ORCID Profile
0000-0003-2379-9225
Current Organisation
Universitiy of Zurich
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Microbial Genetics | Mycology | Plant Biology | Plant Pathology |
Control of Plant Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Expanding Knowledge in the Biological Sciences
Publisher: Wiley
Date: 18-06-2012
Publisher: Oxford University Press (OUP)
Date: 06-2010
Abstract: To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of lification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.
Publisher: Wiley
Date: 05-11-2013
DOI: 10.1111/TPJ.12345
Abstract: The improvement of wheat through breeding has relied strongly on the use of genetic material from related wild and domesticated grass species. The 1RS chromosome arm from rye was introgressed into wheat and crossed into many wheat lines, as it improves yield and fungal disease resistance. Pm8 is a powdery mildew resistance gene on 1RS which, after widespread agricultural cultivation, is now widely overcome by adapted mildew races. Here we show by homology-based cloning and subsequent physical and genetic mapping that Pm8 is the rye orthologue of the Pm3 allelic series of mildew resistance genes in wheat. The cloned gene was functionally validated as Pm8 by transient, single-cell expression analysis and stable transformation. Sequence analysis revealed a complex mosaic of ancient haplotypes among Pm3- and Pm8-like genes from different members of the Triticeae. These results show that the two genes have evolved independently after the ergence of the species 7.5 million years ago and kept their function in mildew resistance. During this long time span the co-evolving pathogens have not overcome these genes, which is in strong contrast to the breakdown of Pm8 resistance since its introduction into commercial wheat 70 years ago. Sequence comparison revealed that evolutionary pressure acted on the same subdomains and sequence features of the two orthologous genes. This suggests that they recognize directly or indirectly the same pathogen effectors that have been conserved in the powdery mildews of wheat and rye.
Publisher: Wiley
Date: 10-10-2012
DOI: 10.1111/PBI.12003
Abstract: Agronomically important traits are frequently controlled by rare, genotype-specific alleles. Such genes can only be mapped in a population derived from the donor genotype. This requires the development of a specific genetic map, which is difficult in wheat because of the low level of polymorphism among elite cultivars. The absence of sufficient polymorphism, the complexity of the hexaploid wheat genome as well as the lack of complete sequence information make the construction of genetic maps with a high density of reproducible and polymorphic markers challenging. We developed a genotype-specific genetic map of chromosome 3B from winter wheat cultivars Arina and Forno. Chromosome 3B was isolated from the two cultivars and then sequenced to 10-fold coverage. This resulted in a single-nucleotide polymorphisms (SNP) database of the complete chromosome. Based on proposed synteny with the Brachypodium model genome and gene annotation, sequences close to coding regions were used for the development of 70 SNP-based markers. They were mapped on a Arina × Forno Recombinant Inbred Lines population and found to be spread over the complete chromosome 3B. While overall synteny was well maintained, numerous exceptions and inversions of syntenic gene order were identified. Additionally, we found that the majority of recombination events occurred in distal parts of chromosome 3B, particularly in hot-spot regions. Compared with the earlier map based on SSR and RFLP markers, the number of markers increased fourfold. The approach presented here allows fast development of genotype-specific polymorphic markers that can be used for mapping and marker-assisted selection.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 18-07-2014
Abstract: An ordered draft sequence of the 17-gigabase hexaploid bread wheat ( Triticum aestivum ) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the ergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Publisher: Springer Science and Business Media LLC
Date: 19-08-2003
DOI: 10.1007/S00122-003-1372-3
Abstract: Stagonospora nodorum is the causal agent of the Stagonospora glume blotch disease in hexaploid wheat. The Swiss winter bread wheat cv. 'Arina' has a highly effective, durable and quantitative glume blotch resistance. We studied 240 single seed descent (SSD)-derived lines of an 'Arina x Forno' F(5:7) population to identify and map quantitative trait loci (QTLs) for glume blotch resistance under natural infestation. Using composite interval mapping (CIM) and LOD>4.5, we detected two chromosomal regions on chromosome arms 3BS and 4BL which were specifically associated with glume blotch resistance. These identified QTLs were designated QSng.sfr-3BS and QSng.sfr-4BL, respectively. QSng.sfr-3BS peaked at the locus Xgwm389 in the telomeric region of the short arm of chromosome 3B and explained 31.2% of the observed phenotypic variance for the resistance within the population. The responsible QSng.sfr-3BS allele originated from the resistant parent 'Arina'. The QTL QSng.sfr-4BL (19.1%) mapped to chromosome arm 4BL ('Forno' allele) very close to two known genes, TaMlo and a catalase ( Cat). Both QTL alleles combined could enhance the resistance level by about 50%. Additionally, they showed significant epistatic effects (4.4%). We found PCR-based microsatellite markers closely linked to QSng.sfr-3BS (gwm389) and QSng.sfr-4BL (gwm251) which make marker-assisted selection (MAS) for Stagonospora glume blotch resistance feasible. We also found one resistance QTL, QSng.sfr-5BL, on the long arm of chromosome 5B which overlapped with QTLs for plant height as well as heading time.
