1
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Nguyen DT, Henningsen EC, Lewis D, Mago R, McNeil M, Suchecki R, Boden S, Sperschneider J, Kianian S, Dodds P, Figueroa M. Genotypic and resistance profile analysis of two oat crown rust differential sets urge coordination and standardisation. Phytopathology 2023. [PMID: 38114076 DOI: 10.1094/phyto-10-23-0353-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Puccinia coronata f. sp. avenae (Pca) is the causal agent of the disease known as crown rust which represents a bottleneck in oat production worldwide. Characterisation of pathogen populations often involves race (pathotype) assignments using differential sets, which are not uniform across countries. This study compared virulence profiles of 25 Pca isolates from Australia using two host differential sets, one from Australia and one from the USA. These differential sets were also genotyped using DArT sequencing technology. Phenotypic and genotypic discrepancies were detected on eight out of 29 common lines between the two sets, indicating that pathogen race assignments based on those lines are not comparable. To further investigate molecular markers that could assist in the stacking of rust resistance genes important for Australia, four published Pc91-linked markers were validated across the differential sets and then screened across a collection of 150 oat cultivars. Drover, Aladdin, and Volta were identified as putative carriers of the Pc91 locus. This is the first report to confirm that the cultivar 'Volta' carries Pc91 and demonstrates the value of implementing molecular markers to characterise materials in breeding pools of oat. Overall, our findings highlight the necessity of examining seed stocks using pedigree and molecular markers to ensure seed uniformity and bring robustness to surveillance methodologies.
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Affiliation(s)
- Duong T Nguyen
- CSIRO, 2221, Agriculture and Food, Adelaide, South Australia, Australia;
| | - Eva Celeste Henningsen
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Australian National University, 2219, Research School of Biology, Canberra, Australian Capital Territory, Australia;
| | - Dave Lewis
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Rohit Mago
- CSIRO, 2221, Agriculture & Food, GPO Box 1700, Canberra, Australian Capital Territory, Australia, 2601;
| | - Meredith McNeil
- CSIRO, 2221, Agriculture and Food, 306 Carmody Road, St Lucia , Queensland, Australia, 4067;
| | | | - Scott Boden
- The University of Adelaide, 1066, School of Food, Agriculture, and Wine, Adelaide, South Australia, Australia;
| | - Jana Sperschneider
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, 57840, 1551 Lindig Street, Saint Paul, Minnesota, United States, 55108;
| | - Peter Dodds
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
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2
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Sperschneider J, Hewitt T, Lewis DC, Periyannan S, Milgate AW, Hickey LT, Mago R, Dodds PN, Figueroa M. Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina. Nat Microbiol 2023; 8:2130-2141. [PMID: 37884814 PMCID: PMC10627818 DOI: 10.1038/s41564-023-01494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Tim Hewitt
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - David C Lewis
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Sambasivam Periyannan
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
- School of Agriculture and Environmental Science, Centre for Crop Health, The University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Andrew W Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, New South Wales, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
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3
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Mago R, Chen C, Xia X, Whan A, Forrest K, Basnet BR, Perera G, Chandramohan S, Randhawa M, Hayden M, Bansal U, Huerta-Espino J, Singh RP, Bariana H, Lagudah E. Correction to: Adult plant stem rust resistance in durum wheat Glossy Huguenot: mapping, marker development and validation. Theor Appl Genet 2022; 135:4565-4566. [PMID: 36394594 DOI: 10.1007/s00122-022-04240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Rohit Mago
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
| | - Chunhong Chen
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Xiaodi Xia
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Alex Whan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Bhoja R Basnet
- CIMMYT, Carretera Mexico‑Veracruz Km 18, El Batan, Texcoco, Estado de Mexico, Mexico
| | - Geetha Perera
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Sutha Chandramohan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Mandeep Randhawa
- ICRAF House, CIMMYT Kenya, United Nations Avenue, Gigiri, Village Market, P.O. Box 1041, Nairobi, 00621, Kenya
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Urmil Bansal
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico, INIFAP, Chapingo, Estado de Mexico, Mexico
| | - Ravi P Singh
- CIMMYT, Carretera Mexico‑Veracruz Km 18, El Batan, Texcoco, Estado de Mexico, Mexico
| | - Harbans Bariana
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| | - Evans Lagudah
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
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4
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Mago R, Chen C, Xia X, Whan A, Forrest K, Basnet BR, Perera G, Chandramohan S, Randhawa M, Hayden M, Bansal U, Huerta-Espino J, Singh RP, Bariana H, Lagudah E. Adult plant stem rust resistance in durum wheat Glossy Huguenot: mapping, marker development and validation. Theor Appl Genet 2022; 135:1541-1550. [PMID: 35199199 DOI: 10.1007/s00122-022-04052-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/28/2022] [Indexed: 05/12/2023]
Abstract
Adult plant stem rust resistance locus, QSrGH.cs-2AL, was identified in durum wheat Glossy Huguenot and mendelised as Sr63. Markers closely linked with Sr63 were developed. An F3 population from a Glossy Huguenot (GH)/Bansi cross used in a previous Australian study was advanced to F6 for molecular mapping of adult plant stem rust resistance. Maturity differences among F6 lines confounded assessments of stem rust response. GH was crossed with a stem rust susceptible F6 recombinant inbred line (RIL), GHB14 (M14), with similar maturity and an F6:7 population was developed through single seed descent method. F7 and F8 RILs were tested along with the parents at different locations. The F6 individual plants and both parents were genotyped using the 90 K single nucleotide polymorphism (SNP) wheat array. Stem rust resistance QTL on the long arms of chromosomes 1B (QSrGH.cs-1BL) and 2A (QSrGH.cs-2AL) were detected. QSrGH.cs-1BL and QSrGH.cs-2AL were both contributed by GH and explained 22% and 18% adult plant stem rust response variation, respectively, among GH/M14 RIL population. RILs carrying combinations of these QTL reduced more than 14% stem rust severity compared to those that possessed QSrGH.cs-1BL and QSrGH.cs-2AL individually. QSrGH.cs1BL was demonstrated to be the same as Sr58/Lr46/Yr29/Pm39 through marker genotyping. Lines lacking QSrGH.cs-1BL were used to Mendelise QSrGH.cs-2AL. Based on genomic locations of previously catalogued stem rust resistance genes and the QSrGH.cs-2AL map, it appeared to represent a new APR locus and was permanently named Sr63. SNP markers associated with Sr63 were converted to kompetetive allele-specific PCR (KASP) assays and were validated on a set of durum cultivars.
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Affiliation(s)
- Rohit Mago
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
| | - Chunhong Chen
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Xiaodi Xia
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Alex Whan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Bhoja R Basnet
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Geetha Perera
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Sutha Chandramohan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Mandeep Randhawa
- ICRAF House, CIMMYT Kenya, United Nations Avenue, Gigiri, Village Market, P.O. Box 1041, 00621, Nairobi, Kenya
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Urmil Bansal
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Julio Huerta-Espino
- Campo Experimental Valle de México, INIFAP, Chapingo, Estado de México, Mexico
| | - Ravi P Singh
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Harbans Bariana
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| | - Evans Lagudah
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
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5
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Ortiz D, Chen J, Outram MA, Saur IM, Upadhyaya NM, Mago R, Ericsson DJ, Cesari S, Chen C, Williams SJ, Dodds PN. The stem rust effector protein AvrSr50 escapes Sr50 recognition by a substitution in a single surface-exposed residue. New Phytol 2022; 234:592-606. [PMID: 35107838 PMCID: PMC9306850 DOI: 10.1111/nph.18011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/12/2022] [Indexed: 05/28/2023]
Abstract
Pathogen effectors are crucial players during plant colonisation and infection. Plant resistance mostly relies on effector recognition to activate defence responses. Understanding how effector proteins escape from plant surveillance is important for plant breeding and resistance deployment. Here we examined the role of genetic diversity of the stem rust (Puccinia graminis f. sp. tritici (Pgt)) AvrSr50 gene in determining recognition by the corresponding wheat Sr50 resistance gene. We solved the crystal structure of a natural variant of AvrSr50 and used site-directed mutagenesis and transient expression assays to dissect the molecular mechanisms explaining gain of virulence. We report that AvrSr50 can escape recognition by Sr50 through different mechanisms including DNA insertion, stop codon loss or by amino-acid variation involving a single substitution of the AvrSr50 surface-exposed residue Q121. We also report structural homology of AvrSr50 to cupin superfamily members and carbohydrate-binding modules indicating a potential role in binding sugar moieties. This study identifies key polymorphic sites present in AvrSr50 alleles from natural stem rust populations that play important roles to escape from Sr50 recognition. This constitutes an important step to better understand Pgt effector evolution and to monitor AvrSr50 variants in natural rust populations.
