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Kenzhebayeva S, Mazkirat S, Shoinbekova S, Atabayeva S, Abekova A, Omirbekova N, Doktyrbay G, Asrandina S, Zharassova D, Amirova A, Serfling A. Phenotyping and Exploitation of Kompetitive Allele-Specific PCR Assays for Genes Underpinning Leaf Rust Resistance in New Spring Wheat Mutant Lines. Curr Issues Mol Biol 2024; 46:689-709. [PMID: 38248347 PMCID: PMC10814123 DOI: 10.3390/cimb46010045] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Leaf rust (Puccinia triticina Eriks) is a wheat disease causing substantial yield losses in wheat production globally. The identification of genetic resources with permanently effective resistance genes and the generation of mutant lines showing increased levels of resistance allow the efficient incorporation of these target genes into germplasm pools by marker-assisted breeding. In this study, new mutant (M3 generation) lines generated from the rust-resistant variety Kazakhstanskaya-19 were developed using gamma-induced mutagenesis through 300-, 350-, and 400-Gy doses. In field trials after leaf rust inoculation, 75 mutant lines showed adult plant resistance. These lines were evaluated for resistance at the seedling stage via microscopy in greenhouse experiments. Most of these lines (89.33%) were characterized as resistant at both developmental stages. Hyperspectral imaging analysis indicated that infected leaves of wheat genotypes showed increased relative reflectance in visible and near-infrared light compared to the non-infected genotypes, with peak means at 462 and 644 nm, and 1936 and 2392 nm, respectively. Five spectral indexes, including red edge normalized difference vegetation index (RNDVI), structure-insensitive pigment index (SIPI), ratio vegetation index (RVSI), water index (WI), and normalized difference water index (NDWI), demonstrated significant potential for determining disease severity at the seedling stage. The most significant differences in reflectance between susceptible and resistant mutant lines appeared at 694.57 and 987.51 nm. The mutant lines developed were also used for the development and validation of KASP markers for leaf rust resistance genes Lr1, Lr2a, Lr3, Lr9, Lr10, and Lr17. The mutant lines had high frequencies of "a" resistance alleles (0.88) in all six Lr genes, which were significantly associated with seedling resistance and suggest the potential of favorable haplotype introgression through functional markers. Nine mutant lines characterized by the presence of "b" alleles in Lr9 and Lr10-except for one line with allele "a" in Lr9 and three mutant lines with allele "a" in Lr10-showed the progressive development of fungal haustorial mother cells 72 h after inoculation. One line from 300-Gy-dosed mutant germplasm with "b" alleles in Lr1, Lr2a, Lr10, and Lr17 and "a" alleles in Lr3 and Lr9 was characterized as resistant based on the low number of haustorial mother cells, suggesting the contribution of the "a" alleles of Lr3 and Lr9.
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Affiliation(s)
- Saule Kenzhebayeva
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (S.S.); (S.A.); (N.O.); (G.D.); (S.A.); (A.A.)
| | - Shynarbek Mazkirat
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty Region, Almalybak 040909, Kazakhstan; (S.M.); (A.A.)
| | - Sabina Shoinbekova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (S.S.); (S.A.); (N.O.); (G.D.); (S.A.); (A.A.)
| | - Saule Atabayeva
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (S.S.); (S.A.); (N.O.); (G.D.); (S.A.); (A.A.)
| | - Alfia Abekova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty Region, Almalybak 040909, Kazakhstan; (S.M.); (A.A.)
| | - Nargul Omirbekova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (S.S.); (S.A.); (N.O.); (G.D.); (S.A.); (A.A.)
| | - Gulina Doktyrbay
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (S.S.); (S.A.); (N.O.); (G.D.); (S.A.); (A.A.)
| | - Saltant Asrandina
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (S.S.); (S.A.); (N.O.); (G.D.); (S.A.); (A.A.)
| | - Dinara Zharassova
- Mangyshlak Experimental Botanical Garden, Ministry of Science and Higher Education of the Republic of Kazakhstan, Aktau R00A3E0, Kazakhstan;
| | - Aigul Amirova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (S.S.); (S.A.); (N.O.); (G.D.); (S.A.); (A.A.)
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI) Federal Research Centre for Cultivated Plants, 06484 Quedlinburg, Germany;
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Norman M, Chen C, Miah H, Patpour M, Sørensen C, Hovmøller M, Forrest K, Kumar S, Prasad P, Gangwar OP, Bhardwaj S, Bariana H, Periyannan S, Bansal U. Sr65: a widely effective gene for stem rust resistance in wheat. Theor Appl Genet 2023; 137:1. [PMID: 38071267 DOI: 10.1007/s00122-023-04507-7] [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] [Received: 07/18/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Sr65 in chromosome 1A of Indian wheat landrace Hango-2 is a potentially useful all-stage resistance gene that currently protects wheat from stem rust in Australia, India, Africa and Europe. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatened global wheat production with the appearance of widely virulent races that included TTKSK and TTRTF. Indian landrace Hango-2 showed resistance to Pgt races in India and Australia. Screening of a Hango-2/Avocet 'S' (AvS) recombinant inbred line population identified two stem rust resistance genes, a novel gene (temporarily named as SrH2) from Hango-2 and Sr26 from AvS. A mapping population segregating for SrH2 alone was developed from two recombinant lines. SrH2 was mapped on the short arm of chromosome 1A, where it was flanked by KASP markers KASP_7944 (proximal) and KASP_12147 (distal). SrH2 was delimited to an interval of 1.8-2.3 Mb on chromosome arm 1AS. The failure to detect candidate genes through MutRenSeq and comparative genomic analysis with the pan-genome dataset indicated the necessity to generate a Hango-2 specific assembly for detecting the gene sequence linked with SrH2 resistance. MutRenSeq however enabled identification of SrH2-linked KASP marker sunCS_265. Markers KASP_12147 and sunCS_265 showed 92% and 85% polymorphism among an Australian cereal cultivar diversity panel and can be used for marker-assisted selection of SrH2 in breeding programs. The effectiveness of SrH2 against Pgt races from Europe, Africa, India, and Australia makes it a valuable resource for breeding stem rust-resistant wheat cultivars. Since no wheat-derived gene was previously located in chromosome arm 1AS, SrH2 represents a new locus and named as SR65.
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Affiliation(s)
- Michael Norman
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Hanif Miah
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Kerrie Forrest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Rd., Bundoora, VIC, 3083, Australia
| | - Subodh Kumar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Pramod Prasad
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Om Prakash Gangwar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Subhash Bhardwaj
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Harbans Bariana
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW, 2753, Australia
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia.
- School of Agriculture and Environmental Science, Centre for Crop Health, University of Southern Queensland, West Street, Toowoomba, QLD, 4350, Australia.
| | - Urmil Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
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Yang L, Liu H, Lei L, Wang J, Zheng H, Xin W, Zou D. Combined QTL-sequencing, linkage mapping, and RNA-sequencing identify candidate genes and KASP markers for low-temperature germination in Oryza sativa L. ssp. Japonica. Planta 2023; 257:122. [PMID: 37202578 DOI: 10.1007/s00425-023-04155-7] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
MAIN CONCLUSION Through QTL-seq, QTL mapping and RNA-seq, six candidate genes of qLTG9 can be used as targets for cold tolerance functional characterization, and six KASP markers can be used for marker-assisted breeding to improve the germination ability of japonica rice at low temperature. The development of direct-seeded rice at high latitudes and altitudes depends on the seed germination ability of rice under a low-temperature environment. However, the lack of regulatory genes for low-temperature germination has severely limited the application of genetics in improving the breeds. Here, we used cultivars DN430 and DF104 with significantly different low-temperature germination (LTG) and 460 F2:3 progeny derived from them to identify LTG regulators by combining QTL-sequencing, linkage mapping, and RNA-sequencing. The QTL-sequencing mapped qLTG9 within a physical interval of 3.4 Mb. In addition, we used 10 Kompetitive allele-specific PCR (KASP) markers provided by the two parents, and qLTG9 was optimized from 3.4 Mb to a physical interval of 397.9 kb and accounted for 20.4% of the phenotypic variation. RNA-sequencing identified qLTG9 as eight candidate genes with significantly different expression within the 397.9 kb interval, six of which possessed SNPs on the promoter and coding regions. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) completely validated the results of these six genes in RNA-sequencing. Subsequently, six non-synonymous SNPs were designed using variants in the coding region of these six candidates. Genotypic analysis of these SNPs in 60 individuals with extreme phenotypes indicated these SNPs determined the differences in cold tolerance between parents. The six candidate genes of qLTG9 and the six KASP markers could be used together for marker-assisted breeding to improve LTG.
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Affiliation(s)
- Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Lei
- Institute of Crop Cultivation and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Honglaing Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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Kaur S, Gill HS, Breiland M, Kolmer JA, Gupta R, Sehgal SK, Gill U. Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis. Front Plant Sci 2023; 14:1090163. [PMID: 36818858 PMCID: PMC9929074 DOI: 10.3389/fpls.2023.1090163] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.
