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Nazareno ES, Matny O, Jin Y, Fetch T, Rouse MN, Steffenson BJ. Virulence Dynamics of the Barley Leaf Rust Pathogen ( Puccinia hordei) in the United States from 1989 to 2020. PLANT DISEASE 2023; 107:3952-3957. [PMID: 37415351 DOI: 10.1094/pdis-03-23-0583-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Barley leaf rust, caused by Puccinia hordei, is an important disease of barley worldwide. The pathogen can develop new races that overcome resistance genes, emphasizing the need for monitoring its virulence. This study characterized 519 P. hordei isolates collected in the United States from the 1989 to 2000 and 2010 to 2020 survey periods on 15 Rph (Reaction to Puccinia hordei) genes. We analyzed linearized infection type data to detect virulence patterns across the United States and in five geographical regions: Pacific/West (PW), Southwest (SW), Midwest (MW), Northeast (NE), and Southeast (SE). Over 32 years, we observed high mean infection scores for Rph1.a, Rph4.d, and Rph8.h; intermediate scores for Rph2.b, Rph9.i, Rph10.o, Rph11.p, and Rph13.x; and low scores for Rph3.c, Rph5.e, Rph5.f, Rph7.g, Rph9.z, Rph14.ab, and Rph15.ad. Virulence for Rph2.b, Rph3.c, Rph5.e, Rph9.z, Rph10.o, Rph11.p, and Rph13.x significantly differed between the two survey periods. From 1989 to 2020, regional patterns of virulence were found for Rph5.e, Rph5.f, Rph7.g, and Rph14.ab, while regionalities of virulence for Rph3.c, Rph9.i, Rph9.z were only observed in the 2010 to 2020 survey period. Virulence associations were also detected in the P. hordei population. Notably, isolates that were virulent to Rph5.e and Rph6.f were more likely to be avirulent to Rph7.g and Rph13.x, and vice versa. In decreasing order of effectiveness, Rph15.ad, Rph5.e, Rph3.c, Rph9.z, Rph7.g, Rph5.f, and Rph14.ab were the most effective Rph genes in the United States from 1989 to 2020. Pyramiding Rph15.ad with other widely effective Rph and adult plant resistance genes may provide long-lasting resistance against P. hordei.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Yue Jin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
- Cereal Disease Laboratory, USDA-Agricultural Research Service, St. Paul, MN, U.S.A
| | - Thomas Fetch
- Morden Research Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
- Cereal Disease Laboratory, USDA-Agricultural Research Service, St. Paul, MN, U.S.A
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
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Sowa S, Sozoniuk M, Toporowska J, Kowalczyk K, Paczos-Grzęda E. Reference genes expression stability in Avena sativa L. during compatible and incompatible interactions with Puccinia graminis. Sci Rep 2022; 12:18369. [PMID: 36319744 PMCID: PMC9626582 DOI: 10.1038/s41598-022-22993-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
A reliable qPCR experiment requires the selection of reference genes with a stable level of expression in a given experimental system. This study attempts to determine the reference genes (RGs) for the A. sativa-P. graminis experimental setup. We evaluated nine candidate reference genes in A. sativa (oat line Pg4 and the cultivar Kasztan) during compatible and incompatible interactions with different pathotypes of Puccinia graminis f. sp. avenae in six time points post-inoculation. The identification of genes with high expression stability was performed by four algorithms (geNorm, NormFinder, BestKeeper and ΔCt method). We found that the most appropriate combination of RGs for RT-qPCR data normalization were HNR (heterogeneous nuclear ribonucleoprotein 27C) + EF1A (elongation factor 1-alpha) + EIF4A (eukaryotic initiation factor 4A-3). The worst candidates for normalization in this dataset were CYP (cyclophilin) and TUA (alpha tubulin). Identified reference genes are suitable candidates for the standardization of gene expression studies in the A. sativa-P. graminis interaction system and potentially other related pathogens. To date, this is the first report of RGs selection in this pathosystem.
