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Si E, Meng Y, Ma X, Li B, Wang J, Yao L, Yang K, Zhang Y, Shang X, Wang H. Genome Resource for Barley Leaf Stripe Pathogen Pyrenophora graminea. PLANT DISEASE 2020; 104:320-322. [PMID: 31804900 DOI: 10.1094/pdis-06-19-1179-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pyrenophora graminea is the causative agent of barley leaf stripe disease. In this study, the strong pathogenic isolate QWC was used to generate DNA for Illumina sequencing. After assembly, its genome size was 42.5 Mb, consisting of 264 scaffolds, and a total of 10,376 genes was predicted. This is the first genome resource available for P. graminea. The genome sequences of P. graminea will accelerate the understanding interaction of P. graminea and barley.
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Affiliation(s)
- Erjing Si
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yaxiong Meng
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaole Ma
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Baochun Li
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Juncheng Wang
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lirong Yao
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ke Yang
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yu Zhang
- Gansu Plant Seed Administrative Station, Lanzhou 730020, China
| | - Xunwu Shang
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
| | - Huajun Wang
- Gansu Provincial Key Laboratory of Aridland and Crop Science/Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
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Ghannam A, Alek H, Doumani S, Mansour D, Arabi MIE. Deciphering the transcriptional regulation and spatiotemporal distribution of immunity response in barley to Pyrenophora graminea fungal invasion. BMC Genomics 2016; 17:256. [PMID: 27004551 PMCID: PMC4804540 DOI: 10.1186/s12864-016-2573-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/07/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Barley leaf stripe disease, caused by the fungus Pyrenophora graminea (Pg), is a worldwide crop disease that results in significant loss of barley yield. The purpose of the present work was to use transcriptomic profiling to highlight barley genes and metabolic pathways affected or altered in response to Pg infection and consequently elucidate their involvement and contribution in resistance to leaf stripe. RESULTS Our study examined and compared the transcriptomes of two barley genotypes using an established differential display reverse-transcription polymerase chain reaction (DDRT-PCR) strategy at 14 and 20 days post-inoculation (dpi). A total of 54 significantly modulated expressed sequence tags (ESTs) were identified. The analysis of gene expression changes during the course of infection with Pg suggested the involvement of 15 upregulated genes during the immunity response. By using network-based analyses, we could establish a significant correlation between genes expressed in response to Pg invasion. Microscopic analysis and quantitative PCR (qPCR) profiling of callose synthase and cellulose synthases revealed a direct involvement of cell wall reinforcement and callose deposition in the Pg-resistant phenotype. CONCLUSIONS We have identified a number of candidate genes possibly involved in the host-pathogen interactions between barley and Pg fungus, 15 of which are specifically expressed in Pg-resistant plants. Collectively, our results suggest that the resistance to leaf stripe in barley proceeds through callose deposition and different oxidation processes.
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Affiliation(s)
- Ahmed Ghannam
- Laboratory of Plant Functional Genomics, Division of Plant Pathology, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria.
| | - Houda Alek
- Laboratory of Plant Functional Genomics, Division of Plant Pathology, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria
| | - Sanaa Doumani
- Laboratory of Plant Functional Genomics, Division of Plant Pathology, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria
| | - Doureid Mansour
- Laboratory of Plant Functional Genomics, Division of Plant Pathology, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria
| | - Mohamad I E Arabi
- Laboratory Plant Disease, Division of Plant Pathology, Department of Molecular Biology and Biotechnology, AECS, P.O. Box 6091, Damascus, Syria
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The CC-NB-LRR-type Rdg2a resistance gene confers immunity to the seed-borne barley leaf stripe pathogen in the absence of hypersensitive cell death. PLoS One 2010; 5. [PMID: 20844752 PMCID: PMC2937021 DOI: 10.1371/journal.pone.0012599] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 08/12/2010] [Indexed: 01/04/2023] Open