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Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Matthew Breiland
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN, United States
| | - Rajeev Gupta
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fargo, ND, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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Broccanello C, Bellin D, DalCorso G, Furini A, Taranto F. Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change. Front Plant Sci 2023; 14:1101271. [PMID: 36778704 PMCID: PMC9911883 DOI: 10.3389/fpls.2023.1101271] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.
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Affiliation(s)
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Antonella Furini
- Department of Biotechnology, University of Verona, Verona, Italy
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Zhao R, Liu B, Wan W, Jiang Z, Chen T, Wang L, Bie T. Mapping and characterization of a novel adult-plant leaf rust resistance gene LrYang16G216 via bulked segregant analysis and conventional linkage method. Theor Appl Genet 2023; 136:1. [PMID: 36645449 DOI: 10.1007/s00122-023-04270-9] [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] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
A novel adult-plant leaf rust resistance gene LrYang16G216 on wheat chromosome 6BL was identified and mapped to a 0.59 cM genetic interval by BSA and conventional linkage method. Leaf rust (Puccinia triticina) is one of the most devastating fungal diseases of wheat (Triticum aestivum L.). Discovery and identification of new resistance genes is essential to develop disease-resistant cultivars. An advanced breeding line Yang16G216 was previously identified to confer adult-plant resistance (APR) to leaf rust. In this research, a recombinant inbred line (RIL) population was constructed from the cross between Yang16G216 and a highly susceptible line Yang16M6393, and genotyped with exome capture sequencing and 55 K SNP array. Through bulked segregant analysis (BSA) and genetic linkage mapping, a stable APR gene, designated as LrYang16G216, was detected and mapped to the distal region of chromosome arm 6BL with a genetic interval of 2.8 cM. For further verification, another RIL population derived from the cross between Yang16G216 and a susceptible wheat variety Yangmai 29 was analyzed using the enriched markers in the target interval, and LrYang16G216 was further narrowed to a 0.59 cM genetic interval flanked by the KASP markers Ax109403980 and Ax95083494, corresponding to the physical position 712.34-713.94 Mb in the Chinese Spring reference genome, in which twenty-six disease resistance-related genes were annotated. Based on leaf rust resistance spectrum, mapping data and physical location, LrYang16G216 was identified to be a novel and effective APR gene. The LrYang16G216 with linked markers will be useful for marker-assisted selection in wheat resistance breeding.
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Affiliation(s)
- Renhui Zhao
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Bingliang Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225007, China
| | - Wentao Wan
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Zhengning Jiang
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Tiantian Chen
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Ling Wang
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Tongde Bie
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China.
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Zhuansun X, Sun J, Liu N, Zhang S, Wang H, Hu Z, Ma J, Sun Q, Xie C. Mapping a leaf rust resistance gene LrOft in durum wheat Ofanto and its suppressor SuLrOft in common wheat. Front Plant Sci 2023; 14:1108565. [PMID: 37152129 PMCID: PMC10161252 DOI: 10.3389/fpls.2023.1108565] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023]
Abstract
Epidemics of leaf rust (caused by the fungal pathogen Puccinia triticina Erikss., Pt) raise concerns regarding sustainability of wheat production. Deployment of resistant cultivars is the most effective and economic strategy for combating this disease. Ofanto is a durum wheat cultivar that exhibits high resistance to Pt race PHT throughout its entire growing period. In the present study, we identified a leaf rust resistance gene in Ofanto and temporarily designated it as LrOft. LrOft was mapped to a 2.5 cM genetic interval in chromosome arm 6BL between Indel markers 6B6941 and 6B50L24. During introgression of LrOft from Ofanto to common wheat it was observed that F1 plants of Ofanto crossed with Shi4185 exhibited leaf rust resistance whereas the F1 of Ofanto crossed with ND4503 was susceptible. In order to map the presumed suppressor locus, a Shi4185/ND4503//Ofanto three-way pentaploid population was generated and SuLrOft was mapped on chromosome arm 2AS. SuLrOft was mapped within a 2.6 cM genetic interval flanked by 2AS50L14 and 2AS50L6. Fine mapping using 2,268 plants of the three-way cross narrowed the suppressor locus to a 68.2-kbp physical interval according to IWGSC RefSeq v1.1. Sequence analysis of genes in the physical interval revealed that TraesCS2A02G110800 encoding an RPP-13-like protein with an NB-ARC domain was a potential candidate for SuLrOft.
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Affiliation(s)
- Xiangxi Zhuansun
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Junna Sun
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Nannan Liu
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Shengnan Zhang
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Huifang Wang
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Zhaorong Hu
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Jun Ma
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Qixin Sun
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
| | - Chaojie Xie
- Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing, China
- *Correspondence: Chaojie Xie,
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Cui Z, Wu W, Fan F, Wang F, Liu D, Di D, Wang H. Transcriptome analysis of Lr19-virulent mutants provides clues for the AvrLr19 of Puccinia triticina. Front Microbiol 2023; 14:1062548. [PMID: 37032911 PMCID: PMC10073493 DOI: 10.3389/fmicb.2023.1062548] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Wheat leaf rust caused by Puccinia triticina (Pt) remains one of the most destructive diseases of common wheat worldwide. Understanding the pathogenicity mechanisms of Pt is important to control wheat leaf rust. Methods The urediniospores of Pt race PHNT (wheat leaf rust resistance gene Lr19-avirulent isolate) were mutagenized with ethyl methanesulfonate (EMS), and two Lr19-virulent mutants named M1 and M2 were isolated. RNA sequencing was performed on samples collected from wheat cultivars Chinese Spring and TcLr19 infected with wild-type (WT) PHNT, M1, and M2 isolates at 14 days post-inoculation (dpi), respectively. Screening AvrLr19 candidates by quantitative reverse transcription PCR (qPCR) and Agrobacterium-mediated transient assays in Nicotiana benthamiana. Results 560 genes with single nucleotide polymorphisms (SNPs) and insertions or deletions (Indels) from non-differentially expressed genes were identified. Among them, 10 secreted proteins were screened based on their fragments per kilobase of exon model per million mapped reads (FPKM) values in the database. qPCR results showed that the expression profiles of 7 secreted proteins including PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, and PTTG_03570 among 10 secreted proteins in mutants were significantly different with that in wild-type isolate after infection wheat TcLr19 and might be related to the recognition between Lr19 and AvrLr19. In addition, a total of 216 differentially expressed genes (DEGs) were obtained from three different sample comparisons including M1-vs-WT, M2-vs-WT, and M1-vs-M2. Among 216 DEGs, 15 were predicted to be secreted proteins. One secreted protein named PTTG_04779 could inhibit programmed progress of cell death (PCD) induced by apoptosis-controlling genes B-cell lymphoma-2 associated X protein (BAX) on Nicotiana benthamiana, indicating that it might play a virulence function in plant. Taken together, total 8 secreted proteins, PTTG_04779, PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, PTTG_03570 are identified as AvrLr19 candidates. Discussion Our results showed that a large number of genes participate in the interaction between Pt and TcLr19, which will provide valuable resources for the identification of AvrLr19 candidates and pathogenesis-related genes.
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Affiliation(s)
- Zhongchi Cui
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Wenyue Wu
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Fan Fan
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Fei Wang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Daqun Liu
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Dianping Di
- Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding, Hebei, China
- *Correspondence: Dianping Di,
| | - Haiyan Wang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
- Haiyan Wang,
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Huerta-Espino J, Singh RP, Villaseñor-Mir HE, Ammar K. Mining Sources of Resistance to Durum Leaf Rust among Tetraploid Wheat Accessions from CIMMYT's Germplasm Bank. Plants (Basel) 2022; 12:49. [PMID: 36616178 PMCID: PMC9823849 DOI: 10.3390/plants12010049] [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] [Received: 10/29/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
A collection of 482 tetraploid wheat accessions from the CIMMYT Germplasm Bank was screened in the greenhouse for resistance to leaf rust disease caused by the fungus Puccinia triticina E. The accessions were screened against two races CBG/BP and BBG/BP in the field at two locations: against race CBG/BP at the Norman E. Borlaug Experimental Station (CENEB) located in the Yaqui Valley in the northern state of Sonora in Mexico during the 2014-2015 growing season; and against race BBG/BP at CIMMYT headquarters in El Batan, Texcoco, in the state of Mexico in the summer of 2015. Among the accessions, 79 durum genotypes were identified, of which 68 continued demonstrating their resistance in the field (past the seedling stage) against the two leaf rust races. An additional set of 41 genotypes was susceptible at the seedling stage, but adult plant race-specific resistance was identified in the field. The 79 seedling-resistant genotypes were tested against 15 different leaf rust races at the seedling stage to measure the usefulness of their resistance in a breeding program. Among the 79 accessions tested, 35 were resistant to all races used in the tests. Two sample sources, CIMMYT (18/35) pre-breeding germplasm and Ethiopian landraces (17/35), showed seedling resistance to all races tested except for seven landraces from Ethiopia, which became susceptible to the Cirno race identified in 2017.