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Affiliation(s)
- Diana Ortiz
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
- National Research Institute for AgricultureFood and Environment, Genetics and Breeding of Fruit and Vegetables UnitMontfavet84143France
| | - Jian Chen
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Megan A. Outram
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Isabel M.L. Saur
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologne50829Germany
- University of Plant SciencesUniversity of CologneCologne50674Germany
- Cluster of Excellence on Plant SciencesCologne50674Germany
| | - Narayana M. Upadhyaya
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Rohit Mago
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Daniel J. Ericsson
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Australian SynchrotronMacromolecular CrystallographyClaytonVic.3168Australia
| | - Stella Cesari
- PHIM Plant Health InstituteUniversité de MontpellierINRAE, CIRADInstitut AgroIRDMontpellier34980France
| | - Chunhong Chen
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Simon J. Williams
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Peter N. Dodds
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
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6
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Duan H, Jones AW, Hewitt T, Mackenzie A, Hu Y, Sharp A, Lewis D, Mago R, Upadhyaya NM, Rathjen JP, Stone EA, Schwessinger B, Figueroa M, Dodds PN, Periyannan S, Sperschneider J. Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data. Genome Biol 2022; 23:84. [PMID: 35337367 PMCID: PMC8957140 DOI: 10.1186/s13059-022-02658-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
Background Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false-positive signals. Results We generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false-positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30–40 times using HiFi sequencing is required for phasing of the leaf rust genome, with 0.7% heterozygosity, and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. Conclusions This first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02658-2.
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Affiliation(s)
- Hongyu Duan
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | - Ashley W Jones
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Tim Hewitt
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Amy Mackenzie
- Research School of Biology, The Australian National University, Canberra, Australia.,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Yiheng Hu
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Anna Sharp
- Research School of Biology, The Australian National University, Canberra, Australia.,Current Address: John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David Lewis
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Narayana M Upadhyaya
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - John P Rathjen
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Eric A Stone
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | | | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Sambasivam Periyannan
- Research School of Biology, The Australian National University, Canberra, Australia.,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, Australia. .,Current Address: Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
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7
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Sperschneider J, Jones AW, Nasim J, Xu B, Jacques S, Zhong C, Upadhyaya NM, Mago R, Hu Y, Figueroa M, Singh KB, Stone EA, Schwessinger B, Wang MB, Taylor JM, Dodds PN. The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation. BMC Biol 2021; 19:203. [PMID: 34526021 PMCID: PMC8444563 DOI: 10.1186/s12915-021-01123-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Background Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive. Results We use sRNA sequencing and methylation data to gain insight into epigenetics in the dikaryotic fungus Puccinia graminis f. sp. tritici (Pgt), which causes the devastating stem rust disease on wheat. We use Hi-C data to define the Pgt centromeres and show that they are repeat-rich regions (~250 kb) that are highly diverse in sequence between haplotypes and, like in plants, are enriched for young TEs. DNA cytosine methylation is particularly active at centromeres but also associated with genome-wide control of young TE insertions. Strikingly, over 90% of Pgt sRNAs and several RNAi genes are differentially expressed during infection. Pgt induces waves of functionally diversified sRNAs during infection. The early wave sRNAs are predominantly 21 nts with a 5′ uracil derived from genes. In contrast, the late wave sRNAs are mainly 22-nt sRNAs with a 5′ adenine and are strongly induced from centromeric regions. TEs that overlap with late wave sRNAs are more likely to be methylated, both inside and outside the centromeres, and methylated TEs exhibit a silencing effect on nearby genes. Conclusions We conclude that rust fungi use an epigenetic silencing pathway that might have similarity with RdDM in plants. The Pgt RNAi machinery and sRNAs are under tight temporal control throughout infection and might ensure genome stability during sporulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01123-z.
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Affiliation(s)
- Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, Australia. .,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
| | - Ashley W Jones
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Jamila Nasim
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Bo Xu
- Thermo Fisher Scientific, 5 Caribbean Drive, Scoresby, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Australia
| | - Chengcheng Zhong
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Narayana M Upadhyaya
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Yiheng Hu
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Karam B Singh
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Australia.,Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, Australia
| | - Eric A Stone
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | - Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Ming-Bo Wang
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Jennifer M Taylor
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
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8
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Upadhyaya NM, Mago R, Panwar V, Hewitt T, Luo M, Chen J, Sperschneider J, Nguyen-Phuc H, Wang A, Ortiz D, Hac L, Bhatt D, Li F, Zhang J, Ayliffe M, Figueroa M, Kanyuka K, Ellis JG, Dodds PN. Genomics accelerated isolation of a new stem rust avirulence gene-wheat resistance gene pair. Nat Plants 2021; 7:1220-1228. [PMID: 34294906 DOI: 10.1038/s41477-021-00971-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved1,2. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases3. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class4, which recognize pathogen effector proteins known as avirulence (Avr) proteins5. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. 6,7), and none in other cereal rusts8,9. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye10. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat-rye hybrid and is a host for Pgt11,12. Sr27 is effective against Ug99 (ref. 13) and other recent Pgt strains14,15. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.
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Affiliation(s)
- Narayana M Upadhyaya
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Vinay Panwar
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Tim Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hoa Nguyen-Phuc
- Department of Ecology and Evolutionary Biology, Vietnam National University, Ho Chi Minh, Vietnam
| | - Aihua Wang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Diana Ortiz
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Génétique et Amélioration des Fruits et Légumes, INRA, Montfavet Cedex, France
| | - Luch Hac
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Feng Li
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jianping Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jeffrey G Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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9
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Zhang J, Hewitt TC, Boshoff WHP, Dundas I, Upadhyaya N, Li J, Patpour M, Chandramohan S, Pretorius ZA, Hovmøller M, Schnippenkoetter W, Park RF, Mago R, Periyannan S, Bhatt D, Hoxha S, Chakraborty S, Luo M, Dodds P, Steuernagel B, Wulff BBH, Ayliffe M, McIntosh RA, Zhang P, Lagudah ES. A recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes. Nat Commun 2021; 12:3378. [PMID: 34099713 PMCID: PMC8184838 DOI: 10.1038/s41467-021-23738-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 05/10/2021] [Indexed: 12/25/2022] Open
Abstract
The re-emergence of stem rust on wheat in Europe and Africa is reinforcing the ongoing need for durable resistance gene deployment. Here, we isolate from wheat, Sr26 and Sr61, with both genes independently introduced as alien chromosome introgressions from tall wheat grass (Thinopyrum ponticum). Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. Using gene-specific markers, we validate the presence of both genes on a single recombinant alien segment developed in wheat. The co-location of these genes on a small non-recombinogenic segment simplifies their deployment as a gene stack and potentially enhances their resistance durability. The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.
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Affiliation(s)
- Jianping Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Timothy C Hewitt
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Ian Dundas
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | | | - Jianbo Li
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | | | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | | | | | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Rohit Mago
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | | | - Dhara Bhatt
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Sami Hoxha
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | | | - Ming Luo
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Peter Dodds
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | | | | | | | - Robert A McIntosh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.
| | - Evans S Lagudah
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia. .,CSIRO Agriculture & Food, Canberra, ACT, Australia.