Publisher: Springer Science and Business Media LLC
Date: 02-08-2011
DOI: 10.1007/S10142-011-0240-5
Abstract: Powdery mildew of wheat (Triticum aestivum L.) is caused by the ascomycete fungus Blumeria graminis f.sp. tritici. Genomic approaches open new ways to study the biology of this obligate biotrophic pathogen. We started the analysis of the Bg tritici genome with the low-pass sequencing of its genome using the 454 technology and the construction of the first genomic bacterial artificial chromosome (BAC) library for this fungus. High-coverage contigs were assembled with the 454 reads. They allowed the characterization of 56 transposable elements and the establishment of the Blumeria repeat database. The BAC library contains 12,288 clones with an average insert size of 115 kb, which represents a maximum of 7.5-fold genome coverage. Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. Analysis of BAC-end sequences revealed a massive invasion of transposable elements accounting for at least 85% of the genome. This explains the unusually large size of this genome which we estimate to be at least 174 Mb, based on a large-scale physical map constructed through the fingerprinting of the BAC library. Our study represents a crucial step in the perspective of the determination and study of the whole Bg tritici genome sequence.
Publisher: Springer Netherlands
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 19-07-2007
DOI: 10.1007/S00122-007-0601-6
Abstract: Association mapping in populations relevant for wheat breeding has a large potential for validating and fine-mapping QTLs identified in F2- or DH (double haploid)-derived populations. In this study, associations between markers in the region of QSng.sfr-3BS, a major QTL for resistance to Stagonospora nodorum glume blotch (SNG), and SNG resistance were investigated by linkage and association analyses. After increasing marker density in 240 F(5:7) recombinant inbred lines (RILs), QSng.sfr-3BS explained 43% of the genetic variance and peaked 0.6 cM proximal from the marker SUN2-3B. Association between SNG resistance and markers mapped in the region of QSng.sfr-3BS was investigated in a population of 44 modern European winter wheat varieties. Two genetically distinct subpopulations were identified within these lines. In agreement with linkage analyses, association mapping by a least squares general linear model (GLM) at marker loci in the region of QSng.sfr-3BS revealed the highest association with SNG resistance for SUN2-3B (p < 0.05). Association mapping can provide an effective mean of relating genotypes to complex quantitative phenotypes in hexaploid wheat. Linkage disequilibrium (r (2)) in chromosome 3B extended less than 0.5 cM in 44 varieties, while it extended about 30 cM in 240 RILs, based on 91 SSR and STS marker-pair comparisons. This indicated that the association mapping population had a marker resolution potential at least 390-fold higher compared to the RIL population.
Publisher: Springer Science and Business Media LLC
Date: 14-07-2013
DOI: 10.1038/NG.2704
Abstract: Wheat powdery mildew, Blumeria graminis forma specialis tritici, is a devastating fungal pathogen with a poorly understood evolutionary history. Here we report the draft genome sequence of wheat powdery mildew, the resequencing of three additional isolates from different geographic regions and comparative analyses with the barley powdery mildew genome. Our comparative genomic analyses identified 602 candidate effector genes, with many showing evidence of positive selection. We characterize patterns of genetic ersity and suggest that mildew genomes are mosaics of ancient haplogroups that existed before wheat domestication. The patterns of ersity in modern isolates suggest that there was no pronounced loss of genetic ersity upon formation of the new host bread wheat 10,000 years ago. We conclude that the ready adaptation of B. graminis f.sp. tritici to the new host species was based on a erse haplotype pool that provided great genetic potential for pathogen variation.
Publisher: Springer Science and Business Media LLC
Date: 05-2019
DOI: 10.1038/S41588-019-0393-Z
Abstract: For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world's most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats. We observe considerable genetic variation at the genic, chromosomal and subgenomic levels, and use this information to decipher the likely origins of modern day wheats, the consequences of range expansion and the allelic variants selected since its domestication. Our data support a reconciled model of wheat evolution and provide novel avenues for future breeding improvement.
Publisher: Research Square Platform LLC
Date: 02-03-2023
DOI: 10.21203/RS.3.RS-2580055/V1
Abstract: One of the most critical steps following genome-wide association studies (GWAS) is the identification and validation of candidate genes underlying genetic associations. Gene presence-absence and copy number variations can significantly h er candidate gene discovery if high-quality genomic resources from specific crop cultivars are unavailable. This is particularly true for disease resistance genes, which are often located in highly dynamic genomic regions. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically erse rice accessions. To facilitate candidate gene identification, we produced de-novo genome assemblies of ten rice accessions that showed rice blast resistance associations. These assemblies facilitated the identification and validation of novel alleles of the rice blast resistance genes Ptr and Pia . Our work shows that GWAS in combination with whole-genome sequencing are powerful tools for gene cloning and uncovers an allelic series for the unusual Ptr rice blast resistance gene.
Publisher: Cold Spring Harbor Laboratory
Date: 12-12-2019
DOI: 10.1101/2019.12.11.869693
Abstract: We present a chromosome-scale annotated assembly of the rye ( Secale cereale L. inbred line ‘Lo7’) genome, which we use to explore Triticeae genomic evolution, and rye’s superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.