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Affiliation(s)
- Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo 56230, Mexico
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico City 06600, Mexico
| | | | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico City 06600, Mexico
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10
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Sunilkumar V, Krishna H, Devate NB, Manjunath KK, Chauhan D, Singh S, Sinha N, Singh JB, Prakasha TL, Pal D, Sivasamy M, Jain N, Singh GP, Singh PK. Marker assisted improvement for leaf rust and moisture deficit stress tolerance in wheat variety HD3086. Front Plant Sci 2022; 13:1035016. [PMID: 36352858 PMCID: PMC9638138 DOI: 10.3389/fpls.2022.1035016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
There is a significant yield reduction in the wheat crop as a result of different biotic and abiotic stresses, and changing climate, among them moisture deficit stress and leaf rust are the major ones affecting wheat worldwide. HD3086 is a high-yielding wheat variety that has been released for commercial cultivation under timely sown irrigated conditions in the Indo-Gangetic plains of India. Variety HD3086 provides a good, stable yield, and it is the choice of millions of farmers in India. It becomes susceptible to the most prevalent pathotypes 77-5 and 77-9 of Puccinia triticina (causing leaf rust) in the production environment and its potential yield cannot be realized under moisture deficit stress. The present study demonstrates the use of a marker-assisted back cross breeding approach to the successful transfer of leaf rust resistance gene Lr24 and QTLs linked to moisture deficit stress tolerance in the background of HD3086. The genotype HI1500 was used as a donor parent that possesses leaf rust-resistant gene Lr24, which confers resistance against the major pathotypes found in the production environment. It possesses inbuilt tolerance under abiotic stresses with superior quality traits. Foreground selection for gene Lr24 and moisture deficit stress tolerance QTLs linked to Canopy temperature (CT), Normal Differential Vegetation Index (NDVI) and Thousand Kernel Weight (TKW) in different generations of the backcrossing and selection. In BC2F2, foreground selection was carried out to identify homozygous lines based on the linked markers and were advanced following pedigree based phenotypic selection. The selected lines were evaluated against P. triticina pathotypes 77-5 and 77-9 under controlled conditions. Recurrent parent recovery of the selected lines ranged from 78-94%. The identified lines were evaluated for their tolerance to moisture stress under field conditions and their resistance to rust under artificial epiphytotic conditions for two years. In BC2F5 generation, eight positive lines for marker alleles were selected which showed resistance to leaf rust and recorded an improvement in component traits of moisture deficit stress tolerance such as CT, NDVI, TKW and yield compared to the recurrent parent HD3086. The derived line is named HD3471 and is nominated for national trials for testing and further release for commercial cultivation.
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Affiliation(s)
- V.P. Sunilkumar
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Narayana Bhat Devate
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | | | - Divya Chauhan
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Shweta Singh
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Nivedita Sinha
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Jang Bahadur Singh
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - T. L. Prakasha
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Dharam Pal
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - M. Sivasamy
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Neelu Jain
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - G. P. Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - P. K. Singh
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
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11
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Sumitomo K, Shirasawa K, Isobe S, Hirakawa H, Harata A, Nakano M, Nakano Y, Yagi M, Hisamatsu T, Yamaguchi H, Taniguchi F. A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome. Hortic Res 2022; 9:uhac170. [PMID: 36324641 PMCID: PMC9613985 DOI: 10.1093/hr/uhac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
White rust caused by Puccinia horiana is one of the most serious diseases of chrysanthemum (Chrysanthemum × morifolium). In this study, we report the DNA markers associated with resistance against P. horiana via a simple approach using the genome of a wild diploid relative, Chrysanthemum seticuspe. First, we identified the important region of the genome in the resistant cultivar "Ariesu" via a genome-wide association study. Simplex single nucleotide polymorphism (SNP) markers mined from ddRAD-Seq were used in a biparental population originating from crosses between resistant "Ariesu" and susceptible "Yellow Queen". The C. seticuspe genome was used as a reference. For the fine mapping of P. horiana resistance locus 2 (Phr2), a comparative whole genome sequencing study was conducted. Although the genome sequences of chrysanthemum cultivars assembled via the short-read approach were fragmented, reliable genome alignments were reconstructed by mapping onto the chromosome level of the C. seticuspe pseudomolecule. Base variants were then identified by comparing the assembled genome sequences of resistant "Ariesu" and susceptible "Yellow Queen". Consequently, SNP markers that were closer to Phr2 compared with ddRAD-Seq markers were obtained. These SNP markers co-segregated with resistance in F1 progenies originating from resistant "Ariesu" and showed robust transferability for detecting Phr2-conferring resistance among chrysanthemum genetic resources. The wild C. seticuspe pseudomolecule, a de facto monoploid genome used for ddRAD-Seq analysis and assembled genome sequence comparison, demonstrated this method's utility as a model for developing DNA markers in hexaploid chrysanthemum cultivars.
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Affiliation(s)
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818 Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818 Japan
| | - Akiho Harata
- Kagoshima Prefectural Institute for Agricultural Development, Minamisatsuma, Kagoshima 899-3401, Japan
- CCS Inc., Kyoto, Kyoto 602-8019, Japan
| | - Michiharu Nakano
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Yoshihiro Nakano
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Tamotsu Hisamatsu
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Hiroyasu Yamaguchi
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Fumiya Taniguchi
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
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12
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Qu X, Li C, Liu H, Liu J, Luo W, Xu Q, Tang H, Mu Y, Deng M, Pu Z, Ma J, Jiang Q, Chen G, Qi P, Jiang Y, Wei Y, Zheng Y, Lan X, Ma J. Quick mapping and characterization of a co-located kernel length and thousand-kernel weight-related QTL in wheat. Theor Appl Genet 2022; 135:2849-2860. [PMID: 35804167 DOI: 10.1007/s00122-022-04154-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
A co-located KL and TKW-related QTL with no negative effect on PH and AD was rapidly identified using BSA and wheat 660 K SNP array. Its effect was validated in a panel of 218 wheat accessions. Kernel length (KL) and thousand-kernel weight (TKW) of wheat (Triticum aestivum L.) contribute significantly to kernel yield. In the present study, a recombinant inbred line (RIL) population derived from the cross between the wheat line S849-8 with larger kernels and more spikelets per spike and the line SY95-71 was developed. Further, of both the bulked segregant analysis (BSA) and the wheat 660 K single nucleotide polymorphism (SNP) array were used to rapidly identify genomic regions for kernel-related traits from this RIL population. Kompetitive Allele Specific PCR markers were further developed in the SNP-enriched region on the 2D chromosome to construct a genetic map. Both QKL.sicau-SSY-2D for KL and QTKW.sicau-SSY-2D for TKW were identified at multiple environments on chromosome arm 2DL. These two QTLs explained 9.68-23.02% and 6.73-18.32% of the phenotypic variation, respectively. The effects of this co-located QTL were successfully verified in a natural population consisting of 218 Sichuan wheat accessions. Interestingly, the major QTL was significantly and positively correlated with spike length, but did not negatively affect spikelet number per spike (SNS), plant height, or anthesis date. These results indicated that it is possible to synchronously improve kernel weight and SNS by using this QTL. Additionally, several genes associated with kernel development and filling rate were predicted and sequenced in the QTL-containing physical intervals of reference genomes of 'Chinese spring' and Aegilops tauschii. Collectively, these results provide a QTL with great breeding potential and its linked markers which should be helpful for fine mapping and molecular breeding.
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Affiliation(s)
- Xiangru Qu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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13
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Raghunandan K, Tanwar J, Patil SN, Chandra AK, Tyagi S, Agarwal P, Mallick N, Murukan N, Kumari J, Sahu TK, Jacob SR, Kumar A, Yadav S, Nyamgoud S, Vinod, Singh AK, Jha SK. Identification of Novel Broad-Spectrum Leaf Rust Resistance Sources from Khapli Wheat Landraces. Plants 2022; 11:1965. [PMID: 35956445 PMCID: PMC9370231 DOI: 10.3390/plants11151965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/24/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022]
Abstract
Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have evolved from wild emmer (Triticum turgidum var. dicoccoides), and harbors a good number of leaf rust resistance genes. In the present study, we are reporting on the screening of one hundred and twenty-three dicoccum wheat germplasm accessions against the leaf rust pathotype 77-5. Among these, an average of 45.50% of the germplasms were resistant, 46.74% were susceptible, and 8.53% had mesothetic reactions. Further, selected germplasm lines with accession numbers IC138898, IC47022, IC535116, IC535133, IC535139, IC551396, and IC534144 showed high level of resistance against the eighteen prevalent pathotypes. The infection type varied from “;”, “;N”, “;N1” to “;NC”. PCR-based analysis of the resistant dicoccum lines with SSR marker gwm508 linked to the Lr53 gene, a leaf rust resistance gene effective against all the prevalent pathotypes of leaf rust in India and identified from a T. turgidum var. dicoccoides germplasm, indicated that Lr53 is not present in the selected accessions. Moreover, we have also generated 35K SNP genotyping data of seven lines and the susceptible control, Mandsaur Local, to study their relationships. The GDIRT tool based on homozygous genotypic differences revealed that the seven genotypes are unique to each other and may carry different resistance genes for leaf rust.