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10
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Hatta MAM, Arora S, Ghosh S, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Steuernagel B, Richardson T, Mago R, Lagudah ES, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan S, Steffenson BJ, Wulff BB. The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley. Plant Biotechnol J 2021; 19:273-284. [PMID: 32744350 PMCID: PMC7868974 DOI: 10.1111/pbi.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 06/17/2020] [Indexed: 05/16/2023]
Abstract
In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
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Affiliation(s)
- M. Asyraf Md Hatta
- John Innes CentreNorwich Research ParkNorwichUK
- Department of Agriculture TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangMalaysia
| | - Sanu Arora
- John Innes CentreNorwich Research ParkNorwichUK
| | - Sreya Ghosh
- John Innes CentreNorwich Research ParkNorwichUK
| | - Oadi Matny
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
| | | | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichUK
| | - Soma Chakraborty
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Matthew N. Rouse
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
- USDA‐ARS Cereal Disease LaboratorySt. PaulMNUSA
| | | | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Brian J. Steffenson
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
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11
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Luo M, Xie L, Chakraborty S, Wang A, Matny O, Jugovich M, Kolmer JA, Richardson T, Bhatt D, Hoque M, Patpour M, Sørensen C, Ortiz D, Dodds P, Steuernagel B, Wulff BBH, Upadhyaya NM, Mago R, Periyannan S, Lagudah E, Freedman R, Lynne Reuber T, Steffenson BJ, Ayliffe M. A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat. Nat Biotechnol 2021; 39:561-566. [PMID: 33398152 DOI: 10.1038/s41587-020-00770-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/12/2020] [Indexed: 01/08/2023]
Abstract
Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness.
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Affiliation(s)
- Ming Luo
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia
| | - Liqiong Xie
- School of Life Science and Technology, Xinjiang University, Urumqi, China
| | | | - Aihua Wang
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia
| | - Oadi Matny
- Department of Plant Pathology, Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Michelle Jugovich
- Department of Plant Pathology, Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | | | | | - Dhara Bhatt
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia
| | - Mohammad Hoque
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Diana Ortiz
- Genetics and Breeding of Fruit and Vegetables Unit, National Research Institute for Agriculture, Food and Environment, Montfavet, France
| | - Peter Dodds
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia
| | | | | | | | - Rohit Mago
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia
| | | | - Evans Lagudah
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia
| | | | - T Lynne Reuber
- 2Blades Foundation, Evanston, IL, USA.,Enko Chem, Woburn, MA, USA
| | - Brian J Steffenson
- Department of Plant Pathology, Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Michael Ayliffe
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia.
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12
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Tabe L, Samuel S, Dunn M, White R, Mago R, Estavillo G, Spielmeyer W. Phenotypes Conferred by Wheat Multiple Pathogen Resistance Locus, Sr2, Include Cell Death in Response to Biotic and Abiotic Stresses. Phytopathology 2019; 109:1751-1759. [PMID: 31199201 DOI: 10.1094/phyto-03-19-0099-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The wheat Sr2 locus confers partial resistance to four biotrophic pathogens: wheat stem rust (Puccinia graminis f. sp. tritici), leaf rust (P. triticina), stripe rust (P. striiformis f. sp. tritici), and powdery mildew (Blumeria graminis f. sp. tritici). In addition, Sr2 is linked with a brown coloration of ears and stems, termed pseudo-black chaff (PBC). PBC, initially believed to be elicited by stem rust infection, was subsequently recognized to occur in the absence of pathogen infection. The current study demonstrates that the resistance response to stem rust is associated with the death of photosynthetic cells around rust infection sites in the inoculated leaf sheath. Similarly, Sr2-dependent resistance to powdery mildew was associated with the death of leaf mesophyll cells around mildew infection sites. We demonstrate that PBC occurring in the absence of pathogen inoculation also corresponds with death and the collapse of photosynthetic cells in the affected parts of stems and ears. In addition, Sr2-dependent necrosis was inducible in leaves by application of petroleum jelly or by heat treatments. Thus, Sr2 was found to be associated with cell death, which could be triggered by either biotic or abiotic stresses. Our results suggest a role for the Sr2 locus in controlling cell death in response to stress.
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Affiliation(s)
- Linda Tabe
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory 2601, Australia
| | - Sharon Samuel
- University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Matthew Dunn
- Research School of Biological Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Rosemary White
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory 2601, Australia
| | - Rohit Mago
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory 2601, Australia
| | - Gonzalo Estavillo
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory 2601, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Wolfgang Spielmeyer
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory 2601, Australia
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13
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Mago R, Zhang P, Xia X, Zhang J, Hoxha S, Lagudah E, Graner A, Dundas I. Transfer of stem rust resistance gene SrB from Thinopyrum ponticum into wheat and development of a closely linked PCR-based marker. Theor Appl Genet 2019; 132:371-382. [PMID: 30377705 DOI: 10.1007/s00122-018-3224-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/25/2018] [Indexed: 05/10/2023]
Abstract
We report transfer of a rust resistance gene named SrB, on the 6Ae#3 chromosome, to wheat by recombination with the 6Ae#1 segment carrying Sr26 and development of a linked marker. A stem rust resistance gene from a South African wheat W3757, temporarily named SrB, has been transferred onto chromosome 6A. Line W3757 is a 6Ae#3 (6D) substitution line in which the Thinopyrum ponticum chromosomes carry SrB. Crosses were made between W3757 and a T6AS·6AL-6Ae#1 recombinant line named WA-5 carrying the stem rust resistance gene Sr26 on a chromosome segment from another accession of Th. ponticum. The 6Ae#1 and 6Ae#3 chromosomes had previously been shown to pair at meiosis and were polymorphic for the distally located RFLP probes BCD001 and MWG798. A recombinant plant (Type A) was identified carrying a distal chromosome segment from the 6Ae#3 chromosome and a sub-terminal segment from the 6Ae#1 chromosome. Rust tests on the recombinant Type A showed the infection type for SrB. Segregation and linkage data combined with genomic in situ hybridization studies demonstrated that SrB had been transferred to wheat chromosome arm 6AL by recombination between the Thinopyrum chromosome segments. A recombinant positive for the 6Ae#1-6Ae#3 chromosome showed enhanced stem rust resistance compared to the 6Ae#3 addition line in repeated rust tests. A diagnostic PCR-based marker was developed for the 6Ae#3 chromosome segment on the Type A recombinant carrying SrB that distinguishes it from the Sr26-containing segment. A stem rust resistant line which combines SrB with Sr26 would be a great addition to the pool of resistant germplasm for wheat breeders to achieve more durable and effective control of stem rust because virulence has not been found for either of these two genes.
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Affiliation(s)
- Rohit Mago
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute, Cobbitty (PBIC), The University of Sydney, Sydney, NSW, 2570, Australia
| | - Xiaodi Xia
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Jianping Zhang
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
- Plant Breeding Institute, Cobbitty (PBIC), The University of Sydney, Sydney, NSW, 2570, Australia
| | - Sami Hoxha
- Plant Breeding Institute, Cobbitty (PBIC), The University of Sydney, Sydney, NSW, 2570, Australia
| | - Evans Lagudah
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
| | - Ian Dundas
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
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14
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Mago R, Till B, Periyannan S, Yu G, Wulff BBH, Lagudah E. Generation of Loss-of-Function Mutants for Wheat Rust Disease Resistance Gene Cloning. Methods Mol Biol 2018; 1659:199-205. [PMID: 28856652 DOI: 10.1007/978-1-4939-7249-4_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
One of the most important tools to identify and validate rust resistance gene function is by producing loss-of-function mutants. Mutants can be produced using irradiation, chemicals, and insertions. Among all the mutagens, ethyl methanesulfonate (EMS) and sodium azide are most favored because of the ease of use and generation of random point mutations in the genome. The mutants so produced facilitate the isolation, identification and cloning of rust resistance genes. In this chapter we describe a protocol for seed mutagenesis of wheat with EMS and sodium azide.