Publisher: Cold Spring Harbor Laboratory
Date: 07-06-2010
Abstract: Colinearity of genes in plant genomes generally decreases with increasing evolutionary distance while the actual number of genes remains more or less constant. To characterize the molecular mechanisms of this “gene movement,” we identified non-colinear genes by three-way comparison of the genomes of Brachypodium , rice, and sorghum. We found that genomic fragments of up to 50 kb containing the non-colinear genes are duplicated to acceptor sites elsewhere in the genome. Apparent movement of genes may usually be the result of subsequent deletions of genes in the donor region. Often, the duplicated fragments are precisely bordered by transposable elements (TEs) at the acceptor site. Highly diagnostic sequence motifs at these borders strongly suggest that these gene movements were the result of double-strand break (DSB) repair through synthesis-dependent strand annealing. In these cases, a copy of the foreign DNA fragment is used as filler DNA to repair the DSB linked with the transposition of TEs. Interestingly, most TEs we found associated with gene movement have a very low copy number in the genome and for several we did not find autonomous copies. This suggests that some of these elements spontaneously arose from unspecific interaction with TE proteins that are encoded by autonomous elements. Additionally, we found evidence that gene movements can also be caused when DSBs are repaired after template slippage or unequal crossing-over events. The observed frequency of gene movements can explain the erosion of gene colinearity between plant genomes during evolution.
Publisher: Springer Science and Business Media LLC
Date: 02-10-2003
DOI: 10.1007/S00122-003-1444-4
Abstract: The Swiss winter bread wheat cv. 'Forno' has a highly effective, durable and quantitative leaf rust ( Puccinia triticina Eriks.) resistance which is associated with leaf tip necrosis (LTN). We studied 240 single seed descent lines of an 'ArinaxForno' F(5:7 )population to identify and map quantitative trait loci (QTLs) for leaf rust resistance and LTN. Percentage of infected leaf area (%) and the response to infection (RI) were evaluated in seven field trials and were transformed to the area under the disease progress curves (AUDPC). Using composite interval mapping and LOD >4.4, we identified eight chromosomal regions specifically associated with resistance. The largest and most consistent leaf rust resistance locus was identified on the short arm of chromosome 7D (32.6% of variance explained for AUDPC_% and 42.6% for AUDPC_RI) together with the major QTL for LTN ( R(2)=55.6%) in the same chromosomal region as Lr34 ( Xgwm295). A second major leaf rust resistance QTL ( R(2)=28% and 31.5%, respectively) was located on chromosome arm 1BS close to Xgwm604 and was not associated with LTN. Additional minor QTLs for LTN (2DL, 3DL, 4BS and 5AL) and leaf rust resistance were identified. These latter QTLs might correspond to the leaf rust resistance genes Lr2 or Lr22 (2DS) and Lr14a (7BL).
Publisher: Wiley
Date: 05-2001
DOI: 10.1046/J.1365-313X.2001.01028.X
Abstract: In plant species with large genomes such as wheat or barley, genome organization at the level of DNA sequence is largely unknown. The largest sequences that are publicly accessible so far from Triticeae genomes are two 60 kb and 66 kb intervals from barley. Here, we report on the analysis of a 211 kb contiguous DNA sequence from diploid wheat (Triticum monococcum L.). Five putative genes were identified, two of which show similarity to disease resistance genes. Three of the five genes are clustered in a 31 kb gene-enriched island while the two others are separated from the cluster and from each other by large stretches of repetitive DNA. About 70% of the contig is comprised of several classes of transposable elements. Ten different types of retrotransposons were identified, most of them forming a pattern of nested insertions similar to those found in maize and barley. Evidence was found for major deletion, insertion and duplication events within the analysed region, suggesting multiple mechanisms of genome evolution in addition to retrotransposon lification. Seven types of foldback transposons, an element class previously not described for wheat genomes, were characterized. One such element was found to be closely associated with genes in several Triticeae species and may therefore be of use for the identification of gene-rich regions in these species.
Publisher: Cold Spring Harbor Laboratory
Date: 10-03-2021
DOI: 10.1101/2021.03.09.433749
Abstract: Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable - a phenomenon that remains poorly understood as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew ( Blumeria graminis ). Here, we used QTL mapping to identify the corresponding wheat mildew avirulence effector AvrPm17 . It is encoded by two paralogous genes that exhibit signatures of re-occurring gene conversion events and are members of a mildew sub-lineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sub-lineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17 . This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangle complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene ersity in pathogen populations becomes an integral part of introgression breeding to ensure effective and durable resistance in wheat. Domesticated and wild wheat relatives provide an important source of new immune receptors for wheat resistance breeding against fungal pathogens. The durability of these resistance genes is variable and difficult to predict, yet it is crucial for effective resistance breeding. We identified a fungal effector protein recognised by an immune receptor introgressed from rye to wheat. We found that variants of the effector allowing the fungus to overcome the resistance are ancient. They were already present in the wheat powdery mildew gene pool before the introgression of the immune receptor and are therefore responsible for the rapid resistance breakdown. Our study demonstrates that the effort to identify new resistance genes should be accompanied by studies of avirulence genes on the pathogen side.