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14
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Han S, Zhou X, Shi L, Zhang H, Geng Y, Fang Y, Xia H, Liu H, Li P, Zhao S, Miao L, Hou L, Zhang Z, Xu J, Ma C, Wang Z, Li H, Zheng Z, Huang B, Dong W, Zhang J, Tang F, Li S, Gao M, Zhang X, Zhao C, Wang X. AhNPR3 regulates the expression of WRKY and PR genes, and mediates the immune response of the peanut (Arachis hypogaea L.). Plant J 2022; 110:735-747. [PMID: 35124871 DOI: 10.1111/tpj.15700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Systemic acquired resistance is an essential immune response that triggers a broad-spectrum disease resistance throughout the plant. In the present study, we identified a peanut lesion mimic mutant m14 derived from an ethyl methane sulfonate-mutagenized mutant pool of peanut cultivar "Yuanza9102." Brown lesions were observed in the leaves of an m14 mutant from seedling stage to maturity. Using MutMap together with bulked segregation RNA analysis approaches, a G-to-A point mutation was identified in the exon region of candidate gene Arahy.R60CUW, which is the homolog of AtNPR3 (Nonexpresser of PR genes) in Arabidopsis. This point mutation caused a transition from Gly to Arg within the C-terminal transactivation domain of AhNPR3A. The mutation of AhNPR3A showed no effect in the induction of PR genes when treated with salicylic acid. Instead, the mutation resulted in upregulation of WRKY genes and several PR genes, including pathogenesis-related thaumatin- and chitinase-encoding genes, which is consistent with the resistant phenotype of m14 to leaf spot disease. Further study on the AhNPR3A gene will provide valuable insights into understanding the molecular mechanism of systemic acquired resistance in peanut. Moreover, our results indicated that a combination of MutMap and bulked segregation RNA analysis is an effective method for identifying genes from peanut mutants.
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Affiliation(s)
- Suoyi Han
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Ximeng Zhou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Lei Shi
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Huayang Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Yun Geng
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Yuanjin Fang
- Kaifeng Academy of Agriculture and Forestry, Kaifeng, 475000, China
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Hua Liu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Lijuan Miao
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhongxin Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jing Xu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Hongyan Li
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Zheng Zheng
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jun Zhang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Fengshou Tang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Shaojian Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Meng Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
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15
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Kumar K, Jan I, Saripalli G, Sharma PK, Mir RR, Balyan HS, Gupta PK. An Update on Resistance Genes and Their Use in the Development of Leaf Rust Resistant Cultivars in Wheat. Front Genet 2022; 13:816057. [PMID: 35432483 PMCID: PMC9008719 DOI: 10.3389/fgene.2022.816057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/16/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Wheat is one of the most important cereal crops in the world. The production and productivity of wheat is adversely affected by several diseases including leaf rust, which can cause yield losses, sometimes approaching >50%. In the present mini-review, we provide updated information on (i) all Lr genes including those derived from alien sources and 14 other novel resistance genes; (ii) a list of QTLs identified using interval mapping and MTAs identified using GWAS (particular those reported recently i.e., after 2018) and their association with known Lr genes; (iii) introgression/pyramiding of individual Lr genes in commercial/prominent cultivars from 18 different countries including India. Challenges and future perspectives of breeding for leaf rust resistance are also provided at the end of this mini-review. We believe that the information in this review will prove useful for wheat geneticists/breeders, not only in the development of leaf rust-resistant wheat cultivars, but also in the study of molecular mechanism of leaf rust resistance in wheat.
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Affiliation(s)
- Kuldeep Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - P. K. Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura, India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- *Correspondence: P. K. Gupta, ,
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Zhao H, Tian R, Xia H, Li C, Li G, Li A, Zhang X, Zhou X, Ma J, Huang H, Zhang K, Thudi M, Ma C, Wang X, Zhao C. High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut. Front Genet 2022; 13:845602. [PMID: 35401655 PMCID: PMC8990815 DOI: 10.3389/fgene.2022.845602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. Here, we report a comprehensive genome variation map based on the genotyping of a panel of 178 peanut cultivars using Axiom_Arachis2 SNP array, including 163 representative varieties of different provinces in China, and 15 cultivars from 9 other countries. According to principal component analysis (PCA) and phylogenetic analysis, the peanut varieties were divided into 7 groups, notable genetic divergences between the different areas were shaped by environment and domestication. Using genome-wide association study (GWAS) analysis, we identified several marker-trait associations (MTAs) and candidate genes potentially involved in regulating several agronomic traits of peanut, including one MTA related with hundred seed weight, one MTA related with total number of branches, and 14 MTAs related with pod shape. This study outlines the genetic basis of these peanut cultivars and provides 13,125 polymorphic SNP markers for further distinguishing and utility of these elite cultivars. In addition, the candidate loci and genes provide valuable information for further fine mapping of QTLs and improving the quality and yield of peanut using a genomic-assisted breeding method.
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Affiliation(s)
- Huiling Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Guanghui Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Aiqin Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xianying Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Ximeng Zhou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jing Ma
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Huailing Huang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Kun Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, China
| | - Mahendar Thudi
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- Rajendra Prasad Central Agricultural University, Samsthipur, India
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
- *Correspondence: Xingjun Wang, ; Chuanzhi Zhao,
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
- *Correspondence: Xingjun Wang, ; Chuanzhi Zhao,
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Zhou J, Singh RP, Ren Y, Bai B, Li Z, Yuan C, Li S, Huerta-Espino J, Liu D, Lan C. Identification of Two New Loci for Adult Plant Resistance to Leaf Rust and Stripe Rust in the Chinese Wheat Variety 'Neimai 836'. Plant Dis 2021; 105:3705-3714. [PMID: 33779256 DOI: 10.1094/pdis-12-20-2654-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The characterization of leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) resistance genes is the basis for breeding resistant wheat varieties and managing epidemics of these diseases in wheat. A cross between the susceptible wheat variety 'Apav#1' and resistant variety 'Neimai 836' was used to develop a mapping population containing 148 F5 recombinant inbred lines (RILs). Leaf rust phenotyping was done in field trials at Ciudad Obregón, Mexico, in 2017 and 2018, and stripe rust data were generated at Toluca, Mexico, in 2017 and in Mianyang, Ezhou, and Gansu, China, in 2019. Inclusive complete interval mapping (ICIM) was used to create a genetic map and identify significant resistance quantitative trait loci (QTL) with 2,350 polymorphic markers from a 15K wheat single-nucleotide polymorphism (SNP) array and simple-sequence repeats (SSRs). The pleiotropic multipathogen resistance gene Lr46/Yr29 and four QTL were identified, including two new loci, QLr.hzau-3BL and QYr.hzau-5AL, which explained 3 to 16% of the phenotypic variation in resistance to leaf rust and 7 to 14% of that to stripe rust. The flanking SNP markers for the two loci were converted to Kompetitive Allele-Specific PCR (KASP) markers and used to genotype a collection of 153 wheat lines, indicating the Chinese origin of the loci. Our results suggest that Neimai 836, which has been used as a parent for many wheat varieties in China, could be a useful source of high-level resistance to both leaf rust and stripe rust.
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Affiliation(s)
- Jingwei Zhou
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico D.F., Mexico
| | - Yong Ren
- Mianyang Academy of Agricultural Science/Mianyang Branch of National Wheat Improvement Center, Mianyang 621023, Sichuan, P.R. China
| | - Bin Bai
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, No. 1 Nongkeyuanxincun, Lanzhou 730070, Gansu Province, P.R. China
| | - Zhikang Li
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Chan Yuan
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Shunda Li
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico Instituto Nacional de Investigaciones Forestales Agricolas y Pecuarias (INIFAP), 56230 Chapingo, Edo. de Mexico, Mexico
| | - Demei Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Crop Molecular Breeding and China and Qinghai Provincial Key Laboratory of Crop Molecular Breeding Northwest Institute of Plateau Biology, Innovation Academy for Seed Design, Xining 810008, P.R. China
| | - Caixia Lan
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
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Li H, Hua L, Rouse MN, Li T, Pang S, Bai S, Shen T, Luo J, Li H, Zhang W, Wang X, Dubcovsky J, Chen S. Mapping and Characterization of a Wheat Stem Rust Resistance Gene in Durum Wheat "Kronos". Front Plant Sci 2021; 12:751398. [PMID: 34721479 PMCID: PMC8555631 DOI: 10.3389/fpls.2021.751398] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/09/2021] [Indexed: 05/22/2023]
Abstract
Wheat stem (or black) rust is one of the most devastating fungal diseases, threatening global wheat production. Identification, mapping, and deployment of effective resistance genes are critical to addressing this challenge. In this study, we mapped and characterized one stem rust resistance (Sr) gene from the tetraploid durum wheat variety Kronos (temporary designation SrKN). This gene was mapped on the long arm of chromosome 2B and confers resistance to multiple virulent Pgt races, such as TRTTF and BCCBC. Using a large mapping population (3,366 gametes), we mapped SrKN within a 0.29 cM region flanked by the sequenced-based markers pku4856F2R2 and pku4917F3R3, which corresponds to 5.6- and 7.2-Mb regions in the Svevo and Chinese Spring reference genomes, respectively. Both regions include a cluster of nucleotide binding leucine-repeat (NLR) genes that likely includes the candidate gene. An allelism test failed to detect recombination between SrKN and the previously mapped Sr9e gene. This result, together with the similar seedling resistance responses and resistance profiles, suggested that SrKN and Sr9e may represent the same gene. We introgressed SrKN into common wheat and developed completely linked markers to accelerate its deployment in the wheat breeding programs. SrKN can be a valuable component of transgenic cassettes or gene pyramids that includes multiple resistance genes to control this devastating disease.
