Mameaux S.,UK National Institute of Agricultural Botany |
Cockram J.,UK National Institute of Agricultural Botany |
Thiel T.,Leibniz Institute of Plant Genetics and Crop Plant Research |
Steuernagel B.,Leibniz Institute of Plant Genetics and Crop Plant Research |
And 8 more authors.
Plant Biotechnology Journal | Year: 2012
The genomes of cereals such as wheat (Triticum aestivum) and barley (Hordeum vulgare) are large and therefore problematic for the map-based cloning of agronomicaly important traits. However, comparative approaches within the Poaceae permit transfer of molecular knowledge between species, despite their divergence from a common ancestor sixty million years ago. The finding that null variants of the rice gene cytokinin oxidase/dehydrogenase 2 (OsCKX2) result in large yield increases provides an opportunity to explore whether similar gains could be achieved in other Poaceae members. Here, phylogenetic, molecular and comparative analyses of CKX families in the sequenced grass species rice, brachypodium, sorghum, maize and foxtail millet, as well as members identified from the transcriptomes/genomes of wheat and barley, are presented. Phylogenetic analyses define four Poaceae CKX clades. Comparative analyses showed that CKX phylogenetic groupings can largely be explained by a combination of local gene duplication, and the whole-genome duplication event that predates their speciation. Full-length OsCKX2 homologues in barley (HvCKX2.1, HvCKX2.2) and wheat (TaCKX2.3, TaCKX2.4, TaCKX2.5) are characterized, with comparative analysis at the DNA, protein and genetic/physical map levels suggesting that true CKX2 orthologs have been identified. Furthermore, our analysis shows CKX2 genes in barley and wheat have undergone a Triticeae-specific gene-duplication event. Finally, by identifying ten of the eleven CKX genes predicted to be present in barley by comparative analyses, we show that next-generation sequencing approaches can efficiently determine the gene space of large-genome crops. Together, this work provides the foundation for future functional investigation of CKX family members within the Poaceae. © 2011 National Institute of Agricultural Botany (NIAB). Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.
Cubizolles N.,French National Institute for Agricultural Research |
Cubizolles N.,University Blaise Pascal |
Rey E.,French National Institute for Agricultural Research |
Rey E.,University Blaise Pascal |
And 36 more authors.
Plant Genome | Year: 2016
Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP) markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific singlenucleotide polymorphism (SNPs) in the hexaploid wheat (Triticum aestivumL.) genome. Here, we report on the development of a high-throughput SNP discovery approach based on sequence capture of ISBP markers. By applying this approach to the reference sequence of chromosome 3B from hexaploid wheat, we designed 39,077 SNPs that are evenly distributed along the chromosome. We demonstrate that these SNPs can be efficiently scored with the KASPar (Kompetitive allele-specific polymerase chain reaction) genotyping technology. Finally, through genetic diversity and genome-wide association studies, we also demonstrate that ISBP-derived SNPs can be used in marker-assisted breeding programs. © Crop Science Society of America.
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 225.97K | Year: 2011
This proposal for LINK funded project will build on a solid base of work currently underway, funded through existing LINK programmes, BBSRC, directly by industry, the Scottish Government and the NIAB Trust fund. The proposed study will seek to initiate a better understanding of wheat root growth, morphology and functional relationships with nutrient and water uptake. Methods to describe roots in a diverse range of winter wheat types will be implemented in controlled glasshouse conditions and in the field. The project will form the foundation for improving nutrient sequestration and conversion in this important UK crop through initiation of pre-breeding and development of ideal root ideotypes suitable for use in current and future wheat production. The consortium will concentrate on efficient or enhanced use of resources, especially nitrogen and phosphate and will consider interactions with water availability. In addition, the importance of interactions with beneficial mycorrhizal fungi on nutrient sequestration and the negative impact of soil-borne pathogenic fungi on susceptible genotypes will be considered under field conditions. Finally, the potential impact of agrochemical seed coats on root performance will be assessed. Overall, research in root biology leading to increases in nutrient uptake efficiency will contribute to reductions in diffuse pollution and will substantially reduce green house gas emission due a reduction in the use of nitrogen fertilisers in wheat cultivation
McGrann G.R.D.,Crop and Soil Systems Group |
Steed A.,John Innes Center |
Burt C.,RAGT Seeds Ltd. |
Nicholson P.,John Innes Center |
Brown J.K.M.,John Innes Center
Journal of Experimental Botany | Year: 2015
Lesion mimic mutants display spontaneous necrotic spots and chlorotic leaves as a result of mis-regulated cell death programmes. Typically these mutants have increased resistance to biotrophic pathogens but their response to facultative fungi that cause necrotrophic diseases is less well studied. The effect of altered cell death regulation on the development of disease caused by Ramularia collo-cygni, Fusarium culmorum and Oculimacula yallundae was explored using a collection of barley necrotic (nec) lesion mimic mutants. nec8 mutants displayed lower levels of all three diseases compared to nec9 mutants, which had increased R. collo-cygni but decreased F. culmorum disease symptoms. nec1 mutants reduced disease development caused by both R. collo-cygni and F. culmorum. The severity of the nec1-induced lesion mimic phenotype and F. culmorum symptom development was reduced by mutation of the negative cell death regulator MLO. The significant reduction in R. collo-cygni symptoms caused by nec1 was completely abolished in the presence of the mlo-5 allele and both symptoms and fungal biomass were greater than in the wild-type. These results indicate that physiological pathways involved in regulation of cell death interact with one another in their effects on different fungal pathogens. © The Author 2015.