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Affiliation(s)
- Rohit Mago
- Agriculture & Food, CSIRO, Canberra, ACT, Australia.
| | - Bradley Till
- Plant Breeding and Genetics Laboratory, International Atomic Energy Agency, Vienna, Austria
| | - Sambasivam Periyannan
- Agriculture & Food, CSIRO, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia.,Plant Breeding Institute, University of Sydney, Sydney, NSW, Australia
| | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, UK
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15
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Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X, Mago R, Newell K, Xia X, Bernoux M, Taylor JM, Steffenson B, Jin Y, Zhang P, Kanyuka K, Figueroa M, Ellis JG, Park RF, Dodds PN. Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat. Science 2018; 358:1607-1610. [PMID: 29269475 DOI: 10.1126/science.aao4810] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/03/2017] [Indexed: 01/03/2023]
Abstract
Race-specific resistance genes protect the global wheat crop from stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) but are often overcome owing to evolution of new virulent races of the pathogen. To understand virulence evolution in Pgt, we identified the protein ligand (AvrSr50) recognized by the Sr50 resistance protein. A spontaneous mutant of Pgt virulent to Sr50 contained a 2.5 mega-base pair loss-of-heterozygosity event. A haustorial secreted protein from this region triggers Sr50-dependent defense responses in planta and interacts directly with the Sr50 protein. Virulence alleles of AvrSr50 have arisen through DNA insertion and sequence divergence, and our data provide molecular evidence that in addition to sexual recombination, somatic exchange can play a role in the emergence of new virulence traits in Pgt.
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Affiliation(s)
- Jiapeng Chen
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia.,Judith and David Coffey Life Lab, Charles Perkins Centre, University of Sydney
| | - Narayana M Upadhyaya
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Diana Ortiz
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Perth, WA, Australia
| | - Feng Li
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Clement Bouton
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Susan Breen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Chongmei Dong
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Bo Xu
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Xiaoxiao Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Kim Newell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Brian Steffenson
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Yue Jin
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA.,United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN, USA
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Melania Figueroa
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Jeffrey G Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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16
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Cesari S, Moore J, Chen C, Webb D, Periyannan S, Mago R, Bernoux M, Lagudah ES, Dodds PN. Cytosolic activation of cell death and stem rust resistance by cereal MLA-family CC-NLR proteins. Proc Natl Acad Sci U S A 2016; 113:10204-9. [PMID: 27555587 PMCID: PMC5018743 DOI: 10.1073/pnas.1605483113] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Plants possess intracellular immune receptors designated "nucleotide-binding domain and leucine-rich repeat" (NLR) proteins that translate pathogen-specific recognition into disease-resistance signaling. The wheat immune receptors Sr33 and Sr50 belong to the class of coiled-coil (CC) NLRs. They confer resistance against a broad spectrum of field isolates of Puccinia graminis f. sp. tritici, including the Ug99 lineage, and are homologs of the barley powdery mildew-resistance protein MLA10. Here, we show that, similarly to MLA10, the Sr33 and Sr50 CC domains are sufficient to induce cell death in Nicotiana benthamiana Autoactive CC domains and full-length Sr33 and Sr50 proteins self-associate in planta In contrast, truncated CC domains equivalent in size to an MLA10 fragment for which a crystal structure was previously determined fail to induce cell death and do not self-associate. Mutations in the truncated region also abolish self-association and cell-death signaling. Analysis of Sr33 and Sr50 CC domains fused to YFP and either nuclear localization or nuclear export signals in N benthamiana showed that cell-death induction occurs in the cytosol. In stable transgenic wheat plants, full-length Sr33 proteins targeted to the cytosol provided rust resistance, whereas nuclear-targeted Sr33 was not functional. These data are consistent with CC-mediated induction of both cell-death signaling and stem rust resistance in the cytosolic compartment, whereas previous research had suggested that MLA10-mediated cell-death and disease resistance signaling occur independently, in the cytosol and nucleus, respectively.
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Affiliation(s)
- Stella Cesari
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - John Moore
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Daryl Webb
- Centre for Advanced Microscopy, Australian National University, Canberra, ACT 0200, Australia
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia;
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17
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Mago R, Zhang P, Vautrin S, Šimková H, Bansal U, Luo MC, Rouse M, Karaoglu H, Periyannan S, Kolmer J, Jin Y, Ayliffe MA, Bariana H, Park RF, McIntosh R, Doležel J, Bergès H, Spielmeyer W, Lagudah ES, Ellis JG, Dodds PN. The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus. Nat Plants 2015; 1:15186. [PMID: 27251721 DOI: 10.1038/nplants.2015.186] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 05/18/2023]
Abstract
We identify the wheat stem rust resistance gene Sr50 (using physical mapping, mutation and complementation) as homologous to barley Mla, encoding a coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) protein. We show that Sr50 confers a unique resistance specificity different from Sr31 and other genes on rye chromosome 1RS, and is effective against the broadly virulent Ug99 race lineage. Extensive haplotype diversity at the rye Sr50 locus holds promise for mining effective resistance genes.
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Affiliation(s)
- Rohit Mago
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Sonia Vautrin
- INRA - CNRGV, 24 Chemin de Borde Rouge - Auzeville, CS 52627, Castanet Tolosan Cedex 31326, France
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Urmil Bansal
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Matthew Rouse
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Haydar Karaoglu
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | | | - James Kolmer
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Yue Jin
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | | | - Harbans Bariana
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Robert F Park
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Robert McIntosh
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Hélène Bergès
- INRA - CNRGV, 24 Chemin de Borde Rouge - Auzeville, CS 52627, Castanet Tolosan Cedex 31326, France
| | | | - Evans S Lagudah
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Jeff G Ellis
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Peter N Dodds
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
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Upadhyaya NM, Garnica DP, Karaoglu H, Sperschneider J, Nemri A, Xu B, Mago R, Cuomo CA, Rathjen JP, Park RF, Ellis JG, Dodds PN. Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes. Front Plant Sci 2015; 5:759. [PMID: 25620970 PMCID: PMC4288056 DOI: 10.3389/fpls.2014.00759] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 12/09/2014] [Indexed: 05/03/2023]
Abstract
The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.
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Affiliation(s)
- Narayana M. Upadhyaya
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Diana P. Garnica
- Research School of Biology, Australian National UniversityCanberra, ACT, Australia
| | - Haydar Karaoglu
- Plant Breeding Institute, Faculty of Agriculture and Environment, The University of SydneyNarellan, NSW, Australia
| | - Jana Sperschneider
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Adnane Nemri
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Bo Xu
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Rohit Mago
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Christina A. Cuomo
- Genome Sequencing and Analysis Program, Broad Institute of MIT and HarvardCambridge, MA, USA
| | - John P. Rathjen
- Research School of Biology, Australian National UniversityCanberra, ACT, Australia
| | - Robert F. Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, The University of SydneyNarellan, NSW, Australia
| | - Jeffrey G. Ellis
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Peter N. Dodds
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
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Mago R, Tabe L, Vautrin S, Šimková H, Kubaláková M, Upadhyaya N, Berges H, Kong X, Breen J, Doležel J, Appels R, Ellis JG, Spielmeyer W. Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biol 2014; 14:379. [PMID: 25547135 PMCID: PMC4305260 DOI: 10.1186/s12870-014-0379-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 12/11/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The adult plant stem rust resistance gene Sr2 was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently, Sr2 has been widely deployed and has provided durable partial resistance to all known races of Puccinia graminis f. sp. tritici. This report describes the physical map of the Sr2-carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non-Sr2 wheat cv Chinese Spring. RESULTS Sr2 was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope Sr2 region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying Sr2 possessed the GLP cluster; while, of those lacking Sr2, some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of Sr2. Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP. CONCLUSION Physical mapping and sequence comparison showed major haplotype divergence at the Sr2 locus between Hope and Chinese Spring. Candidate genes within the Sr2 region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that Sr2 does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes Lr34 and Yr36.