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Affiliation(s)
- Hongna Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Lei Hua
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Matthew N. Rouse
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Tianya Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Shuyong Pang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shengsheng Bai
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Tao Shen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Jing Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Hongyu Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
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Li M, Wang Y, Liu X, Li X, Wang H, Bao Y. Molecular Cytogenetic Identification of a Novel Wheat- Thinopyrum ponticum 1J S (1B) Substitution Line Resistant to Powdery Mildew and Leaf Rust. Front Plant Sci 2021; 12:727734. [PMID: 34659293 PMCID: PMC8519347 DOI: 10.3389/fpls.2021.727734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Thinopyrum ponticum (2n = 10x = 70) is a wild relative of wheat with high tolerance to both biotic and abiotic stresses; it has been wildly used in wheat genetic improvement. A disomic substitution line named SN19647 was derived from a cross between Triticum aestivum and the wheat-Th. ponticum partial amphiploid SNTE20 (2n = 8x = 56). It was evaluated for disease resistance and characterized via sequential fluorescence in situ hybridization (FISH)-genomic in situ hybridization (GISH) and molecular markers. The results showed that SN19647 carried resistance to both powdery mildew and leaf rust. It contained 42 chromosomes with a pair of wheat chromosome 1B replaced by a pair of JS chromosomes from Th. ponticum. In addition to chromosomal substitution events, structural variation also occurred on wheat chromosomes 2A, 5A, 6B, and 7B. Based on marker analysis, 19 markers specific to the JS chromosome were obtained, of which seventeen markers belonged to homoeologous group one. These results indicated that SN19647 was a 1JS (1B) substitution line. Compared with the known 1JS (1D) substitution line CH10A5, it was found that 17 markers generated different specific bands to Th. ponticum, confirming the novelty of the 1JS chromosome in SN19647. Therefore, SN19647, resistant to powdery mildew and leaf rust, was a novel 1JS (1B) substitution line that can be used in wheat genetic improvement.
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Affiliation(s)
- Mingzhu Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaojuan Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
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20
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Zhang Q, Wei W, Zuansun X, Zhang S, Wang C, Liu N, Qiu L, Wang W, Guo W, Ma J, Peng H, Hu Z, Sun Q, Xie C. Fine Mapping of the Leaf Rust Resistance Gene Lr65 in Spelt Wheat 'Altgold'. Front Plant Sci 2021; 12:666921. [PMID: 34262578 PMCID: PMC8274547 DOI: 10.3389/fpls.2021.666921] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Wheat leaf rust (also known as brown rust), caused by the fungal pathogen Puccinia triticina Erikss. (Pt), is one by far the most troublesome wheat disease worldwide. The exploitation of resistance genes has long been considered as the most effective and sustainable method to control leaf rust in wheat production. Previously the leaf rust resistance gene Lr65 has been mapped to the distal end of chromosome arm 2AS linked to molecular marker Xbarc212. In this study, Lr65 was delimited to a 0.8 cM interval between flanking markers Alt-64 and AltID-11, by employing two larger segregating populations obtained from crosses of the resistant parent Altgold Rotkorn (ARK) with the susceptible parents Xuezao and Chinese Spring (CS), respectively. 24 individuals from 622 F2 plants of crosses between ARK and CS were obtained that showed the recombination between Lr65 gene and the flanking markers Alt-64 and AltID-11. With the aid of the CS reference genome sequence (IWGSC RefSeq v1.0), one SSR marker was developed between the interval matched to the Lr65-flanking marker and a high-resolution genetic linkage map was constructed. The Lr65 was finally located to a region corresponding to 60.11 Kb of the CS reference genome. The high-resolution genetic linkage map founded a solid foundation for the map-based cloning of Lr65 and the co-segregating marker will facilitate the marker-assisted selection (MAS) of the target gene.
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21
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Zhang Y, Wang Z, Quan W, Zhang X, Feng J, Ren J, Jiang X, Zhang Z. Mapping of a QTL with major effect on reducing leaf rust severity at the adult plant growth stage on chromosome 2BL in wheat landrace Hongmazha. Theor Appl Genet 2021; 134:1363-1376. [PMID: 33550471 DOI: 10.1007/s00122-021-03776-4] [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] [Received: 08/29/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
A major QTL (QLr.cau-2BL) for APR to leaf rust was detected on 2BL; an SSR marker was developed to closely link with QLr.cau-2BL and validated for effectiveness of MAS. The wheat landrace Hongmazha (HMZ) possesses adult plant resistance (APR) to leaf rust. To detect and validate quantitative trait locus (QTL) for the APR, four wheat populations were assessed for leaf rust severity in a total of eight field and greenhouse experiments. The mapping population Aquileja × HMZ (120 recombinant inbred lines, RILs) was genotyped using 90 K SNP markers. A major QTL (QLr.cau-2BL) was detected between the markers IWB3854 and IWB21922 on chromosome 2BL. IWB3854 and IWB21922 were positioned at approximately 531.14 Mb and 616.48 Mb, respectively, on 2BL of IWGSC RefSeq v1.0 physical map. Based on the sequences between 531.14 and 616.48 Mb on 2BL of IWGSC RefSeq v1.0, 415 simple sequence repeat (SSR) markers were developed. These markers and 28 previously published SSR makers were screened; the resulted polymorphic markers were used to genotype the relatively larger population RL6058 × HMZ (371 RILs). QLr.cau-2BL was mapped within a 1.5 cM interval on 2BL map of RL6058 × HMZ, and a marker (Ta2BL_ssr7) was identified to closely link with QLr.cau-2BL. Effectiveness of selection for QLr.cau-2BL based on Ta2BL_ssr7 was validated using two populations (RL6058 × HMZ F2:3 and Jimai22 × HMZ BC4F2:3). In addition, polymorphism at Ta2BL_ssr7 was detected among a panel of 282 commercial wheat cultivars. We believe, therefore, that Ta2BL_ssr7 should be useful for introducing QLr.cau-2BL into commercial wheat cultivars and for accumulating QLr.cau-2BL with other APR QTL.
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Affiliation(s)
- Yibin Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wei Quan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Xiang Zhang
- National Fisheries Technology Extension Center, Beijing, 100125, People's Republic of China
| | - Jing Feng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Junda Ren
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Xu Jiang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Zhang P, Yan X, Gebrewahid TW, Zhou Y, Yang E, Xia X, He Z, Li Z, Liu D. Genome-wide association mapping of leaf rust and stripe rust resistance in wheat accessions using the 90K SNP array. Theor Appl Genet 2021; 134:1233-1251. [PMID: 33492413 DOI: 10.1007/s00122-021-03769-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/09/2021] [Indexed: 05/22/2023]
Abstract
A genome-wide association analysis identified diverse loci for seedling and adult plant resistance to leaf rust and stripe rust. KASP markers were developed and validated for marker-assisted selection. Wheat leaf rust and stripe rust cause significant losses in many wheat producing regions worldwide. The objective of this study was to identify chromosome regions conferring resistance to both leaf rust and stripe rust at the seedling and adult plant stages. A diversity panel of 268 wheat lines, including 207 accessions from different wheat growing regions in China, and 61 accessions from foreign countries, were evaluated for leaf rust response at seedling stage using eight Chinese Puccinia triticina pathotypes, and also tested for leaf rust and stripe rust at adult plant stage in multiple field environments. The panel was genotyped with the Wheat 90 K Illumina iSelect SNP array. Genome-wide association mapping (GWAS) was performed using the mixed linear model (MLM). Twenty-two resistance loci including the known Lr genes, Lr1, Lr26, Lr3ka, LrZH22, and 18 potentially new loci were identified associated with seedling resistance, explaining 4.6 to 25.2% of the phenotypic variance. Twenty-two and 23 adult plant resistance (APR) QTL associated with leaf and stripe rust, respectively, were identified at adult stage, explaining 4.2-11.5% and 4.4-9.7% of the phenotypic variance. Among them, QLr-2BS was the potentially most valuable all-stage resistance gene. Seven and six consistent APR QTL were identified in multiple environments including best linear unbiased prediction (BLUP) data, respectively. Comparison with previously mapped resistance loci indicated that three of the seven leaf rust resistance APR QTL, and two of the six stripe rust resistance APR QTL were new. Four potentially pleiotropic APR QTL, including Lr46/Yr29, QLr-2AL.1/QYr-2AL.1, QLr-2AL.2/QYr-2AL.2, and QLr-5BL/QYr-5BL.1, were identified. Twelve associated SNPs were converted into kompetitive allele-specific PCR (KASP) markers and verified in bi-parental populations. The study reports genetic loci conferring resistance to both diseases, and the closely linked markers should be applicable for marker-assisted wheat breeding.