Publisher: Springer Science and Business Media LLC
Date: 26-07-2022
DOI: 10.1038/S41467-022-31975-0
Abstract: The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global s le of 172 mildew genomes. Our analyses show that B.g. tritici emerged in the Fertile Crescent during wheat domestication. After it spread throughout Eurasia, colonization brought it to America, where it hybridized with unknown grass mildew species. Recent trade brought USA strains to Japan, and European strains to China. In both places, they hybridized with local ancestral strains. Thus, although mildew spreads by wind regionally, our results indicate that humans drove its global spread throughout history and that mildew rapidly evolved through hybridization.
Publisher: Springer Science and Business Media LLC
Date: 04-05-2014
DOI: 10.1007/S00122-014-2311-1
Abstract: This article covers detailed characterization and naming of QSr.sun - 5BL as Sr56 . Molecular markers linked with adult plant stem rust resistance gene Sr56 were identified and validated for marker-assisted selection. The identification of new sources of adult plant resistance (APR) and effective combinations of major and minor genes is well appreciated in breeding for durable rust resistance in wheat. A QTL, QSr.sun-5BL, contributed by winter wheat cultivar Arina providing 12-15 % reduction in stem rust severity, was reported in an Arina/Forno recombinant inbred line (RIL) population. Following the demonstration of monogenic segregation for APR in the Arina/Yitpi RIL population, the resistance locus was formally named Sr56. Saturation mapping of the Sr56 region using STS (from EST and DArT clones), SNP (9 K) and SSR markers from wheat chromosome survey sequences that were ordered based on synteny with Brachypodium distachyon genes in chromosome 1 resulted in the flanking of Sr56 by sun209 (SSR) and sun320 (STS) at 2.6 and 1.2 cM on the proximal and distal ends, respectively. Investigation of conservation of gene order between the Sr56 region in wheat and B. distachyon showed that the syntenic region defined by SSR marker interval sun209-sun215 corresponded to approximately 192 kb in B. distachyon, which contains five predicted genes. Conservation of gene order for the Sr56 region between wheat and Brachypodium, except for two inversions, provides a starting point for future map-based cloning of Sr56. The Arina/Forno RILs carrying both Sr56 and Sr57 exhibited low disease severity compared to those RILs carrying these genes singly. Markers linked with Sr56 would be useful for marker-assisted pyramiding of this gene with other major and APR genes for which closely linked markers are available.
Publisher: Springer Science and Business Media LLC
Date: 08-02-2023
DOI: 10.1186/S12915-023-01513-5
Abstract: Worldwide wheat production is under constant threat by fast-evolving fungal pathogens. In the last decades, wheat breeding for disease resistance heavily relied on the introgression of chromosomal segments from related species as genetic sources of new resistance. The Pm8 resistance gene against the powdery mildew disease has been introgressed from rye into wheat as part of a large 1BL.1RS chromosomal translocation encompassing multiple disease resistance genes and yield components. Due to its high agronomic value, this translocation has seen continuous global use since the 1960s on large growth areas, even after Pm8 resistance was overcome by the powdery mildew pathogen. The long-term use of Pm8 at a global scale provided the unique opportunity to study the consequences of such extensive resistance gene application on pathogen evolution. Using genome-wide association studies in a population of wheat mildew isolates, we identified the avirulence effector AvrPm8 specifically recognized by Pm8 . Haplovariant mining in a global mildew population covering all major wheat growing areas of the world revealed 17 virulent haplotypes of the AvrPm8 gene that grouped into two functional categories. The first one comprised amino acid polymorphisms at a single position along the AvrPm8 protein, which we confirmed to be crucial for the recognition by Pm8. The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame such as disruptions of the start codon, gene truncations, gene deletions, and interference with mRNA splicing. With the exception of a single, likely ancient, gain-of-virulence mutation found in mildew isolates around the world, all AvrPm8 virulence haplotypes were found in geographically restricted regions, indicating that they occurred recently as a consequence of the frequent Pm8 use. In this study, we show that the broad and prolonged use of the Pm8 gene in wheat production worldwide resulted in a multitude of gain-of-virulence mechanisms affecting the AvrPm8 gene in the wheat powdery mildew pathogen. Based on our findings, we conclude that both standing genetic variation as well as locally occurring new mutations contributed to the global breakdown of the Pm8 resistance gene introgression.
Publisher: Informa UK Limited
Date: 15-12-2022
Publisher: Oxford University Press (OUP)
Date: 14-11-2008
Abstract: A large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic ersity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes erged only a few thousand years ago, while some barley and Ae. tauschii haplotypes erged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.
Publisher: Public Library of Science (PLoS)
Date: 21-11-2013
Publisher: Springer Science and Business Media LLC
Date: 30-07-2003
DOI: 10.1007/S00122-003-1361-6
Abstract: We constructed a genetic linkage map based on a cross between two Swiss winter wheat ( Triticum aestivum L.) varieties, Arina and Forno. Two-hundred and forty F(5) single-seed descent (SSD)-derived lines were analysed with 112 restriction fragment length polymorphism (RFLP) anonymous probes, 18 wheat cDNA clones coding for putative stress or defence-related proteins and 179 simple-sequence repeat (SSR) primer-pairs. The 309 markers revealed 396 segregating loci. Linkage analysis defined 27 linkage groups that could all be assigned to chromosomes or chromosome arms. The resulting genetic map comprises 380 loci and spans 3,086 cM with 1,131 cM for the A genome, 920 cM for the B genome and 1,036 cM for the D genome. Seventeen percent of the loci showed a significant ( P < 0.05) deviation from a 1:1 ratio, most of them in favour of the Arina alleles. This map enabled the mapping of QTLs for resistance against several fungal diseases such as Stagonospora glume blotch, leaf rust and Fusarium head blight. It will also be very useful for wheat genetic mapping, as it combines RFLP and SSR markers that were previously located on separate maps.