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Affiliation(s)
- Rohit Mago
- />CSIRO Agriculture Flagship, Canberra, ACT 2601 Australia
| | - Linda Tabe
- />CSIRO Agriculture Flagship, Canberra, ACT 2601 Australia
| | - Sonia Vautrin
- />INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Hana Šimková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Marie Kubaláková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Hélène Berges
- />INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Xiuying Kong
- />Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 PR China
| | - James Breen
- />Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 WA Australia
- />Current address: Australian Centre for Ancient DNA (ACAD), University of Adelaide, Adelaide, SA 5005 Australia
| | - Jaroslav Doležel
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Rudi Appels
- />Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 WA Australia
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Upadhyaya NM, Mago R, Staskawicz BJ, Ayliffe MA, Ellis JG, Dodds PN. A bacterial type III secretion assay for delivery of fungal effector proteins into wheat. Mol Plant Microbe Interact 2014; 27:255-64. [PMID: 24156769 DOI: 10.1094/mpmi-07-13-0187-fi] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Large numbers of candidate effectors from fungal pathogens are being identified through whole-genome sequencing and in planta expression studies. Although Agrobacterium-mediated transient expression has enabled high-throughput functional analysis of effectors in dicot plants, this assay is not effective in cereal leaves. Here, we show that a nonpathogenic Pseudomonas fluorescens engineered to express the type III secretion system (T3SS) of P. syringae and the wheat pathogen Xanthomonas translucens can deliver fusion proteins containing T3SS signals from P. syringae (AvrRpm1) and X. campestris (AvrBs2) avirulence (Avr) proteins, respectively, into wheat leaf cells. A calmodulin-dependent adenylate cyclase reporter protein was delivered effectively into wheat and barley by both bacteria. Absence of any disease symptoms with P. fluorescens makes it more suitable than X. translucens for detecting a hypersensitive response (HR) induced by an effector protein with avirulence activity. We further modified the delivery system by removal of the myristoylation site from the AvrRpm1 fusion to prevent its localization to the plasma membrane which could inhibit recognition of an Avr protein. Delivery of the flax rust AvrM protein by the modified delivery system into transgenic tobacco leaves expressing the corresponding M resistance protein induced a strong HR, indicating that the system is capable of delivering a functional rust Avr protein. In a preliminary screen of effectors from the stem rust fungus Puccinia graminis f. sp. tritici, we identified one effector that induced a host genotype-specific HR in wheat. Thus, the modified AvrRpm1:effector-Pseudomonas fluorescens system is an effective tool for large-scale screening of pathogen effectors for recognition in wheat.
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Mago R, Verlin D, Zhang P, Bansal U, Bariana H, Jin Y, Ellis J, Hoxha S, Dundas I. Development of wheat-Aegilops speltoides recombinants and simple PCR-based markers for Sr32 and a new stem rust resistance gene on the 2S#1 chromosome. Theor Appl Genet 2013; 126:2943-55. [PMID: 23989672 DOI: 10.1007/s00122-013-2184-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/16/2013] [Indexed: 05/20/2023]
Abstract
Wheat- Aegilops speltoides recombinants carrying stem rust resistance genes Sr32 and SrAes1t effective against Ug99 and PCR markers for marker-assisted selection. Wild relatives of wheat are important resources for new rust resistance genes but underutilized because the valuable resistances are often linked to negative traits that prevent deployment of these genes in commercial wheats. Here, we report ph1b-induced recombinants with reduced alien chromatin derived from E.R. Sears' wheat-Aegilops speltoides 2D-2S#1 translocation line C82.2, which carries the widely effective stem rust resistance gene Sr32. Infection type assessments of the recombinants showed that the original translocation in fact carries two stem rust resistance genes, Sr32 on the short arm and a previously undescribed gene SrAes1t on the long arm of chromosome 2S#1. Recombinants with substantially shortened alien chromatin were produced for both genes, which confer resistance to stem rust races in the TTKSK (Ug99) lineage and representative races of all Australian stem rust lineages. Selected recombinants were back crossed into adapted Australian cultivars and PCR markers were developed to facilitate the incorporation of these genes into future wheat varieties. Our recombinants and those from several other labs now show that Sr32, Sr39, and SrAes7t on the short arm and Sr47 and SrAes1t on the long arm of 2S#1 form two linkage groups and at present no rust races are described that can distinguish these resistance specificities.
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Affiliation(s)
- Rohit Mago
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia,
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Hurni S, Brunner S, Buchmann G, Herren G, Jordan T, Krukowski P, Wicker T, Yahiaoui N, Mago R, Keller B. Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew. Plant J 2013; 76:957-69. [PMID: 24124925 DOI: 10.1111/tpj.12345] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/25/2013] [Accepted: 10/04/2013] [Indexed: 05/18/2023]
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 divergence 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.
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Affiliation(s)
- Severine Hurni
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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Spielmeyer W, Mago R, Wellings C, Ayliffe M. Lr67 and Lr34 rust resistance genes have much in common--they confer broad spectrum resistance to multiple pathogens in wheat. BMC Plant Biol 2013; 13:96. [PMID: 23819608 PMCID: PMC3716802 DOI: 10.1186/1471-2229-13-96] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/27/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Adult plant rust resistance genes Lr67 and Lr34 confer race non-specific resistance to multiple fungal pathogens of wheat. Induced, susceptible mutants were characterised for both genes. RESULTS Three categories of Lr34 mutants were identified that were either partial susceptible, fully susceptible or hyper-susceptible to stripe rust and leaf rust. The likely impact of the mutational change on the predicted Lr34 protein correlated with differences in response to rust infection. Four independent Lr67 mutants were recovered that were susceptible to stripe rust, leaf rust and stem rust pathogens, including one possible hyper-susceptible Lr67 mutant. CONCLUSIONS Detailed study of Lr34 mutants revealed that subtle changes in resistance response to multiple pathogens were correlated with mutational changes in the predicted protein. Recovery of independent Lr67 mutants indicates that as for Lr34, a single gene at the Lr67 locus is likely to confer resistance to multiple pathogens. The infection phenotypes of Lr67 mutants closely resembled that of Lr34 mutants.
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Affiliation(s)
| | - Rohit Mago
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - Colin Wellings
- Plant Breeding Institute, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Michael Ayliffe
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia
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Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H, Mago R, McIntosh R, Dodds P, Dvorak J, Lagudah E. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 2013; 341:786-8. [PMID: 23811228 DOI: 10.1126/science.1239028] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as "Ug99" have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea.
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Affiliation(s)
- Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Canberra, ACT 2601, Australia
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Abstract
Rice is atypical in that it is an agricultural cereal that is immune to fungal rust diseases. This report demonstrates that several cereal rust species (Puccinia graminis f. sp tritici, P. triticina, P. striiformis, and P. hordei) can infect rice and produce all the infection structures necessary for plant colonization, including specialized feeding cells (haustoria). Some rust infection sites are remarkably large and many plant cells are colonized, suggesting that nutrient uptake occurs to support this growth. Rice responds with an active, nonhost resistance (NHR) response that prevents fungal sporulation and that involves callose deposition, production of reactive oxygen species, and, occasionally, cell death. Genetic variation for the efficacy of NHR to wheat stem rust and wheat leaf rust was observed. Unlike cereal rusts, the rust pathogen (Melampsora lini) of the dicotyledenous plant flax (Linum usitatissimum) rarely successfully infects rice due to an apparent inability to recognize host-derived signals. Morphologically abnormal infection structures are produced and appressorial-like structures often don't coincide with stomata. These data suggest that basic compatibility is an important determinate of nonhost infection outcomes of rust diseases on cereals, with cereal rusts being more capable of infecting a cereal nonhost species compared with rust species that are adapted for dicot hosts.
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Affiliation(s)
- Michael Ayliffe
- CSIRO Plant Indudtry, Box 1600, Canberra, ACT, 2601, Australia.
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26
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Mago R, Tabe L, McIntosh RA, Pretorius Z, Kota R, Paux E, Wicker T, Breen J, Lagudah ES, Ellis JG, Spielmeyer W. A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew. Theor Appl Genet 2011; 123:615-23. [PMID: 21573954 DOI: 10.1007/s00122-011-1611-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 04/26/2011] [Indexed: 05/21/2023]
Abstract
Sr2 is the only known durable, race non-specific adult plant stem rust resistance gene in wheat. The Sr2 gene was shown to be tightly linked to the leaf rust resistance gene Lr27 and to powdery mildew resistance. An analysis of recombinants and mutants suggests that a single gene on chromosome arm 3BS may be responsible for resistance to these three fungal pathogens. The resistance functions of the Sr2 locus are compared and contrasted with those of the adult plant resistance gene Lr34.