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Affiliation(s)
- Peipei Zhang
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Xiaocui Yan
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Takele-Weldu Gebrewahid
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
- College of Agriculture, Aksum University, Shire-Indaslassie 314, Tigray, Ethiopia
| | - Yue Zhou
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, 071001, Hebei, People's Republic of China
| | - Ennian Yang
- Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Crop Research Institute, Sichuan Academy of Agricultural Science, #4 Shizishan Rd, Jinjiang, Chengdu, 610066, Sichuan, People's Republic of China
| | - Xianchun Xia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Zhonghu He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Zaifeng Li
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China.
| | - Daqun Liu
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China.
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23
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Kumar S, Bhardwaj SC, Gangwar OP, Sharma A, Qureshi N, Kumaran VV, Khan H, Prasad P, Miah H, Singh GP, Sharma K, Verma H, Forrest KL, Trethowan RM, Bariana HS, Bansal UK. Lr80: A new and widely effective source of leaf rust resistance of wheat for enhancing diversity of resistance among modern cultivars. Theor Appl Genet 2021; 134:849-858. [PMID: 33388887 DOI: 10.1007/s00122-020-03735-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
A new leaf rust resistance gene Lr80 was identified and closely linked markers were developed for its successful pyramiding with other marker-tagged genes to achieve durable control of leaf rust. Common wheat landrace Hango-2, collected in 2006 from the Himalayan area of Hango, District Kinnaur, in Himachal Pradesh, exhibited a very low infection type (IT;) at the seedling stage to all Indian Puccinia triticina (Pt) pathotypes, except the pathotype 5R9-7 which produced IT 3+. Genetic analysis based on Agra Local/Hango-2-derived F3 families indicated monogenic control of leaf rust resistance, and the underlying locus was temporarily named LrH2. Bulked segregant analysis using 303 simple sequence repeat (SSR) markers located LrH2 in the short arm of chromosome 2D. An additional set of 10 chromosome 2DS-specific markers showed polymorphism between the parents and these were mapped on the entire Agra Local/Hango-2 F3 population. LrH2 was flanked by markers cau96 (distally) and barc124 (proximally). The 90 K Infinium SNP array was used to identify SNP markers linked with LrH2. Markers KASP_17425 and KASP_17148 showed association with LrH2. Comparison of seedling leaf rust response data and marker locations across different maps demonstrated the uniqueness of LrH2 and it was formally named Lr80. The Lr80-linked markers KASP_17425, KASP_17148 and barc124 amplified alleles/products different to Hango-2 in 82 Australian cultivars indicating their robustness for marker-assisted selection of this gene in wheat breeding programs.
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Affiliation(s)
- Subodh Kumar
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Subhash C Bhardwaj
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India.
| | - Om P Gangwar
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Akanksha Sharma
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia
| | - Naeela Qureshi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, Victoria, 3083, Australia
| | - Vikas V Kumaran
- Indian Council of Agricultural Research (ICAR), Indian Agricultural Research Institute Regional Station, Wellington, Nilgiris, Tamil Nadu, 643231, India
| | - Hanif Khan
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Pramod Prasad
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Hanif Miah
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia
| | - Gyanendra P Singh
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Kiran Sharma
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Hemlata Verma
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Kerrie L Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, Victoria, 3083, Australia
| | - Richard M Trethowan
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia
| | - Harbans S Bariana
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia.
| | - Urmil K Bansal
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia.
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Aoun M, Rouse MN, Kolmer JA, Kumar A, Elias EM. Genome-Wide Association Studies Reveal All-Stage Rust Resistance Loci in Elite Durum Wheat Genotypes. Front Plant Sci 2021; 12:640739. [PMID: 33912208 PMCID: PMC8072158 DOI: 10.3389/fpls.2021.640739] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/17/2021] [Indexed: 05/11/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt), stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), and stem rust caused by Puccinia graminis f. sp. tritici (Pgt) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type-Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13a, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat.
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Affiliation(s)
- Meriem Aoun
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- *Correspondence: Meriem Aoun,
| | - Matthew N. Rouse
- Cereal Disease Laboratory, United States Department of Agriculture–Agricultural Research Service, St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture–Agricultural Research Service, St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Elias M. Elias,
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25
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Dinkar V, Jha SK, Mallick N, Niranjana M, Agarwal P, Sharma JB, Vinod. Molecular mapping of a new recessive wheat leaf rust resistance gene originating from Triticum spelta. Sci Rep 2020; 10:22113. [PMID: 33335131 PMCID: PMC7746701 DOI: 10.1038/s41598-020-78679-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/04/2020] [Accepted: 11/27/2020] [Indexed: 11/09/2022] Open
Abstract
TSD276-2, a wheat genetic stock derived from the cross Agra Local/T. spelta 276 showed broad spectrum resistance against leaf rust pathogen. Genetic analysis was undertaken using F1, F2, F2:3 and BC1F1 generations derived from the cross TSD276-2/Agra Local. The results revealed a single recessive gene for leaf rust resistance, tentatively named as LrTs276-2, in TSD276-2. Molecular mapping of leaf rust resistance gene LrTs276-2 in TSD276-2 was done using SNP-based PCR and SSR markers. For Bulked Segregant Analysis (BSA), two bulks viz. resistant bulk and susceptible bulk, and the parents TSD276-2 and Agra Local were genotyped for SNPs using AFFYMETRIX 35K Wheat Breeders' AXIOM array. T. spelta 276 was also genotyped and used as a check. BSA indicated that the gene for leaf rust resistance in TSD276-2 is located on chromosome arm 1DS. Putatively linked SNPs on chromosome arm 1DS were converted into PCR-based markers. Polymorphic SSR markers on chromosome arm 1DS were also identified. Final linkage map was constructed using one SNP-based PCR and three SSR markers. The rust reaction and chromosomal location suggest that LrTs276-2 is a new leaf rust resistance gene which may be useful in broadening the genetic base of leaf rust resistance in wheat.
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Affiliation(s)
- Vishal Dinkar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S K Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niharika Mallick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - M Niranjana
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Priyanka Agarwal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - J B Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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26
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Sapkota S, Mergoum M, Kumar A, Fiedler JD, Johnson J, Bland D, Lopez B, Sutton S, Ghimire B, Buck J, Chen Z, Harrison S. A novel adult plant leaf rust resistance gene Lr2K38 mapped on wheat chromosome 1AL. Plant Genome 2020; 13:e20061. [PMID: 33169935 DOI: 10.1002/tpg2.20061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Soft red winter wheat (SRWW) cultivar AGS 2038 has a high level of seedling and adult plant leaf rust (LR) resistance. To map and characterize LR resistance in AGS 2038, a recombinant inbred line (RIL) population consisting of 225 lines was developed from a cross between AGS 2038 and moderately resistant line UGA 111729. The parents and RIL population were phenotyped for LR response in three field environments at Plains and Griffin, GA, in the 2017-2018 and 2018-2019 growing seasons, one greenhouse environment at the adult-plant stage, and at seedling stage. The RIL population was genotyped with the Illumina iSelect 90K SNP marker array, and a total of 7667 polymorphic markers representing 1513 unique loci were used to construct a linkage map. Quantitative trait loci (QTL) analysis detected six QTL, QLr.ags-1AL, QLr.ags-2AS, QLr.ags-2BS1, QLr.ags-2BS2, QLr.ags-2BS3, and QLr.ags-2DS, for seedling and adult plant LR resistance. Of these, the major adult plant leaf rust resistance QTL, QLr.ags-1AL, was detected on all field and greenhouse adult plant tests and explained up to 34.45% of the phenotypic variation. QLr.ags-1AL, tightly flanked by IWB20487 and IWA4022 markers, was contributed by AGS 2038. Molecular marker analysis using a diagnostic marker linked to Lr59 showed that QLr.ags-1AL was different from Lr59, the only known LR resistance gene on 1AL. Therefore, the QTL was temporarily designated as Lr2K38. Lr2K38-linked marker IWB20487 was highly polymorphic among 30 SRWW lines and should be useful for selecting the Lr2K38 in wheat breeding programs.