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Affiliation(s)
- Sylwia Sowa
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Magdalena Sozoniuk
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Joanna Toporowska
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Krzysztof Kowalczyk
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Edyta Paczos-Grzęda
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
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Gordon TC, Jin Y, Tinker NA, Bekele WA, Gale S, Bockelman H, Bonman JM. Comparative sequencing and SNP marker validation for oat stem rust resistance gene Pg6 in a diverse collection of Avena accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1307-1318. [PMID: 35113191 PMCID: PMC9033690 DOI: 10.1007/s00122-022-04032-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Comparative sequence analysis was used to design a SNP marker that aided in the identification of new sources of oat stem rust resistance. New races of Puccinia graminis f. sp. avenae (Pga) threaten global oat production. An A. strigosa accession known to carry the broadly effective oat stem rust resistance gene, Pg6, was crossed with two susceptible A. strigosa accessions to generate 198 F2:3 families and 190 F5:6 RILs. The RIL population was used to determine that Pg6 was a single dominant gene located between 475 and 491 Mbp on diploid chromosome AA2 of the A. atlantica genome. This region was further refined by identifying SNPs associated with Pg6 resistance in a panel of previously sequenced A-genome accessions. Twenty-four markers were developed from SNPs that showed perfect association between the Pg6 phenotype and 11 sequenced Avena diploid accessions. These markers were validated in the RILs and F2:3 families, and the markers most closely linked with resistance were tested in a diverse panel of 253 accessions consisting of oat stem rust differentials, all available diploid Avena spp. accessions, and 41 A. vaviloviana accessions from the National Small Grains Collection. One SNP marker located at 483, 439, 497 bp on AA2, designated as AA2_483439497, was perfectly associated with the Pg6 phenotype in Avena strigosa diploids and was within several Kb of a resistance gene analog, RPP13. The marker results and seedling testing against Pga races DBD, KBD, TJS, and TQL enabled the postulation of Pg6 and potential new sources of resistance in the Avena panel. These results will be used to infer Pg6 presence in other germplasm collections and breeding programs and can assist with introgression, gene pyramiding, and cloning of Pg6.
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Affiliation(s)
- Tyler C Gordon
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA.
| | - Yue Jin
- Cereal Disease Laboratory, USDA-ARS, 1551 Lindig Street, St. Paul, MN, 55108, USA
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Samuel Gale
- Cereal Disease Laboratory, USDA-ARS, 1551 Lindig Street, St. Paul, MN, 55108, USA
| | - Harold Bockelman
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - J Michael Bonman
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
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Li T, Xu Y, Zhang X, Wu X, Zhang Y, Xuan Y, Wang S. Virulence Characterization of Puccinia graminis f. sp. avenae and Resistance of Oat Cultivars in China. PLANT DISEASE 2022; 106:901-905. [PMID: 34546784 DOI: 10.1094/pdis-06-21-1239-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Oat stem rust, caused by Puccinia graminis f. sp. avenae, is one of the most devastating diseases of oat. The most cost-effective and environmentally friendly strategy to control this disease is the use of resistant cultivars. However, P. graminis f. sp. avenae can overcome the resistance of cultivars by rapidly changing its virulence. Thus, information on the virulence of P. graminis f. sp. avenae populations and resistance of cultivars is critical to control the disease. The current study was conducted to monitor the virulence composition and dynamics of the P. graminis f. sp. avenae population in China and to evaluate resistance of oat cultivars. Oat leaves naturally infected by P. graminis f. sp. avenae were collected in 2018 and 2019, and 159 isolates were derived from single uredinia. The isolates were tested on 12 international differential lines, and eight races, TJJ, TBD, TJB, TJD, TJL, TJN, TGD, and TKN, were identified for the first time in China. The predominant race was TJD, virulent against Pg1, Pg2, Pg3, Pg4, Pg8, Pg9, and Pg15, accounting for 35.8 and 37.8% in 2018 and 2019, respectively. The sub-predominant races were TJN (30.2% in 2018, 28.3% in 2019) and TKN (20.8% in 2018, 12.3% in 2019). All isolates were virulent to Pg1, Pg2, Pg3, and Pg4, and avirulent to Pg6 and Pg16. The three predominant races (TJD, TJN, and TKN) were used to evaluate resistance in 30 Chinese oat cultivars at the seedling and adult plant stages. Five cultivars, Bayan 1, Baiyan 2, Baiyan 3, Baiyan 5, and Baiyan 9, were highly resistant to the three races at both seedling and adult plant stages. The results of the virulences and frequencies of P. graminis f. sp. avenae races and the resistant cultivars will be useful in elucidating the pathogen migration and evolution and for breeding oat cultivars with stem rust resistance.