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Affiliation(s)
- R Mago
- CSIRO Plant Industry, Canberra 2601, Australia
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27
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Mago R, Simkova H, Brown-Guedira G, Dreisigacker S, Breen J, Jin Y, Singh R, Appels R, Lagudah ES, Ellis J, Dolezel J, Spielmeyer W. An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat. Theor Appl Genet 2011; 122:735-44. [PMID: 21060985 DOI: 10.1007/s00122-010-1482-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 10/22/2010] [Indexed: 05/08/2023]
Abstract
The stem rust resistance gene Sr2 has provided broad-spectrum protection against stem rust (Puccinia graminis Pers. f. sp. tritici) since its wide spread deployment in wheat from the 1940s. Because Sr2 confers partial resistance which is difficult to select under field conditions, a DNA marker is desirable that accurately predicts Sr2 in diverse wheat germplasm. Using DNA sequence derived from the vicinity of the Sr2 locus, we developed a cleaved amplified polymorphic sequence (CAPS) marker that is associated with the presence or absence of the gene in 115 of 122 (95%) diverse wheat lines. The marker genotype predicted the absence of the gene in 100% of lines which were considered to lack Sr2. Discrepancies were observed in lines that were predicted to carry Sr2 but failed to show the CAPS marker. Given the high level of accuracy observed, the marker provides breeders with a selection tool for one of the most important disease resistance genes of wheat.
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Affiliation(s)
- R Mago
- CSIRO Plant Industry, Canberra, Australia
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Abstract
The haustorium is a distinguishing feature of biotrophic plant pathogens. Several highly diverged -pathogen classes have independently evolved haustoria, suggesting that they represent an effective adaptation for growing within living plant tissue. Despite their clear importance in biotrophy, they have been difficult to study due to the close association of biotrophic pathogens with their host and the inability to produce haustoria in vitro. These drawbacks have been circumvented in the study of rust fungi by the development of a haustoria isolation technique. The strong binding of the lectin concanavalin A (ConA) to rust haustoria allows these structures to be purified from infected plant tissue by affinity chromatography on a ConA-Sepharose macrobead column. The isolation process results in substantial yields of intact haustoria that retain their cytoplasmic contents, making them amenable to experimentation. The construction of cDNA libraries from isolated rust haustoria and their subsequent sequence analysis have provided significant insight into haustoria function at a molecular level, revealing important roles in nutrient acquisition and the delivery of pathogenicity effector proteins. The generation of a rust haustorium-specific cDNA library is described in this chapter.
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Affiliation(s)
- Ann-Maree Catanzariti
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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29
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Hiebert CW, Thomas JB, McCallum BD, Humphreys DG, DePauw RM, Hayden MJ, Mago R, Schnippenkoetter W, Spielmeyer W. An introgression on wheat chromosome 4DL in RL6077 (Thatcher*6/PI 250413) confers adult plant resistance to stripe rust and leaf rust (Lr67). Theor Appl Genet 2010; 121:1083-91. [PMID: 20552325 DOI: 10.1007/s00122-010-1373-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 05/21/2010] [Indexed: 05/18/2023]
Abstract
Adult plant resistance (APR) to leaf rust and stripe rust derived from the wheat (Triticum aestivum L.) line PI250413 was previously identified in RL6077 (=Thatcher*6/PI250413). The leaf rust resistance gene in RL6077 is phenotypically similar to Lr34 which is located on chromosome 7D. It was previously hypothesized that the gene in RL6077 could be Lr34 translocated to another chromosome. Hybrids between RL6077 and Thatcher and between RL6077 and 7DS and 7DL ditelocentric stocks were examined for first meiotic metaphase pairing. RL6077 formed chain quadrivalents and trivalents relative to Thatcher and Chinese Spring; however both 7D telocentrics paired only as heteromorphic bivalents and never with the multivalents. Thus, chromosome 7D is not involved in any translocation carried by RL6077. A genome-wide scan of SSR markers detected an introgression from chromosome 4D of PI250413 transferred to RL6077 through five cycles of backcrossing to Thatcher. Haplotype analysis of lines from crosses of Thatcher × RL6077 and RL6058 (Thatcher*6/PI58548) × RL6077 showed highly significant associations between introgressed markers (including SSR marker cfd71) and leaf rust resistance. In a separate RL6077-derived population, APR to stripe rust was also tightly linked with cfd71 on chromosome 4DL. An allele survey of linked SSR markers cfd71 and cfd23 on a set of 247 wheat lines from diverse origins indicated that these markers can be used to select for the donor segment in most wheat backgrounds. Comparison of RL6077 with Thatcher in field trials showed no effect of the APR gene on important agronomic or quality traits. Since no other known Lr genes exist on chromosome 4DL, the APR gene in RL6077 has been assigned the name Lr67.
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Affiliation(s)
- Colin W Hiebert
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada.
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Breen J, Li D, Dunn DS, Békés F, Kong X, Zhang J, Jia J, Wicker T, Mago R, Ma W, Bellgard M, Appels R. Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain. BMC Plant Biol 2010; 10:99. [PMID: 20507562 PMCID: PMC2887456 DOI: 10.1186/1471-2229-10-99] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 05/27/2010] [Indexed: 05/16/2023]
Abstract
BACKGROUND Expansins form a large multi-gene family found in wheat and other cereal genomes that are involved in the expansion of cell walls as a tissue grows. The expansin family can be divided up into two main groups, namely, alpha-expansin (EXPA) and beta-expansin proteins (EXPB), with the EXPB group being of particular interest as group 1-pollen allergens. RESULTS In this study, three beta-expansin genes were identified and characterized from a newly sequenced region of the Triticum aestivum cv. Chinese Spring chromosome 3B physical map at the Sr2 locus (FPC contig ctg11). The analysis of a 357 kb sub-sequence of FPC contig ctg11 identified one beta-expansin genes to be TaEXPB11, originally identified as a cDNA from the wheat cv Wyuna. Through the analysis of intron sequences of the three wheat cv. Chinese Spring genes, we propose that two of these beta-expansin genes are duplications of the TaEXPB11 gene. Comparative sequence analysis with two other wheat cultivars (cv. Westonia and cv. Hope) and a Triticum aestivum var. spelta line validated the identification of the Chinese Spring variant of TaEXPB11. The expression in maternal and grain tissues was confirmed by examining EST databases and carrying out RT-PCR experiments. Detailed examination of the position of TaEXPB11 relative to the locus encoding Sr2 disease resistance ruled out the possibility of this gene directly contributing to the resistance phenotype. CONCLUSIONS Through 3-D structural protein comparisons with Zea mays EXPB1, we proposed that variations within the coding sequence of TaEXPB11 in wheats may produce a functional change within features such as domain 1 related to possible involvement in cell wall structure and domain 2 defining the pollen allergen domain and binding to IgE protein. The variation established in this gene suggests it is a clearly identifiable member of a gene family and reflects the dynamic features of the wheat genome as it adapted to a range of different environments and uses. Accession Numbers: ctg11 =FN564426Survey sequences of TaEXPB11ws and TsEXPB11 are provided request.