Abstract
Background Leaf stripe disease on barley (Hordeum vulgare) is caused by the seed-transmitted hemi-biotrophic fungus Pyrenophora graminea. Race-specific resistance to leaf stripe is controlled by two known Rdg (Resistance to Drechslera graminea) genes: the H. spontaneum-derived Rdg1a and Rdg2a, identified in H. vulgare. The aim of the present work was to isolate the Rdg2a leaf stripe resistance gene, to characterize the Rdg2a locus organization and evolution and to elucidate the histological bases of Rdg2a-based leaf stripe resistance. Principal Findings We describe here the positional cloning and functional characterization of the leaf stripe resistance gene Rdg2a. At the Rdg2a locus, three sequence-related coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NB-LRR) encoding genes were identified. Sequence comparisons suggested that paralogs of this resistance locus evolved through recent gene duplication, and were subjected to frequent sequence exchange. Transformation of the leaf stripe susceptible cv. Golden Promise with two Rdg2a-candidates under the control of their native 5′ regulatory sequences identified a member of the CC-NB-LRR gene family that conferred resistance against the Dg2 leaf stripe isolate, against which the Rdg2a-gene is effective. Histological analysis demonstrated that Rdg2a-mediated leaf stripe resistance involves autofluorescing cells and prevents pathogen colonization in the embryos without any detectable hypersensitive cell death response, supporting a cell wall reinforcement-based resistance mechanism. Conclusions This work reports about the cloning of a resistance gene effective against a seed borne disease. We observed that Rdg2a was subjected to diversifying selection which is consistent with a model in which the R gene co-evolves with a pathogen effector(s) gene. We propose that inducible responses giving rise to physical and chemical barriers to infection in the cell walls and intercellular spaces of the barley embryo tissues represent mechanisms by which the CC-NB-LRR-encoding Rdg2a gene mediates resistance to leaf stripe in the absence of hypersensitive cell death.
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Biselli C, Urso S, Bernardo L, Tondelli A, Tacconi G, Martino V, Grando S, Valè G. Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1207-1218. [PMID: 20041226 DOI: 10.1007/s00122-009-1248-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 12/12/2009] [Indexed: 05/28/2023]
Abstract
Leaf stripe of barley, caused by Pyrenophora graminea, is an important seed-borne disease in organically grown as well as in conventionally grown Nordic and Mediterranean barley districts. Two barley segregating populations represented by 103 recombinant inbred lines (RILs) of the cross L94 (susceptible) x Vada (resistant) and 194 RILs of the cross Arta (susceptible) x Hordeum spontaneum 41-1 (resistant) were analysed with two highly virulent leaf stripe isolates, Dg2 and Dg5, to identify loci for P. graminea resistance. A major gene with its positive allele contributed by Vada and H. spontaneum 41-1 was detected in both populations and for both pathogen isolates on chromosome 2HL explaining 44.1 and 91.8% R (2), respectively for Dg2 and Dg5 in L94 x Vada and 97.8 and 96.1% R (2), respectively for Dg2 and Dg5 in Arta x H. spontaneum 41-1. Common markers in the gene region of the two populations enabled map comparison and highlighted an overlapping for the region of the resistance locus. Since the map position of the resistance locus identified in this report is the same as that for the leaf stripe resistance gene Rdg1a, mapped earlier in Alf and derived from the 'botanical' barley line H. laevigatum, we propose that leaf stripe resistance in Vada and H. spontaneum 41-1 is governed by the same gene, namely by Rdg1a, and that Rdg1a resistance could be traced back to H. spontaneum, the progenitor of cultivated barley. PCR-based molecular markers that can be used for marker-assisted selection (MAS) of Rdg1a were identified. An Rdg1a syntenic interval with the rice chromosome arm 4L was identified on the basis of rice orthologs of EST-based barley markers. Analysis of the rice genes annotated into the syntenic interval did not reveal sequences strictly belonging to the major class (nucleotide-binding site plus leucine-rich repeat) of the resistance genes. Nonetheless, four genes coding for domains that are present in the major disease-resistance genes, namely receptor-like protein kinase and ATP/GTP-binding proteins, were identified together with a homolog of the barley powdery mildew resistance gene mlo. Three (out of five) homologs of these genes were mapped in the Rdg1a region in barley and the mlo homolog map position was tightly associated with the LOD score peak in both populations.