Publisher: Public Library of Science (PLoS)
Date: 10-03-2014
Publisher: Proceedings of the National Academy of Sciences
Date: 29-06-2015
Abstract: Northern corn leaf blight (NCLB) is one of the most devastating fungal diseases of maize. The Htn1 disease resistance gene confers quantitative field resistance against most NCLB isolates. Here we show that Htn1 encodes a putative wall-associated receptor-like kinase (RLK). RLKs act as important components of the first tier of the plant innate immune system by perceiving pathogen- or host-derived elicitors on the cell surface. RLKs are often associated with resistance to nonadapted pathogens and are a component of nonhost resistance. Our work demonstrates that the Htn1-RLK plays an important role in host resistance against adapted fungal pathogens.
Publisher: Springer Science and Business Media LLC
Date: 25-11-2020
DOI: 10.1038/S41586-020-2961-X
Abstract: Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2,3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic ersity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to erse environments, grain yield and quality, and resistance to stresses 4,5 . We provide ex les outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.
Publisher: Springer Science and Business Media LLC
Date: 11-02-2021
DOI: 10.1038/S41467-020-20777-X
Abstract: Plasma membrane-associated and intracellular proteins and protein complexes play a pivotal role in pathogen recognition and disease resistance signaling in plants and animals. The two predominant protein families perceiving plant pathogens are receptor-like kinases and nucleotide binding-leucine-rich repeat receptors (NLR), which often confer race-specific resistance. Leaf rust is one of the most prevalent and most devastating wheat diseases. Here, we clone the race-specific leaf rust resistance gene Lr14a from hexaploid wheat. The cloning of Lr14a is aided by the recently published genome assembly of Arina LrFor , an Lr14a -containing wheat line. Lr14a encodes a membrane-localized protein containing twelve ankyrin (ANK) repeats and structural similarities to Ca 2+ -permeable non-selective cation channels. Transcriptome analyses reveal an induction of genes associated with calcium ion binding in the presence of Lr14a . Haplotype analyses indicate that Lr14a- containing chromosome segments were introgressed multiple times into the bread wheat gene pool, but we find no variation in the Lr14a coding sequence itself. Our work demonstrates the involvement of an ANK-transmembrane (TM)-like type of gene family in race-specific disease resistance in wheat. This forms the basis to explore ANK-TM-like genes in disease resistance breeding.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 17-08-2018
Abstract: Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Ex les of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science , this issue p. eaar7191 see also p. eaar6089
Publisher: Wiley
Date: 14-11-2018
DOI: 10.1111/NPH.15529
Publisher: Springer Science and Business Media LLC
Date: 25-05-2007
DOI: 10.1007/S00122-007-0543-Z
Abstract: Diploid A genome species of wheat harbour immense variability for biotic stresses and productivity traits, and these could be transferred efficiently to hexaploid wheat through marker assisted selection, provided the target genes are tagged at diploid level first. Here we report an integrated molecular linkage map of A genome diploid wheat based on 93 recombinant inbred lines (RILs) derived from Triticum boeoticum x Triticum monococcum inter sub-specific cross. The parental lines were analysed with 306 simple sequence repeat (SSR) and 194 RFLP markers, including 66 bin mapped ESTs. Out of 306 SSRs tested for polymorphism, 74 (24.2%) did not show lification (null) in both the parents. Overall, 171 (73.7%) of the 232 remaining SSR and 98 (50.5%) of the 194 RFLP markers were polymorphic. Both A and D genome specific SSR markers showed similar transferability to A genome of diploid wheat species. The 176 polymorphic markers, that were assayed on a set of 93 RILs, yielded 188 polymorphic loci and 177 of these as well as two additional morphological traits mapped on seven linkage groups with a total map length of 1,262 cM, which is longer than most of the available A genome linkage maps in diploid and hexaploid wheat. About 58 loci showed distorted segregation with majority of these mapping on chromosome 2A(m). With a few exceptions, the position and order of the markers was similar to the ones in other maps of the wheat A genome. Chromosome 1A(m) of T. monococcum and T. boeoticum showed a small paracentric inversion relative to the A genome of hexaploid wheat. The described linkage map could be useful for gene tagging, marker assisted gene introgression from diploid into hexaploid wheat as well as for map based cloning of genes from diploid A genome species and orthologous genes from hexaploid wheat.