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Affiliation(s)
- James Breen
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
- Molecular Plant Breeding Co-operative Research Centre (MPBCRC), Murdoch University, South Street, Perth 6150, Australia
| | - Dora Li
- Molecular Plant Breeding Co-operative Research Centre (MPBCRC), Murdoch University, South Street, Perth 6150, Australia
- State Agricultural Biotechnology Centre (SABC), Murdoch University, Murdoch University, South Street, Perth 6150, Australia
| | - David S Dunn
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
- Centre for Clinical Immunology and Biomedical Statistics, Murdoch University, South Street, Perth WA 6150, Australia
| | - Ferenc Békés
- CSIRO Plant Industries, PO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Xiuying Kong
- Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, PR China
| | - Juncheng Zhang
- Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, PR China
| | - Jizeng Jia
- Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, PR China
| | - Thomas Wicker
- Institute of Plant Biology, University Zurich, Zollikerstrasse 107, Zurich, CH-8008 Switzerland
| | - Rohit Mago
- CSIRO Plant Industries, PO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Wujun Ma
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
- State Agricultural Biotechnology Centre (SABC), Murdoch University, Murdoch University, South Street, Perth 6150, Australia
- Department of Agriculture and Food, Western Australia (DAFWA), 3 Baron Hay Court, Perth, 6151 Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
- Molecular Plant Breeding Co-operative Research Centre (MPBCRC), Murdoch University, South Street, Perth 6150, Australia
| | - Rudi Appels
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
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Mago R, Zhang P, Bariana HS, Verlin DC, Bansal UK, Ellis JG, Dundas IS. Development of wheat lines carrying stem rust resistance gene Sr39 with reduced Aegilops speltoides chromatin and simple PCR markers for marker-assisted selection. Theor Appl Genet 2009; 119:1441-50. [PMID: 19756473 DOI: 10.1007/s00122-009-1146-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 08/21/2009] [Indexed: 05/20/2023]
Abstract
The use of major resistance genes is a cost-effective strategy for preventing stem rust epidemics in wheat crops. The stem rust resistance gene Sr39 provides resistance to all currently known pathotypes of Puccinia graminis f. sp. tritici (Pgt) including Ug99 (TTKSK) and was introgressed together with leaf rust resistance gene Lr35 conferring adult plant resistance to P. triticina (Pt), into wheat from Aegilops speltoides. It has not been used extensively in wheat breeding because of the presumed but as yet undocumented negative agronomic effects associated with Ae. speltoides chromatin. This investigation reports the production of a set of recombinants with shortened Ae. speltoides segments through induction of homoeologous recombination between the wheat and the Ae. speltoides chromosome. Simple PCR-based DNA markers were developed for resistant and susceptible genotypes (Sr39#22r and Sr39#50s) and validated across a set of recombinant lines and wheat cultivars. These markers will facilitate the pyramiding of ameliorated sources of Sr39 with other stem rust resistance genes that are effective against the Pgt pathotype TTKSK and its variants.
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Affiliation(s)
- Rohit Mago
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia.
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Simková H, Safár J, Suchánková P, Kovárová P, Bartos J, Kubaláková M, Janda J, Cíhalíková J, Mago R, Lelley T, Dolezel J. A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS). BMC Genomics 2008; 9:237. [PMID: 18495015 PMCID: PMC2410134 DOI: 10.1186/1471-2164-9-237] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Accepted: 05/21/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C approximately 7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation. RESULTS We demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using HindIII and EcoRI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning. CONCLUSION We present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.
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Affiliation(s)
- Hana Simková
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic.
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Colas I, Shaw P, Prieto P, Wanous M, Spielmeyer W, Mago R, Moore G. Effective chromosome pairing requires chromatin remodeling at the onset of meiosis. Proc Natl Acad Sci U S A 2008; 105:6075-80. [PMID: 18417451 PMCID: PMC2329686 DOI: 10.1073/pnas.0801521105] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Indexed: 11/18/2022] Open
Abstract
During meiosis, homologous chromosomes (homologues) recognize each other and then intimately associate. Studies exploiting species with large chromosomes reveal that chromatin is remodeled at the onset of meiosis before this intimate association. However, little is known about the effect the remodeling has on pairing. We show here in wheat that chromatin remodeling of homologues can only occur if they are identical or nearly identical. Moreover, a failure to undergo remodeling results in reduced pairing between the homologues. Thus, chromatin remodeling at the onset of meiosis enables the chromosomes to become competent to pair and recombine efficiently.
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Affiliation(s)
- Isabelle Colas
- *John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, United Kingdom
| | - Peter Shaw
- *John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, United Kingdom
| | - Pilar Prieto
- Instituto de Agricultura Sostenible, Alameda del Obispo s/n, Apartado 4084, 14080 Córdoba, Spain
| | - Michael Wanous
- Biology Department, Augustana College, 2001 South Summit Avenue, Sioux Falls, SD 57197; and
| | - Wolfgang Spielmeyer
- Commonwealth Scientific and Industrial Research Organization, Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization, Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Graham Moore
- *John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, United Kingdom
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Ellis JG, Mago R, Kota R, Dodds PN, McFadden H, Lawrence G, Spielmeyer W, Lagudah E. Wheat rust resistance research at CSIRO. ACTA ACUST UNITED AC 2007. [DOI: 10.1071/ar06151] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Although chemical control is available for rust diseases in wheat, economic and environmental factors favour genetic solutions. Maintenance and improvement of levels of resistance and durability of the genetic control of the 3 wheat rust diseases will occur with the application of DNA markers for pyramiding resistance genes. Information about the molecular basis of rust resistance, including durable, adult-plant resistance, coming from studies in model species such as flax and flax rust and from studies of wheat and barley, will provide knowledge for new biotechnological approaches to rust resistance. Increasing cereal gene sequence data will improve the efficiency of cloning disease resistance genes and, together with the rapid progress in understanding the molecular basis of rust resistance, will make it possible to construct transgenic plants with multiple rust resistance genes at a single locus, which will provide efficient breeding and increased durability of rust resistance.
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Dundas IS, Anugrahwati DR, Verlin DC, Park RF, Bariana HS, Mago R, Islam AKMR. New sources of rust resistance from alien species: meliorating linked defects and discovery. ACTA ACUST UNITED AC 2007. [DOI: 10.1071/ar07056] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper presents a review of projects undertaken over the past 2 decades aimed at improving the yield and/or quality attributes of translocation lines carrying rust resistance genes from species related to wheat, so as to make these lines more suitable for use in breeding programs. Homeologous recombination between the alien chromosome segments and normal wheat chromosomes was induced in a ph1bph1b background. Lines with shortened alien chromatin were selected using dissociation patterns of molecular-based markers. A new line of bread wheat was developed containing a shortened chromosome 1RS segment carrying rust resistance gene SrR (Secale cereale L.), in which a defect affecting dough-quality appears to have been deleted. In addition, several advanced lines were produced with modified 6Ae#1L chromosome segments with Sr26 (Thinopyrum ponticum), 2S#1 chromosome segments with Sr32, and a previously unnamed gene, a 2S#2 chromosome segment with Sr39 (Triticum speltoides), 4G#1 chromosome segments with Sr37, and 2G#2 chromosome segments with Sr40 (T. timopheevii).
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36
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Mago R, Miah H, Lawrence GJ, Wellings CR, Spielmeyer W, Bariana HS, McIntosh RA, Pryor AJ, Ellis JG. High-resolution mapping and mutation analysis separate the rust resistance genes Sr31, Lr26 and Yr9 on the short arm of rye chromosome 1. Theor Appl Genet 2005; 112:41-50. [PMID: 16283230 DOI: 10.1007/s00122-005-0098-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 08/20/2005] [Indexed: 05/05/2023]
Abstract
The stem, leaf and stripe rust resistance genes Sr31, Lr26 and Yr9, located on the short arm of rye chromosome 1, have been widely used in wheat by means of wheat-rye translocation chromosomes. Previous studies have suggested that these resistance specificities are encoded by either closely-linked genes, or by a single gene capable of recognizing all three rust species. To investigate these issues, two 1BL.1RS wheat lines, one with and one without Sr31, Lr26 and Yr9, were used as parents for a high-resolution F2 mapping family. Thirty-six recombinants were identified between two PCR markers 2.3 cM apart that flanked the resistance locus. In one recombinant, Lr26 was separated from Sr31 and Yr9. Mutation studies recovered mutants that separated all three rust resistance genes. Thus, together, the recombination and mutation studies suggest that Sr31, Lr26 and Yr9 are separate closely-linked genes. An additional 16 DNA markers were mapped in this region. Multiple RFLP markers, identified using part of the barley Mla powdery mildew resistance gene as probe, co-segregated with Sr31 and Yr9. One deletion mutant that had lost Sr31, Lr26 and Yr9 retained all Mla markers, suggesting that the family of genes on 1RS identified by the Mla probe does not contain the Sr31, Lr26 or Yr9 genes. The genetic stocks and DNA markers generated from this study should facilitate the future cloning of Sr31, Lr26 and Yr9.
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Affiliation(s)
- R Mago
- CSIRO Plant Industry, GPO Box 1600, 2601 Canberra, ACT, Australia.