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Affiliation(s)
- Chiara Biselli
- CRA-GPG Genomic Research Centre, Via S. Protaso 302, 29017, Fiorenzuola d'Arda (PC), Italy
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HAEGI ANITA, BONARDI VERA, DALL’AGLIO ELENA, GLISSANT DAVID, TUMINO GIORGIO, COLLINS NICHOLASC, BULGARELLI DAVIDE, INFANTINO ALESSANDRO, STANCA AMICHELE, DELLEDONNE MASSIMO, VALÈ GIAMPIERO. Histological and molecular analysis of Rdg2a barley resistance to leaf stripe. MOLECULAR PLANT PATHOLOGY 2008; 9:463-78. [PMID: 18705861 PMCID: PMC6640343 DOI: 10.1111/j.1364-3703.2008.00479.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Barley (Hordeum vulgare L.) leaf stripe is caused by the seed-borne fungus Pyrenophora graminea. We investigated microscopically and molecularly the reaction of barley embryos to leaf stripe inoculation. In the resistant genotype NIL3876-Rdg2a, fungal growth ceased at the scutellar node of the embryo, while in the susceptible near-isogenic line (NIL) Mirco-rdg2a fungal growth continued past the scutellar node and into the embryo. Pathogen-challenged embryos of resistant and susceptible NILs showed different levels of UV autofluorescence and toluidine blue staining, indicating differential accumulation of phenolic compounds. Suppression subtractive hybridization and cDNA amplified fragment-length polymorphism (AFLP) analyses of embryos identified P. graminea-induced and P. graminea-repressed barley genes. In addition, cDNA-AFLP analysis identified six pathogenicity-associated fungal genes expressed during barley infection but at low to undetectable levels during growth on artificial media. Microarrays representing the entire set of differentially expressed cDNA-AFLP fragments and 100 barley homologues of previously described defence-related genes were used to study gene expression changes at 7 and 14 days after inoculation in the resistant and susceptible NILs. A total of 171 significantly modulated barley genes were identified and assigned to four groups based on timing and genotype dependence of expression. Analysis of the changes in gene expression during the barley resistance response to leaf stripe suggests that the Rdg2a-mediated response includes cell-wall reinforcement, signal transduction, generation of reactive oxygen species, cell protection, jasmonate signalling and expression of plant effector genes. The identification of genes showing leaf stripe inoculation or resistance-dependent expression sets the stage for further dissection of the resistance response of barley embryo cells to leaf stripe.
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Affiliation(s)
- ANITA HAEGI
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Patologia Vegetale, 00156 Roma, Italy
| | - VERA BONARDI
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, 37134 Verona, Italy
- Present address:
Department of BiologyCoker Hall 108, CB 3280University of North CarolinaChapel Hill NC27599‐3280USA
| | - ELENA DALL’AGLIO
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Genomica e la Postgenomica Animale e Vegetale, 29017 Fiorenzuola d’Arda, Italy
| | - DAVID GLISSANT
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, 37134 Verona, Italy
| | - GIORGIO TUMINO
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Genomica e la Postgenomica Animale e Vegetale, 29017 Fiorenzuola d’Arda, Italy
- Present address:
Università degli Studi di MilanoDipartimento di BiologiaSezione di Fisiologia Vegetale–Fotosintesi20133 MilanoItaly
| | - NICHOLAS C. COLLINS
- Australian Centre for Plant Functional Genomics, University of Adelaide, Glen Osmond SA 5064, Australia
| | - DAVIDE BULGARELLI
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Genomica e la Postgenomica Animale e Vegetale, 29017 Fiorenzuola d’Arda, Italy
| | - ALESSANDRO INFANTINO
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Patologia Vegetale, 00156 Roma, Italy
| | - A. MICHELE STANCA
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Genomica e la Postgenomica Animale e Vegetale, 29017 Fiorenzuola d’Arda, Italy
| | - MASSIMO DELLEDONNE
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, 37134 Verona, Italy
| | - GIAMPIERO VALÈ
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Genomica e la Postgenomica Animale e Vegetale, 29017 Fiorenzuola d’Arda, Italy
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Marcel TC, Aghnoum R, Durand J, Varshney RK, Niks RE. Dissection of the barley 2L1.0 region carrying the 'Laevigatum' quantitative resistance gene to leaf rust using near-isogenic lines (NIL) and subNIL. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1604-15. [PMID: 17990968 DOI: 10.1094/mpmi-20-12-1604] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Partial resistance to leaf rust (Puccinia hordei G. H. Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation, resulting in a long latency period in greenhouse tests. The three most consistent quantitative trait loci (QTL) uncovered in the L94 x 'Vada' mapping population were introgressed by marker-assisted backcrossing into the susceptible L94 background to obtain near-isogenic lines (NIL). We also developed the reciprocal Vada-NIL for the susceptibility alleles of those QTL. The QTL Rphq2 affected latency period of P. hordei more than the QTL Rphq3 and Rphq4. The NIL confirmed the contribution of Rphq2 to partial resistance by prolonging the latency period by 28 h on L94-Rphq2 and shortening the latency period by 23 h on Vada-rphq2. On the basis of flanking restriction fragment length polymorphism-based markers, Rphq2 appeared to be located near the telomeric end of the long arm of chromosome 2H, in a physical region of high recombination, making it the target QTL for map-based cloning. Microscopic observations on the NIL confirmed the nonhypersensitive nature of the resistance conferred by Rphq2. A high-resolution genetic map of the Rphq2 region was constructed using a population of 38 subNIL with overlapping L94 introgressions in Vada background across the region. Rphq2 mapped approximately 2 centimorgans (cM) proximal from the MlLa locus. By bulked segregant analysis and use of synteny with rice, we developed additional markers and fine-mapped Rphq2 to a genetic interval of 0.11 cM that corresponds to a stretch of sequence of, at most, 70 kb in rice. Analysis of this rice sequence revealed predicted genes encoding two proteins with unknown function, retrotransposon proteins, peroxidase proteins, and a protein similar to a mitogen-activated protein kinase kinase kinase (MAP3K). Possible homologs of those peroxidases and MAP3K in barley are candidates for the gene that contributes to partial resistance to P. hordei.