Publisher: Wiley
Date: 26-11-2012
DOI: 10.1111/TPJ.12048
Abstract: A 454 sequencing snapshot was utilised to investigate the genome composition and nucleotide ersity of transposable elements (TEs) for several Triticeae taxa, including Triticum aestivum, Hordeum vulgare, Hordeum spontaneum and Secale cereale together with relatives of the A, B and D genome donors of wheat, Triticum urartu (A), Aegilops speltoides (S) and Aegilops tauschii (D). Additional taxa containing the A genome, Triticum monococcum and its wild relative Triticum boeoticum, were also included. The main focus of the analysis was on the genomic composition of TEs as these make up at least 80% of the overall genome content. Although more than 200 TE families were identified in each species, approximately 50% of the overall genome comprised 12-15 TE families. The BARE1 element was the largest contributor to all genomes, contributing more than 10% to the overall genome. We also found that several TE families differ strongly in their abundance between species, indicating that TE families can thrive extremely successfully in one species while going virtually extinct in another. Additionally, the nucleotide ersity of BARE1 populations within in idual genomes was measured. Interestingly, the nucleotide ersity in the domesticated barley H. vulgare cv. Barke was found to be twice as high as in its wild progenitor H. spontaneum, suggesting that the domesticated barley gained nucleotide ersity from the addition of different genotypes during the domestication and breeding process. In the rye/wheat lineage, sequence ersity of BARE1 elements was generally higher, suggesting that factors such as geographical distribution and mating systems might play a role in intragenomic TE ersity.
Publisher: Oxford University Press (OUP)
Date: 05-2011
Abstract: All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were s led per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely erse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.
Publisher: Wiley
Date: 30-12-2010
Publisher: Springer Science and Business Media LLC
Date: 26-10-2006
Abstract: During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing"), promising a ~100-fold increase in throughput over Sanger technology – an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley. To study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC) clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences. Our data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing and targeted sequence analysis can result in large regions of high-quality finished genomic sequences.
Publisher: Springer Science and Business Media LLC
Date: 20-05-2012
Publisher: Springer Science and Business Media LLC
Date: 19-03-2021
DOI: 10.1038/S42003-021-01908-6
Abstract: The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 ( Rg-B1 ) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20 th century. We used genotyping-by-sequencing to characterize a global ersity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the ersity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.
Publisher: Wiley
Date: 25-08-2009
Publisher: Wiley
Date: 09-11-2009
Publisher: Elsevier BV
Date: 03-2011
DOI: 10.1016/J.FGB.2010.10.003
Abstract: The two fungal pathogens Blumeria graminis f. sp. tritici (B.g. tritici) and hordei (B.g. hordei) cause powdery mildew specifically in wheat or barley. They have the same life cycle, but their growth is restricted to the respective host. Here, we compared the sequences of two loci in both cereal mildews to determine their ergence time and their relationship with the evolution of their hosts. We sequenced a total of 273.3kb derived from B.g. tritici BAC sequences and compared them with the orthologous regions in the B.g. hordei genome. Protein-coding genes were colinear and well conserved. In contrast, the intergenic regions showed very low conservation mostly due to different integration patterns of transposable elements. To estimate the ergence time of B.g. tritici and B.g. hordei, we used conserved intergenic sequences including orthologous transposable elements. This revealed that B.g. tritici and B.g. hordei have erged about 10 million years ago (MYA), two million years after wheat and barley (12 MYA). These data suggest that B.g. tritici and B.g. hordei have co-evolved with their hosts during most of their evolutionary history after host ergence, possibly after a short phase of host expansion when the same pathogen could still grow on the two erged hosts.
Publisher: Springer Science and Business Media LLC
Date: 18-03-2021
DOI: 10.1038/S41588-021-00807-0
Abstract: Rye ( Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a erse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye’s incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye–wheat introgressions.
Publisher: Wiley
Date: 27-08-2001
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/FP17024
Abstract: The prototype light-induced fluorescence transient (LIFT) instrument provides continuous, minimally intrusive, high time resolution (~2 s) assessment of photosynthetic performance in terrestrial plants from up to 2 m. It induces a chlorophyll fluorescence transient by a series of short flashes in a saturation sequence (180 ~1μs flashlets in μs) to achieve near-full reduction of the primary acceptor QA, followed by a relaxation sequence (RQA 90 flashlets at exponentially increasing intervals over ~30 ms) to observe kinetics of QA re-oxidation. When fitted by the fast repetition rate (FRR) model (Kolber et al. 1998) the QA flash of LIFT/FRR gives smaller values for FmQA from dark adapted leaves than FmPAM from pulse litude modulated (PAM) assays. The ratio FmQA/FmPAM resembles the ratio of fluorescence yield at the J/P phases of the classical O-J-I-P transient and we conclude that the difference simply is due to the levels of PQ pool reduction induced by the two techniques. In a strong PAM-analogous WL pulse in the dark monitored by the QA flash of LIFT/FRR φPSIIWL ≈ φPSIIPAM. The QA flash also tracks PQ pool reduction as well as the associated responses of ETR QA → PQ and PQ → PSI, the relative functional (σPSII) and optical absorption (aPSII) cross-sections of PSII in situ with a time resolution of ~2 s as they relax after the pulse. It is impractical to deliver strong WL pulses at a distance in the field but a longer PQ flash from LIFT/FRR also achieves full reduction of PQ pool and delivers φPSIIPQ ≈ φPSIIPAM to obtain PAM-equivalent estimates of ETR and NPQ at a distance. In situ values of σPSII and aPSII from the QA flash with smaller antenna barley (chlorina-f2) and Arabidopsis mutants (asLhcb2–12, ch1–3 Lhcb5) are proportionally similar to those previously reported from in vitro assays. These direct measurements are further validated by changes in antenna size in response to growth irradiance. We illustrate how the QA flash facilitates our understanding of photosynthetic regulation during sun flecks in natural environments at a distance, with a time resolution of a few seconds.