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37
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Mago R, Bariana HS, Dundas IS, Spielmeyer W, Lawrence GJ, Pryor AJ, Ellis JG. Development of PCR markers for the selection of wheat stem rust resistance genes Sr24 and Sr26 in diverse wheat germplasm. Theor Appl Genet 2005; 111:496-504. [PMID: 15918008 DOI: 10.1007/s00122-005-2039-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 04/12/2005] [Indexed: 05/02/2023]
Abstract
The use of major resistance genes is the most cost-effective strategy for preventing stem rust epidemics in Australian wheat crops. The long-term success of this strategy is dependent on combining resistance genes that are effective against all predominant races of the pathogen, a task greatly assisted by the use of molecular markers linked to individual resistance genes. The wheat stem rust resistance genes Sr24 and Sr26 (derived from Agropyron elongatum) and SrR and Sr31 (derived from rye) are available in wheat as segments of alien chromosome translocated to wheat chromosomes. Each of these genes provides resistance to all races of wheat stem rust currently found in Australia . We have developed robust PCR markers for Sr24 and Sr26 (this study) and SrR and Sr31 (previously reported) that are applicable across a wide selection of Australian wheat germplasm. Wheat lines have recently become available in which the size of the alien segments containing Sr26, SrR and Sr31 has been reduced. Newly developed PCR-markers can be used to identify the presence of the shorter alien segment in all cases. Assuming that these genes have different gene-for-gene specificities and that the wheat industry will discourage the use of varieties carrying single genes only, the newly developed PCR markers will facilitate the incorporation of two or more of the genes Sr24, Sr26, SrR and Sr31 into wheat lines and have the potential to provide durable control to stem rust in Australia and elsewhere.
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Affiliation(s)
- R Mago
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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38
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Mago R, Spielmeyer W, Lawrence GJ, Ellis JG, Pryor AJ. Resistance genes for rye stem rust (SrR) and barley powdery mildew (Mla) are located in syntenic regions on short arm of chromosome. Genome 2004; 47:112-21. [PMID: 15060608 DOI: 10.1139/g03-096] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic stocks were developed for the localization and eventual cloning of the stem rust resistance gene SrR that occurs in wheat lines carrying the 1RS translocation from Secale cereale 'Imperial' rye. We have used a mutation-based approach for molecular analysis of the SrR region in rye. Forty-one independent mutants resulting in loss of SrR resistance were isolated: many of these were deletions of various sizes that were used to locate SrR with respect to chromosome group 1S markers. The analysis of the mutants showed that markers about 1 Mb apart flanking the barley Mla locus also flank SrR. Additionally, three of the approximately 20 closely related sequences of Mla in rye are deleted in each of six interstitial deletion mutants of SrR. The results indicate that the SrR region in rye is syntenic to the Mla region in barley or that SrR is possibly orthologous to the Mla locus.
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Affiliation(s)
- R Mago
- CSIRO Plant Industry, Canberra, Australia.
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Mago R, Spielmeyer W, Lawrence J, Lagudah S, Ellis G, Pryor A. Identification and mapping of molecular markers linked to rust resistance genes located on chromosome 1RS of rye using wheat-rye translocation lines. Theor Appl Genet 2002; 104:1317-1324. [PMID: 12582587 DOI: 10.1007/s00122-002-0879-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2001] [Accepted: 10/25/2001] [Indexed: 05/18/2023]
Abstract
The short arm of rye ( Secale cereale) chromosome 1 has been widely used in breeding programs to incorporate new disease resistance genes into wheat. Using wheat-rye translocation and recombinant lines, molecular markers were isolated and mapped within chromosomal regions of 1RS carrying rust resistance genes Lr26, Sr31, Yr9 from 'Petkus' and SrR from 'Imperial' rye. RFLP markers previously mapped to chromosome 1HS of barley - flanking the complex Mla powdery mildew resistance gene locus - and chromosome 1DS of Aegilops tauschii - flanking the Sr33 stem rust resistance gene - were shown to map on either side of rust resistance genes on 1RS. Three non cross-hybridising Resistance Gene Analog markers, one of them being derived from the Mla gene family, were mapped within same region of 1RS. PCR-based markers were developed which were tightly linked to the rust resistance genes in 'Imperial' and 'Petkus' rye and which have potential for use in marker-assisted breeding.
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Affiliation(s)
- R. Mago
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia,
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Saxena D, Gowri PM, Mago R, Srivastav S. Removal of copper by Pseudomonas putida strain S4 isolated from copper mines. Indian J Exp Biol 2001; 39:590-3. [PMID: 12562024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
A bacterial strain, Pseudomonas putida S4, was isolated from smelter drainage of copper mines. The strain exhibited resistance to several heavy metals, like aluminium (Al), zinc (Zn), nickel (Ni), cobalt (Co) besides copper (Cu). Strain S4 could accumulate Cu from the Cu-supplemented growth medium. In the present study, we have demonstrated the Cu2+ removal capacity of this strain from various samples such as mine effluent, low-grade ore and ore-tailings, collected from the mining site. Moreover, approximately 80% of the accumulated Cu2+ could be recovered from the loaded biomass by a simple desorption procedure.
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Affiliation(s)
- D Saxena
- Department of Genetics, University of Delhi, South Campus, New Deihil 10021, India
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Mago R, Bilker W, Ten Have T, Harralson T, Streim J, Parmalee P, Katz IR. Clinical laboratory measures in relation to depression, disability, and cognitive impairment in elderly patients. Am J Geriatr Psychiatry 2001; 8:327-32. [PMID: 11069273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
To characterize the dimensions of physiological abnormalities that commonly occur in older individuals in a residential care setting and to evaluate their association with clinical measures, the authors conducted an exploratory factor analysis on clinical laboratory measures from a sample of 231 elderly residents (mean age: 86) living in a nursing home and congregate apartment facility. An eight-factor solution accounted for 70.2% of the variance in these measures; factors identified were interpreted as indices of renal function, protein/calorie/nutritional status, serum electrolytes/osmolarity, liver function, acute-phase processes, plasma lipids, acid/base status, and renal-tubular function. The nutritional factor was significantly associated with measures of disability and the presence of depression. The acute-phase processes factor was significantly associated with cognitive impairment.
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Affiliation(s)
- R Mago
- The University of Pennsylvania Health System, Department of Psychiatry, Section on Geriatric Psychiatry, Philadelphia 19104, USA
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Behura SK, Sahu SC, Rajamani S, Devi A, Mago R, Nair S, Mohan M. Differentiation of Asian rice gall midge, Orseolia oryzae (Wood-Mason), biotypes by sequence characterized amplified regions (SCARs). Insect Mol Biol 1999; 8:391-397. [PMID: 10469256 DOI: 10.1046/j.1365-2583.1999.83126.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We developed a polymerase chain reaction (PCR)-based assay that distinguished five different biotypes of the Asian gall midge (Orseolia oryzae), a major insect pest of rice. A total of 400 random primers were screened using random amplified polymorphic DNAs (RAPDs). Five diagnostic PCR products were isolated, cloned, sequenced and converted to sequence characterized amplified regions (SCARs). Primers specific to these SCARs were able to amplify specific DNA fragments from genomic DNAs of five biotypes of gall midge in a multiplexed-PCR-based assay. The amplified DNA fragments were used as diagnostic markers to identify different biotypes of gall midge. The SCAR primers were also capable of differentiating the Asian from the African rice gall midge (Orseolia oryzivora) as well as detecting a variant of biotype 5 which caused an outbreak in Kerala, India. Unlike the use of plant host differentials and midge feeding behaviour for identifying biotypes, this assay is fast, reliable and unaffected by environmental factors.
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Affiliation(s)
- S K Behura
- Central Rice Research Institute (CRRI), Cuttack-753 006, Orissa, India
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Abstract
Zinc resistance in
Pseudomonas
sp. strain UDG26 was inducible. Induction led to enhanced uptake of the metal. A zinc-sensitive variant (UDG86) took up significantly less metal ion than the resistant one did. The affinity of uninduced and sensitive cells to zinc was less than that of resistant, induced cells. Metal accumulation by induced cells was not inhibited by azide, while 2,4-dinitrophenol and
N-N′
-dicyclohexylcarbodiimide enhanced zinc uptake because of inhibition of efflux. Transcription and translation inhibitors drastically reduced zinc accumulation, bringing it to the level found in the sensitive strain. These results suggest the involvement of protein(s) in zinc resistance.
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Affiliation(s)
- R Mago
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
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