Agency: GTR | Branch: BBSRC | Program: | Phase: Studentship | Award Amount: 0.00 | Year: 2015
Wheat, grown on more land than any other crop, is the most important food grain source for mankind, it provides 20% of our calories, is the major source of protein for the poor, and is by far, the major European crop. Fusarium head blight (FHB) is a major threat to wheat production. FHB reduces yields and leads to the accumulation of mycotoxins in grain. Most UK wheat varieties are highly susceptible to FHB and achieving resistance remains a major challenge internationally. Traditionally, research has focussed on identifying FHB resistance and introgressing genes of major effect into commercial varieties. In this project we aim to exploit our discovery that wheat is complicit in its own downfall. This is because carries FHB susceptibility factors that actually assist the fungus. This finding means that a new approach can be taken - the targeted elimination of susceptibility. We have identified three locations in the wheat genome that confer susceptibility to FHB. The aim of this project will be to physically map these regions with the long term intention of isolating the genes responsible. A pre-existing gamma-irradiated population of a FHB susceptible wheat cultivar will be used to generate a deletion map of the target regions. Previous studies have established the deletion frequency within these materials. A tiling path of overlapping chromosomal deletions covering the FHB susceptibility loci will be constructed and used to dissect each of them by putting together genomic and FHB resistance data. In this way the position of the FHB susceptibility factor will be refined. The gene content of the newly defined loci will be revealed by alignment of deletions to closely related cereal species for which genome sequence is available (gene content prediction by synteny) and increasingly by the more direct comparison with the rapidly emerging wheat genome sequence. These approaches will allow the identification of candidate FHB susceptibility genes, which will then be studied in detail for expression profiles. If time permits wheat TILLING populations will be screened to identify and disease screen mutants in the susceptibility factor candidates. In addition to providing an outstanding opportunity to work at the forefront of crop science, this project includes collaboration with a dynamic wheat research team with the company RAGT to provide the student with an insight into commercial plant breeding.
Mcgrann G.R.D.,John Innes Center |
Mcgrann G.R.D.,Crop and Soil Systems Group |
Steed A.,John Innes Center |
Burt C.,John Innes Center |
And 8 more authors.
Molecular Plant Pathology | Year: 2015
NAC proteins are plant transcription factors that are involved in tolerance to abiotic and biotic stresses, as well as in many developmental processes. Stress-responsive NAC1 (SNAC1) transcription factor is involved in drought tolerance in barley and rice, but has not been shown previously to have a role in disease resistance. Transgenic over-expression of HvSNAC1 in barley cv. Golden Promise reduced the severity of Ramularia leaf spot (RLS), caused by the fungus Ramularia collo-cygni, but had no effect on disease symptoms caused by Fusarium culmorum, Oculimacula yallundae (eyespot), Blumeria graminis f. sp. hordei (powdery mildew) or Magnaporthe oryzae (blast). The HvSNAC1 transcript was weakly induced in the RLS-susceptible cv. Golden Promise during the latter stages of R.collo-cygni symptom development when infected leaves were senescing. Potential mechanisms controlling HvSNAC1-mediated resistance to RLS were investigated. Gene expression analysis revealed no difference in the constitutive levels of antioxidant transcripts in either of the over-expression lines compared with cv. Golden Promise, nor was any difference in stomatal conductance or sensitivity to reactive oxygen species-induced cell death observed. Over-expression of HvSNAC1 delayed dark-induced leaf senescence. It is proposed that mechanisms controlled by HvSNAC1 that are involved in tolerance to abiotic stress and that inhibit senescence also confer resistance to R.collo-cygni and suppress RLS symptoms. This provides further evidence for an association between abiotic stress and senescence in barley and the development of RLS. © 2014 John Innes Centre.
Farrell A.D.,University of the West Indies |
Kettlewell P.S.,Harper Adams University College |
Simmonds J.,John Innes Center |
Flintham J.E.,John Innes Center |
And 3 more authors.
Molecular Breeding | Year: 2013
The occurrence of late maturity alpha-amylase (LMA) was investigated using two doubled haploid wheat populations segregating for the dwarfing gene Rht-D1b and the 1B/1R translocation. Genotypes were assessed in the field and in controlled environments where a cold-shock treatment was used to induce LMA. Results from field-grown genotypes from the cross Spark × Rialto suggest that the absence of Rht-D1b or the presence of the 1B/1R translocation increases the expression of LMA.These two genetic factors were found to act independently and to have a positive interaction (complementary epistasis). In Option × Potent genotypes fixed for Rht-D1b, the 1B/1R effect was similar to that seen in the equivalent Spark × Rialto genotypes. Under controlled environment conditions, genotypes with the 1B/1R translocation showed a higher occurrence of LMA under both control and cold-shock conditions. 1B/1R was present in the majority of genotypes expressing LMA under control and cold-shock conditions. The results point to the novel finding that the 1B/1R translocation increases the expression of alpha-amylase in LMA-prone germplasm independently of effects of Rht-D1b, whereas previously it had been thought to act by a modification of the Rht-D1b effect. © 2013 Springer Science+Business Media Dordrecht.