Publisher: Proceedings of the National Academy of Sciences
Date: 20-07-2022
Abstract: Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable—a phenomenon that remains poorly understood, as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew ( Blumeria graminis ). Here, we used quantitative trait locus (QTL) mapping to identify the corresponding wheat mildew avirulence effector AvrPm17 . It is encoded by two paralogous genes that exhibit signatures of reoccurring gene conversion events and are members of a mildew sublineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sublineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangling complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene ersity in pathogen populations become an integral part of introgression breeding to ensure effective and durable resistance in wheat.
Publisher: Wiley
Date: 22-04-2019
DOI: 10.1111/NPH.15815
Publisher: Frontiers Media SA
Date: 30-01-2018
Publisher: Springer Science and Business Media LLC
Date: 19-11-2016
DOI: 10.1007/S00122-016-2829-5
Abstract: Fine mapping of Yr47 and Lr52 in chromosome arm 5BS of wheat identified close linkage of the marker sun180 to both genes and its robustness for marker-assisted selection was demonstrated. The widely effective and genetically linked rust resistance genes Yr47 and Lr52 have previously been mapped in the short arm of chromosome 5B in two F
Publisher: Proceedings of the National Academy of Sciences
Date: 14-11-2000
Abstract: For many agronomically important plant genes, only their position on a genetic map is known. In the absence of an efficient transposon tagging system, such genes have to be isolated by map-based cloning. In bread wheat Triticum aestivum , the genome is hexaploid, has a size of 1.6 × 10 10 bp, and contains more than 80% of repetitive sequences. So far, this genome complexity has not allowed chromosome walking and positional cloning. Here, we demonstrate that chromosome walking using bacterial artificial chromosome (BAC) clones is possible in the diploid wheat Triticum monococcum (A m genome). BAC end sequences were mostly repetitive and could not be used for the first walking step. New probes corresponding to rare low-copy sequences were efficiently identified by low-pass DNA sequencing of the BACs. Two walking steps resulted in a physical contig of 450 kb on chromosome 1A m S. Genetic mapping of the probes derived from the BAC contig demonstrated perfect colinearity between the physical map of T. monococcum and the genetic map of bread wheat on chromosome 1AS. The contig genetically spans the Lr10 leaf rust disease resistance locus in bread wheat, with 0.13 centimorgans corresponding to 300 kb between the closest flanking markers. Comparison of the genetic to physical distances has shown large variations within 350 kb of the contig. The physical contig can now be used for the isolation of the orthologous regions in bread wheat. Thus, subgenome chromosome walking in wheat can produce large physical contigs and saturate genomic regions to support positional cloning.
Publisher: Springer Science and Business Media LLC
Date: 20-06-2008
Publisher: Proceedings of the National Academy of Sciences
Date: 25-11-2003
Abstract: More than 50 leaf rust resistance ( Lr ) genes against the fungal pathogen Puccinia triticina have been identified in the wheat gene pool, and a large number of them have been extensively used in breeding. Of the 50 Lr genes, all are known only from their phenotype and/or map position except for Lr21 , which was cloned recently. For many years, the problems of molecular work in the large (1.6 × 10 10 bp), highly repetitive (80%), and hexaploid bread wheat ( Triticum aestivum L.) genome have h ered map-based cloning. Here, we report the isolation of the Lr gene Lr10 from hexaploid wheat by using a combination of subgenome map-based cloning and haplotype studies in the genus Triticum. Lr10 is a single-copy gene on chromosome 1AS. It encodes a CC-NBS-LRR type of protein with an N-terminal domain, which is under ersifying selection. When overexpressed in transgenic wheat plants, Lr10 confers enhanced resistance to leaf rust. Lr10 has similarities to RPM1 in Arabidopsis thaliana and to resistance gene analogs in rice and barley, but is not closely related to other wheat Lr genes based on Southern analysis. We conclude that map-based cloning of genes of agronomic importance in hexaploid wheat is now feasible, opening perspectives for molecular bread wheat improvement trough transgenic strategies and diagnostic allele detection.