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Affiliation(s)
- Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Jason D Fiedler
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Jerry Johnson
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Dan Bland
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Benjamin Lopez
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Steve Sutton
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - James Buck
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Zhenbang Chen
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA
| | - Stephen Harrison
- School of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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Babu P, Baranwal DK, Harikrishna, Pal D, Bharti H, Joshi P, Thiyagarajan B, Gaikwad KB, Bhardwaj SC, Singh GP, Singh A. Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance. Front Plant Sci 2020; 11:567147. [PMID: 33013989 PMCID: PMC7516254 DOI: 10.3389/fpls.2020.567147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2023]
Abstract
Wheat is an important source of dietary protein and calories for the majority of the world's population. It is one of the largest grown cereal in the world occupying over 215 M ha. Wheat production globally is challenged by biotic stresses such as pests and diseases. Of the 50 diseases of wheat that are of economic importance, the three rust diseases are the most ubiquitous causing significant yield losses in the majority of wheat production environments. Under severe epidemics they can lead to food insecurity threats amid the continuous evolution of new races of the pathogens, shifts in population dynamics and their virulence patterns, thereby rendering several effective resistance genes deployed in wheat breeding programs vulnerable. This emphasizes the need to identify, characterize, and deploy effective rust-resistant genes from diverse sources into pre-breeding lines and future wheat varieties. The use of genetic resistance has been marked as eco-friendly and to curb the further evolution of rust pathogens. Deployment of multiple rust resistance genes including major and minor genes in wheat lines could enhance the durability of resistance thereby reducing pathogen evolution. Advances in next-generation sequencing (NGS) platforms and associated bioinformatics tools have revolutionized wheat genomics. The sequence alignment of the wheat genome is the most important landmark which will enable genomics to identify marker-trait associations, candidate genes and enhanced breeding values in genomic selection (GS) studies. High throughput genotyping platforms have demonstrated their role in the estimation of genetic diversity, construction of the high-density genetic maps, dissecting polygenic traits, and better understanding their interactions through GWAS (genome-wide association studies) and QTL mapping, and isolation of R genes. Application of breeder's friendly KASP assays in the wheat breeding program has expedited the identification and pyramiding of rust resistance alleles/genes in elite lines. The present review covers the evolutionary trends of the rust pathogen and contemporary wheat varieties, and how these research strategies galvanized to control the wheat killer genus Puccinia. It will also highlight the outcome and research impact of cost-effective NGS technologies and cloning of rust resistance genes amid the public availability of common and tetraploid wheat reference genomes.
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Affiliation(s)
- Prashanth Babu
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Harikrishna
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Dharam Pal
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Hemlata Bharti
- Directorate of Medicinal and Aromatic Plants Research (ICAR), Anand, India
| | - Priyanka Joshi
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | | | | | | | - Anupam Singh
- DCM SHRIRAM-Bioseed Research India, ICRISAT, Hyderabad, India
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28
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Rani K, Raghu BR, Jha SK, Agarwal P, Mallick N, Niranjana M, Sharma JB, Singh AK, Sharma NK, Rajkumar S, Tomar SMS. A novel leaf rust resistance gene introgressed from Aegilops markgrafii maps on chromosome arm 2AS of wheat. Theor Appl Genet 2020; 133:2685-2694. [PMID: 32507913 DOI: 10.1007/s00122-020-03625-w] [Citation(s) in RCA: 9] [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: 10/17/2019] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
A novel leaf rust resistance gene, LrM, introgressed from Aegilops markgrafii and mapped on chromosome 2AS using SSR- and SNP-based PCR markers will aid in broadening the genetic base of rust resistance in wheat. A new leaf rust resistance gene tentatively named LrM was introgressed from the diploid non-progenitor species Ae. markgrafii (2n = 2x = 14, genome CC) into common wheat using the nulli-5B mechanism. The introgression line ER9-700 showed a high degree of resistance against a wide spectrum of Puccinia triticina pathotypes. Genetic analysis was performed using the F1, F2, F2:3 and BC1F1 generations derived from the cross ER9-700/Agra Local. The results showed a single dominant gene for leaf rust resistance. The resistance gene LrM was mapped on chromosome arm 2AS using SSR- and SNP-based PCR markers. Preliminary mapping with SSR markers in the F2:3 population from the cross ER9-700/Agra Local identified two SSR markers flanking the LrM. SNPs were identified in the genomic region flanked by SSR markers, and SNP-based PCR markers were developed to construct the final map. Three SNP-based PCR markers co-segregated and mapped closest to the resistance gene at a distance of 2 cM. The gene LrM was distinguished from all the other genes designated and mapped on chromosome arm 2AS by molecular markers and rust reaction. All five markers used in the mapping amplified identical alleles in the donor Ae. markgrafii accession and introgression line ER9-700. The chromosomal location and rust reaction suggest that LrM is a novel leaf rust resistance gene that may be useful in broadening the genetic base of leaf rust resistance in wheat.
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Affiliation(s)
- K Rani
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- ICAR-Directorate of Groundnut Research, Junagadh, 362001, India
| | - B R Raghu
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- ICAR-Indian Institute of Horticultural Research, Bengaluru, 560089, India
| | - S K Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Priyanka Agarwal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niharika Mallick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - M Niranjana
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - J B Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A K Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - N K Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Rajkumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - S M S Tomar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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29
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Genievskaya Y, Turuspekov Y, Rsaliyev A, Abugalieva S. Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan. PeerJ 2020; 8:e9820. [PMID: 32944423 PMCID: PMC7469934 DOI: 10.7717/peerj.9820] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 04/24/2020] [Accepted: 08/05/2020] [Indexed: 11/20/2022] Open
Abstract
Common or bread wheat (Triticum aestivum L.) is the most important cereal crop in the world, including Kazakhstan, where it is a major agricultural commodity. Fungal pathogens producing leaf, stem, and yellow (stripe) rusts of wheat may cause yield losses of up to 50-60%. One of the most effective methods for preventing these losses is to develop resistant cultivars with high yield potential. This goal can be achieved using complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. In this study, a panel consisting of 215 common wheat cultivars and breeding lines from Kazakhstan, Russia, Europe, USA, Canada, Mexico, and Australia, with a wide range of resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR) diseases, was analyzed under field conditions in Southern Kazakhstan. The collection was genotyped using the 20K Illumina iSelect DNA array, where 11,510 informative single-nucleotide polymorphism markers were selected for further genome-wide association study (GWAS). Evaluation of the phenotypic diversity over 2 years showed a mostly mixed reaction to LR, mixed reaction/moderate susceptibility to SR, and moderate resistance to YR among wheat accessions from Kazakhstan. GWAS revealed 45 marker-trait associations (MTAs), including 23 for LR, 14 for SR, and eight for YR resistances. Three MTAs for LR resistance and one for SR resistance appeared to be novel. The MTAs identified in this work can be used for marker-assisted selection of common wheat in Kazakhstan in breeding new cultivars resistant to LR, SR, and YR diseases. These findings can be helpful for pyramiding genes with favorable alleles in promising cultivars and lines.
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Affiliation(s)
- Yuliya Genievskaya
- Plant Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Yerlan Turuspekov
- Plant Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Biodiversity and Bioresources, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aralbek Rsaliyev
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky, Zhambyl Region, Kazakhstan
| | - Saule Abugalieva
- Plant Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Kazakh National Agrarian University, Almaty, Kazakhstan
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30
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Ghimire B, Sapkota S, Bahri BA, Martinez-Espinoza AD, Buck JW, Mergoum M. Fusarium Head Blight and Rust Diseases in Soft Red Winter Wheat in the Southeast United States: State of the Art, Challenges and Future Perspective for Breeding. Front Plant Sci 2020; 11:1080. [PMID: 32765563 PMCID: PMC7378807 DOI: 10.3389/fpls.2020.01080] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/30/2020] [Indexed: 05/21/2023]
Abstract
Among the biotic constraints to wheat (Triticum aestivum L.) production, fusarium head blight (FHB), caused by Fusarium graminearum, leaf rust (LR), caused by Puccinia triticina, and stripe rust (SR) caused by Puccinia striiformis are problematic fungal diseases worldwide. Each can significantly reduce grain yield while FHB causes additional food and feed safety concerns due to mycotoxin contamination of grain. Genetic resistance is the most effective and sustainable approach for managing wheat diseases. In the past 20 years, over 500 quantitative trait loci (QTLs) conferring small to moderate effects for the different FHB resistance types have been reported in wheat. Similarly, 79 Lr-genes and more than 200 QTLs and 82 Yr-genes and 140 QTLs have been reported for seedling and adult plant LR and SR resistance, respectively. Most QTLs conferring rust resistance are race-specific generally conforming to a classical gene-for-gene interaction while resistance to FHB exhibits complex polygenic inheritance with several genetic loci contributing to one resistance type. Identification and deployment of additional genes/QTLs associated with FHB and rust resistance can expedite wheat breeding through marker-assisted and/or genomic selection to combine small-effect QTL in the gene pool. LR disease has been present in the southeast United States for decades while SR and FHB have become increasingly problematic in the past 20 years, with FHB arguably due to increased corn acreage in the region. Currently, QTLs on chromosome 1B from Jamestown, 1A, 1B, 2A, 2B, 2D, 4A, 5A, and 6A from W14, Ning7840, Ernie, Bess, Massey, NC-Neuse, and Truman, and 3B (Fhb1) from Sumai 3 for FHB resistance, Lr9, Lr10, Lr18, Lr24, Lr37, LrA2K, and Lr2K38 genes for LR resistance, and Yr17 and YrR61 for SR resistance have been extensively deployed in southeast wheat breeding programs. This review aims to disclose the current status of FHB, LR, and SR diseases, summarize the genetics of resistance and breeding efforts for the deployment of FHB and rust resistance QTL on soft red winter wheat cultivars, and present breeding strategies to achieve sustainable management of these diseases in the southeast US.