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Affiliation(s)
- Tianya Li
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Yiwei Xu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Xue Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Xianxin Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Yazhao Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
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Kebede AZ, Bekele WA, Mitchell Fetch JW, Beattie AD, Chao S, Tinker NA, Fetch TG, McCartney CA. Localization of the Stem Rust Resistance Gene Pg2 to Linkage Group Mrg20 in Cultivated Oat ( Avena sativa). PHYTOPATHOLOGY 2020; 110:1721-1726. [PMID: 32915112 DOI: 10.1094/phyto-03-20-0076-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stem rust is an important disease of cultivated oat (Avena sativa) caused by Puccinia graminis f. sp. avenae. In North America, host resistance is the primary strategy to control this disease and is conferred by a relatively small number of resistance genes. Pg2 is a widely deployed stem rust resistance gene that originates from cultivated oat. Oat breeders wish to develop cultivars with multiple Pg genes to slow the breakdown of single gene resistance, and often require DNA markers suited for marker-assisted selection. Our objectives were to (i) construct high density linkage maps for a major oat stem rust resistance gene using three biparental mapping populations, (ii) develop Kompetitive allele-specific PCR (KASP) assays for Pg2-linked single-nucleotide polymorphisms (SNPs), and (iii) test the prediction accuracy of those markers with a diverse panel of spring oat lines and cultivars. Genotyping-by-sequencing SNP markers linked to Pg2 were identified in an AC Morgan/CDC Morrison recombinant inbred line (RIL) population. Pg2-linked SNPs were then analyzed in an AC Morgan/RL815 F2 population and an AC Morgan/CDC Dancer RIL population. Linkage analysis identified a common location for Pg2 in all three populations on linkage group Mrg20 of the oat consensus genetic map. The most predictive markers were identified and converted to KASP assays for use in oat breeding programs. When used in combination, the KASP assays for the SNP loci avgbs2_126549.1.46 and avgbs_cluster_23819.1.27 were highly predictive of Pg2 status in panel of 54 oat breeding lines and cultivars.
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Affiliation(s)
- Aida Z Kebede
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Jennifer W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB R7C 1A1, Canada
| | - Aaron D Beattie
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Shiaoman Chao
- Cereal Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Fargo, ND 58102-2765, U.S.A
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Thomas G Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB R7C 1A1, Canada
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
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Kebede AZ, Admassu-Yimer B, Bekele WA, Gordon T, Bonman JM, Babiker E, Jin Y, Gale S, Wight CP, Tinker NA, Menzies JG, Beattie AD, Mitchell Fetch J, Fetch TG, Esvelt Klos K, McCartney CA. Mapping of the stem rust resistance gene Pg13 in cultivated oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:259-270. [PMID: 31637459 DOI: 10.1007/s00122-019-03455-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/09/2019] [Indexed: 05/19/2023]
Abstract
The widely deployed, oat stem rust resistance gene Pg13 was mapped by linkage analysis and association mapping, and KASP markers were developed for marker-assisted selection in breeding programs. Pg13 is one of the most extensively deployed stem rust resistance genes in North American oat cultivars. Identification of markers tightly linked to this gene will be useful for routine marker-assisted selection, identification of gene pyramids, and retention of the gene in backcrosses and three-way crosses. To this end, high-density linkage maps were constructed in four bi-parental mapping populations using SNP markers identified from 6K oat Infinium iSelect and genotyping-by-sequencing platforms. Additionally, genome-wide associations were identified using two sets of association panels consisting of diverse elite oat lines in one set and landrace accessions in the other. The results showed that Pg13 was located at approximately 67.7 cM on linkage group Mrg18 of the consensus genetic map. The gene co-segregated with the 7C-17A translocation breakpoint and with crown rust resistance gene Pc91. Co-segregating markers with the best prediction accuracy were identified at 67.7-68.5 cM on Mrg18. KASP assays were developed for linked SNP loci for use in oat breeding.
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Affiliation(s)
- Aida Z Kebede
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Belayneh Admassu-Yimer
- Small Grains and Potato Germplasm Research Unit, Oak Ridge Institute for Science and Education (ORISE) Research Participant, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Tyler Gordon
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - J Michael Bonman
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - Ebrahiem Babiker
- Southern Horticultural Research Laboratory, USDA-ARS, 810 Hwy 26, West Polarville, MS, 39470-0287, USA
| | - Yue Jin
- Cereal Disease Laboratory, USDA-ARS, 1551 Lindig Street, St. Paul, MN, 55108, USA
| | - Sam Gale
- Cereal Disease Laboratory, USDA-ARS, 1551 Lindig Street, St. Paul, MN, 55108, USA
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Aaron D Beattie
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Jennifer Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Thomas G Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Kathy Esvelt Klos
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
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Oat Fungal Diseases and the Application of Molecular Marker Technology for Their Control. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1188-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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