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Affiliation(s)
- Thierry C Marcel
- Laboratory of Plant Breeding, Wageningen University, The Netherlands
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Wilfert L, Gadau J, Baer B, Schmid-Hempel P. Natural variation in the genetic architecture of a host-parasite interaction in the bumblebee Bombus terrestris. Mol Ecol 2007; 16:1327-39. [PMID: 17391417 DOI: 10.1111/j.1365-294x.2007.03234.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The genetic architecture of fitness-relevant traits in natural populations is a topic that has remained almost untouched by quantitative genetics. Given the importance of parasitism for the host's fitness, we used QTL mapping to study the genetic architecture of traits relevant for host-parasite interactions in the trypanosome parasite, Crithidia bombi and its host, Bombus terrestris. The three traits analysed were the parasite's infection intensity, the strength of the general immune response (measured as the encapsulation of a novel antigen) and body size. The genetic architecture of these traits was examined in three natural, unmanipulated mapping populations of B. terrestris. Our results indicate that the intracolonial phenotypic variation of all three traits is based on a network of QTLs and epistatic interactions. While these networks are similar between mapping populations in complexity and number of QTLs, as well as in their epistatic interactions, the variability in the position of QTL and the interacting loci was high. Only one QTL for body size was plausibly found in at least two populations. QTLs for encapsulation and Crithidia infection intensity were located on the same linkage groups.
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Affiliation(s)
- L Wilfert
- ETH Zürich, Institute for Integrative Biology (IBZ), Experimental Ecology Group, ETH-Zentrum CHN, CH-8092 Zürich, Switzerland.
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Bulgarelli D, Collins NC, Tacconi G, Dellaglio E, Brueggeman R, Kleinhofs A, Stanca AM, Valè G. High-resolution genetic mapping of the leaf stripe resistance gene Rdg2a in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1401-1408. [PMID: 14689188 DOI: 10.1007/s00122-003-1557-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2003] [Accepted: 11/24/2003] [Indexed: 05/24/2023]
Abstract
The dominant gene Rdg2a of barley conferring resistance to the hemi-biotrophic seed-borne pathogen Pyrenophora graminea is located in the distal region of chromosome arm 1 (7H)S. As the first step towards isolating the gene, a high-resolution genetic map of the region was constructed using an F(2) population of 1,400 plants (Thibaut Rdg2axMirco). The map included six classes of resistance gene analogues (RGAs) tightly associated with Rdg2a. Rdg2a was delimited to a genetic interval of 0.14 cM between the RGAs ssCH4 and MWG851. Additional markers were generated using the sequence from the corresponding region on rice chromosome 6, allowing delimitation of the Rdg2a syntenic interval in rice to a 115 kbp stretch of sequence. Analysis of the rice sequence failed to reveal any genes with similarity to characterized resistance genes. Therefore, either the rice-barley synteny is disrupted in this region, or Rdg2a encodes a novel type of resistance protein.
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Affiliation(s)
- D Bulgarelli
- Istituto sperimentale per la Cerealicoltura, Sezione di Fiorenzuola d'Arda, Via S. Protaso 302, 29017 Fiorenzuola d'Arda, Italy
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