Burt C.,John Innes Center |
Hollins T.W.,RAGT Seeds Ltd |
Powell N.,John Innes Center |
Nicholson P.,John Innes Center
Plant Pathology | Year: 2010
Eyespot is an economically important stem-base disease of wheat caused by two fungal species: Oculimacula yallundae and Oculimacula acuformis. This study investigated the efficacy of two sources of resistance, viz. the genes Pch1, introgressed into hexaploid wheat from Aegilops ventricosa, and Pch2, identified in wheat cv. Cappelle Desprez, against O. yallundae and O. acuformis separately. In a series of seedling bioassays Pch1 was found to be highly effective against both species. Although Pch2 was found to confer resistance against both pathogen species, it was significantly less effective against penetration from O. yallundae than O. acuformis. Furthermore, a quantitative trait locus (QTL) analysis was not able to locate any resistance to O. yallundae on chromosome 7A of Cappelle Desprez. This has important implications for the use of Pch2 in commercial cultivars as it is necessary to have genes that confer resistance to both pathogens for effective eyespot control. In addition, a set of 22 T. monococcum accessions was screened for resistance to both O. yallundae and O. acuformis to identify potentially novel resistances and to assess the accessions for evidence of differential resistance to the eyespot species. Significant differences in resistance to the two pathogens were identified in four of these lines, providing evidence for differential resistance in T. monococcum. This study demonstrates that future screening for novel sources of eyespot resistance should investigate both pathogen species. © 2010 The Authors. Plant Pathology © 2010 BSPP.
Summers R.W.,RAGT Seeds Ltd |
Brown J.K.M.,John Innes Center
Plant Pathology | Year: 2013
Breeding of arable crops such as wheat has led to substantial improvements in yield, quality of produce, traits of agronomic value and resistance to disease and abiotic stress. Resistance to many diseases and pests of wheat has improved through a combination of innovation by breeders, driven by competition, and independent assessment of cultivars in Recommended List trials. In addition to pleiotropic effects of resistance genes, two further limitations on breeding for disease resistance are linkage drag and competition drag. Linkage drag, the slow rate of decline of linkage disequilibrium between closely linked genes, can be especially significant in wheat, particularly after the introgression of chromosome segments from related wild grasses. For example it slowed the deployment of the Pch1 gene for resistance to eyespot in leading cultivars because Pch1 is on a chromosome segment that also reduces yield. Linkage drag also inhibited the use of Pm16 for resistance to powdery mildew. Competition drag can be described as the delay in the deployment of a useful gene because of the additional time needed to raise yield and quality to the standard of the current market-leading cultivars. This is exemplified by the near-absence of resistance to Soil-borne cereal mosaic virus in most modern varieties, despite no evidence for detrimental pleiotropic effects. Changes in agricultural practice and regulation of pesticides are increasing demand for durable resistance to disease but wherever possible, improvement of resistance should not constrain selection for yield which remains the most significant trait in leading wheat cultivars for the UK. © 2013 British Society for Plant Pathology.
Burt C.,John Innes Center |
Hollins T.W.,RAGT Seeds Ltd. |
Nicholson P.,John Innes Center
Theoretical and Applied Genetics | Year: 2011
Eyespot is an economically important fungal disease of wheat and other cereals caused by two fungal species: Oculimacula yallundae and Oculimacula acuformis. However, only two eyespot resistance genes have been characterised and molecular markers made available to plant breeders. These resistances are Pch1, introduced into wheat from the relative Aegilops ventricosa, and Pch2, originally identified in the cultivar Cappelle Desprez (CD). There are drawbacks associated with both resistances; Pch1 is linked to deleterious traits carried on the Ae. ventricosa introgression and Pch2 has been shown to have limited effectiveness. An additional resistance has been reported on chromosome 5A of CD that confers resistance to eyespot in adult plants. In the present study, we demonstrate that resistance on this chromosome is effective against both O. yallundae and O. acuformis eyespot pathogens and confers resistance at both seedling and adult plant stages. This resistance was mapped in both seedling bioassays and field trials in a 5A recombinant population derived from a cross between CD and a CD single chromosome substitution line carrying 5A from the susceptible line Bezostaya. The resistance was also mapped using seedling bioassays in a 5A recombinant population derived from a cross between the susceptible line Chinese Spring (CS) and a single chromosome substitution line carrying 5A from CD. A single major QTL on the long arm of chromosome 5A was detected in all experiments. Furthermore, the SSR marker Xgwm639 was found to be closely associated with the resistance and could be used for marker-assisted selection of the eyespot resistance by plant breeders. © 2010 Springer-Verlag.