several different components of resistance to Rhynchosporium secalis in barley was investigated in a mapping population derived from a cross between winter and spring barley types. Both the severity of visual disease symptoms and amount of R. secalis DNA in leaf tissues were assessed in field trials in Scotland in the 2007/2008 and 2008/2009 growing seasons. Relative expression of symptoms was defined as the residual values from a linear regression of amount of R. secalis DNA against visual plot disease score at GS 50. Amount of R. secalis DNA and visual disease score were highly correlated traits and identified nearly identical QTL. The genetic control of relative expression of symptoms was less clear. However, a QTL on chromosome 7H was identified as having a significant effect on the expression of visual disease symptoms relative to overall amount of R. secalis colonisation. © 2011 Springer Science+Business Media B.V. Source


Niks R.E.,Wageningen University | Alemu S.K.,Ethiopian Institute of Agricultural Research | Marcel T.C.,French National Institute for Agricultural Research | Marcel T.C.,Agro ParisTech | van Heyzen S.,KWS UK Ltd
Euphytica | Year: 2015

Barley (Hordeum vulgare L.) mapping populations have been developed that are useful to study the inheritance of quantitative resistance to adapted and unadapted rust fungi. In a recent host range study, we found that the parents of those mapping populations also differed in their resistance to the crown rust Puccinia coronata (PcE) of couch grass (Elymus repens), as well as three isolates of P. striiformis, representing formae speciales hordei (Psh), tritici (Pst) and bromi (Psb). Available mapping populations were phenotyped at the seedling stage to map the genes conferring resistance to these rust isolates. Resistances to PcE, Psb and Pst inherit quantitatively. This contrasted with reports that barley nonhost resistance to unadapted formae speciales of P. striiformis is based on major genes. We mapped QTLs effective against PcE using relative latency period and relative infection frequency. Some QTLs for resistance were contributed by ‘Vada’ and ‘Cebada Capa’, others by SusPtrit. One PcE-resistance QTL on 3H, contributed by ‘Cebada Capa’, co-localised with a QTL effective against four unadapted grass rust species, indicating either a single gene with broad-spectrum effectiveness or a cluster of rather specific genes. Chromosome arm 7HL from Vada seems particularly rich in genes for resistance to rust fungi. Resistance to Pst and Psb, measured as the number of uredinia, tended to co-localise with each other and mapped to 1HS, 2HL and 7HL. The nearly complete resistance of Ethiopian line L94 to Psh was due to a major gene mapped on chromosome 4H. That gene is likely the recessive gene rpsGZ, which was previously reported in the Ethiopian line Grannenlose Zweizeilige. © 2015, The Author(s). Source

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