Publisher: Wiley
Date: 20-04-2017
DOI: 10.1111/PBI.12723
Publisher: Wiley
Date: 15-11-2016
DOI: 10.1111/PBI.12647
Publisher: Wiley
Date: 24-03-2021
DOI: 10.1111/TPJ.15183
Publisher: Springer Science and Business Media LLC
Date: 10-03-2004
DOI: 10.1007/S00122-004-1628-6
Abstract: Fusarium head blight (FHB) of wheat is a widespread and destructive disease which occurs in humid and semi-humid areas. FHB epidemics can cause serious yield and quality losses under favorable climatic conditions, but the major concern is the contamination of grains with mycotoxins. Resistance to FHB is quantitatively inherited and greatly influenced by the environment. Its evaluation is costly and time-consuming. The genetic basis of FHB resistance has mainly been studied in spring wheat. The objective of this study was to map quantitative trait loci (QTLs) for resistance to FHB in a population of 240 recombinant inbred lines (RILs) derived from a cross between the two Swiss winter wheat cultivars Arina (resistant) and Forno (susceptible). The RILs were genotyped with microsatellite and RFLP markers. The resulting genetic map comprises 380 loci and spans 3,086 cM. The 240 RILs were evaluated for resistance to FHB in six field trials over 3 years. Composite interval mapping (CIM) analyses carried out on FHB AUDPC (i.e. mean values across six environments) revealed eight QTLs which altogether explained 47% of the phenotypic variance. The three main QTLs were mapped on the long arms of chromosomes 6D ( R(2)=22%), 5B ( R(2)=14%) and 4A ( R(2)=10%). The QTL detected on 5B originated from the susceptible parent Forno. Other QTLs with smaller effects on FHB resistance were detected on chromosomes 2AL, 3AL, 3BL, 3DS and 5AL.
Publisher: Cold Spring Harbor Laboratory
Date: 25-08-2022
DOI: 10.1101/2022.08.24.505094
Abstract: The Pm8 resistance gene against the powdery mildew disease has been introgressed from rye into wheat as part of a large 1BL.1RS chromosomal translocation. Due to its high agronomic value, this translocation has seen continuous global use since the 1960’s on large growth areas, even after Pm8 resistance was overcome. This allows studying the effect of long and widespread resistance gene use on a pathogen population. Using genome wide association studies in a global population of wheat mildew isolates, we identified the avirulence effector AvrPm8 specifically recognized by Pm8 . Haplovariant mining in the global population revealed 17 virulent haplotypes of the AvrPm8 gene that grouped into two categories. The first one from geographically erse regions comprised two single amino acid polymorphisms at the same position in the AvrPm8 protein, which we confirmed to be crucial for recognition by Pm8. The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame. Most in idual gain-of-virulence mutations were found in geographically restricted regions, indicating they occurred recently as a consequence of the frequent Pm8 use. We conclude that both standing genetic variation as well as locally occurring new mutations contributed to the global breakdown of the Pm8 resistance gene introgression.
Publisher: Springer Science and Business Media LLC
Date: 12-11-2019
DOI: 10.1038/S41588-018-0266-X
Abstract: Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world's major genebanks. Our large s le size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.
Publisher: Wiley
Date: 15-12-2020
DOI: 10.1111/NPH.17075
Abstract: Pm1a , the first powdery mildew resistance gene described in wheat, is part of a complex resistance (R) gene cluster located in a distal region of chromosome 7AL that has suppressed genetic recombination. A nucleotide‐binding, leucine‐rich repeat (NLR) immune receptor gene was isolated using mutagenesis and R gene enrichment sequencing (MutRenSeq). Stable transformation confirmed Pm1a identity which induced a strong resistance phenotype in transgenic plants upon challenge with avirulent Blumeria graminis (wheat powdery mildew) pathogens. A high‐density genetic map of a B . graminis family segregating for Pm1a avirulence combined with pathogen genome resequencing and RNA sequencing (RNAseq) identified AvrPm1a effector gene candidates. In planta expression identified an effector, with an N terminal Y/FxC motif, that induced a strong hypersensitive response when co‐expressed with Pm1a in Nicotiana benthamiana . Single chromosome enrichment sequencing (ChromSeq) and assembly of chromosome 7A suggested that suppressed recombination around the Pm1a region was due to a rearrangement involving chromosomes 7A, 7B and 7D. The cloning of Pm1a and its identification in a highly rearranged region of chromosome 7A provides insight into the role of chromosomal rearrangements in the evolution of this complex resistance cluster.
Publisher: Springer Science and Business Media LLC
Date: 08-2002
Publisher: Canadian Science Publishing
Date: 08-2002
DOI: 10.1139/G02-040
Abstract: The Lr20Sr15Pm1 resistance locus in hexaploid wheat confers resistance to three different fungal wheat pathogens (leaf rust, stem rust, and powdery mildew). It was previously localized in the distal region of chromosome arm 7AL. As a first step towards the isolation of this complex locus, we performed molecular mapping of the Lr20 and Pm1 genes in three F 2 populations. In two populations, a cluster of 8 and 12 markers, respectively, cosegregated with the resistance genes. In a third population based on a cross between a susceptible lr20 mutant and a resistant cultivar, all clustered markers were monomorphic. However, in this population the recombination frequency proximal to the Lr20 gene was up to 60 times higher, indicating that the complete genetic linkage of the clustered markers is not due to a close physical linkage of the probes but is caused by suppressed recombination. This was supported by the analysis of Triticum monococcum BAC clones where no physical linkage between cosegregating probes was observed. Suppressed recombination at the Lr20Pm1 locus is likely the result of an alien introgression of chromatin from an unidentified wild relative species or is due to chromosomal rearrangements.Key words: wheat, leaf rust, powdery mildew, resistance, suppressed recombination.
Start Date: 08-2021
End Date: 08-2024
Amount: $525,000.00
Funder: Australian Research Council
View Funded Activity