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Affiliation(s)
- Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Suraj Sapkota
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Bochra A. Bahri
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | | | - James W. Buck
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, United States
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31
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Dinh HX, Singh D, Periyannan S, Park RF, Pourkheirandish M. Molecular genetics of leaf rust resistance in wheat and barley. Theor Appl Genet 2020; 133:2035-2050. [PMID: 32128617 DOI: 10.1007/s00122-020-03570-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
The demand for cereal grains as a main source of energy continues to increase due to the rapid increase in world population. The leaf rust diseases of cereals cause significant yield losses, posing challenges for global food security. The deployment of resistance genes has long been considered as the most effective and sustainable way to control cereal leaf rust diseases. While genetic resistance has reduced the impact of these diseases in agriculture, losses still occur due to the ability of the respective rust pathogens to change and render resistance genes ineffective plus the slow pace at which resistance genes are discovered and characterized. This article highlights novel recently developed strategies based on advances in genome sequencing that have accelerated gene isolation by overcoming the complexity of cereal genomes. The leaf rust resistance genes cloned so far from wheat and barley belong to various protein families, including nucleotide binding site/leucine-rich repeat receptors and transporters. We review recent studies that are beginning to reveal the defense mechanisms conferred by the leaf rust resistance genes identified to date in cereals and their roles in either pattern-triggered immunity or effector-triggered immunity.
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Affiliation(s)
- Hoan X Dinh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Davinder Singh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra, 2601, Australia
| | - Robert F Park
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia.
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32
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Qiu L, Wang H, Li Y, Wang W, Liu Y, Mu J, Geng M, Guo W, Hu Z, Ma J, Sun Q, Xie C. Fine Mapping of the Wheat Leaf Rust Resistance Gene LrLC10 ( Lr13) and Validation of Its Co-segregation Markers. Front Plant Sci 2020; 11:470. [PMID: 32477377 PMCID: PMC7232556 DOI: 10.3389/fpls.2020.00470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Wheat leaf rust, caused by the fungus Puccinia triticina Eriks. (Pt), is a destructive disease found throughout common wheat production areas worldwide. At its adult stage, wheat cultivar Liaochun10 is resistant to leaf rust and the gene for that resistance has been mapped on chromosome 2BS. It was designated LrLC10 and is the same gene as cataloged gene Lr13 by pedigree analysis and allelism test. We fine-mapped it using recessive class analysis (RCA) of the homozygous susceptible F2 plants derived from crosses using Liaochun10 as the resistant, male parent. Taking advantage of the re-sequencing data of Liaochun10 and its counterpart susceptible parent, we converted nucleotide polymorphisms in the LrLC10 interval between the resistant and susceptible parents into molecular markers to saturate the LrLC10 genetic linkage map. Four indel markers were added in the 1.65 cM map of LrLC10 flanked by markers CAUT163 and Lseq22. Thirty-two recombinants were identified by those two markers from the 984 F2 homozygous susceptible plants and were further genotyped with additional ten markers. LrLC10 was finally placed in a 314.3 kb region on the Chinese Spring reference sequence (RefSeq v1.0) that contains three high confidence genes: TraesCS2B01G182800, TraesCS2B01G182900, and TraesCS2B01G183000. Sequence analysis showed several variations in TraesCS2B01G182800 and TraesCS2B01G183000 between resistant and susceptible parents. One KASP marker and an indel marker were designed based on the differences in those two genes, respectively, and were validated to be diagnostic co-segregating markers for LrLC10. Our results both improve marker-assisted selection and help with the map-based cloning of LrLC10.
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Affiliation(s)
- Lina Qiu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Huifang Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yinghui Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Weidong Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yujia Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Junyi Mu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Miaomiao Geng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
- College of Agronomy Hebei Agricultural University, Hebei Agricultural University, Baoding, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jun Ma
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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Prasad P, Savadi S, Bhardwaj SC, Gupta PK. The progress of leaf rust research in wheat. Fungal Biol 2020; 124:537-550. [PMID: 32448445 DOI: 10.1016/j.funbio.2020.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/25/2023]
Abstract
Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.
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Affiliation(s)
- Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Siddanna Savadi
- ICAR-Directorate of Cashew Research, Puttur, Karnataka, 574202, India
| | - S C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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Mohler V, Schmolke M, Zeller FJ, Hsam SLK. Genetic analysis of Aegilops tauschii-derived seedling resistance to leaf rust in synthetic hexaploid wheat. J Appl Genet 2020; 61:163-168. [PMID: 31981185 PMCID: PMC7148280 DOI: 10.1007/s13353-020-00541-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/05/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 10/29/2022]
Abstract
Seedling resistance to leaf rust available in the synthetic hexaploid wheat line Syn137 was characterised by means of cytogenetic and linkage mapping. Monosomic analysis located a single dominant gene for leaf rust resistance on chromosome 5D. Molecular mapping not only confirmed this location but also positioned the gene to the distal part of the long arm of chromosome 5D. A test of allelism showed that the gene, tentatively named LrSyn137, is independent but closely linked to Lr1. It appears that Syn137 is occasionally heterogeneous for Lr1 since the analysis of the Lr1-specific marker RGA567-5 in the genetic mapping population indicated the presence of Lr1. Syn137 represents another source of genetic variation that can be useful for the diversification of leaf rust resistance in wheat cultivars.
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Affiliation(s)
- Volker Mohler
- Bayerische Landesanstalt für Landwirtschaft (LfL), Institut für Pflanzenbau und Pflanzenzüchtung (IPZ), Am Gereuth 8, 85354, Freising, Germany.
| | - Michael Schmolke
- Plant Breeding, Centre for Food and Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Friedrich J Zeller
- Plant Breeding, Centre for Food and Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Sai L K Hsam
- Plant Breeding, Centre for Food and Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
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Zhang P, Li X, Gebrewahid TW, Liu H, Xia X, He Z, Li Z, Liu D. QTL Mapping of Adult-Plant Resistance to Leaf and Stripe Rust in Wheat Cross SW 8588/Thatcher using the Wheat 55K SNP Array. Plant Dis 2019; 103:3041-3049. [PMID: 31613193 DOI: 10.1094/pdis-02-19-0380-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Wheat leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) cause large production losses in many regions of the world. The objective of this study was to identify quantitative trait loci (QTL) for resistance to leaf rust and stripe rust in a recombinant inbred line population derived from a cross between wheat cultivars SW 8588 and Thatcher. The population and parents were genotyped with the Wheat 55K SNP Array and SSR markers and phenotyped for leaf rust severity at Zhoukou in Henan Province and Baoding in Hebei Province. Stripe rust responses were also evaluated at Chengdu in Sichuan Province, and at Baoding. Seven and six QTL were detected for resistance to leaf rust and stripe rust, respectively. Four QTL on chromosomes 1BL, 2AS, 5AL, and 7BL conferred resistance to both rusts. The QTL on 1BL and 2AS were identified as Lr46/Yr29 and Lr37/Yr17, respectively. QLr.hebau-2DS from Thatcher, identified as Lr22b that was previously thought to be ineffective in China, contributed a large effect for leaf rust resistance. QLr.hebau-5AL/QYr.hebau-5AL, QLr.hebau-3BL, QLr.hebau-6DS, QYr.hebau-4BS, and QYr.hebau-6DS are likely to be new QTL, but require further validation. Kompetitive allele-specific PCR (KASP) markers for QLr.hebau-2DS and QLr.hebau-5AL/QYr.hebau-5AL were successfully developed and validated in a diverse wheat panel from Sichuan Province, indicating their usefulness under different genetic backgrounds. These QTL and their closely linked SNP and SSR markers will be useful for fine mapping, candidate gene discovery, and marker-assisted selection in breeding for durable resistance to both leaf and stripe rusts.
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Affiliation(s)
- Peipei Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xing Li
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Takele-Weldu Gebrewahid
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
- College of Agriculture, Aksum University, Shire-Indaslassie, Tigray 314, Ethiopia
| | - Hexing Liu
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing 100081, China
| | - Zaifeng Li
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Daqun Liu
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
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Zhang P, Lan C, Asad MA, Gebrewahid TW, Xia X, He Z, Li Z, Liu D. QTL mapping of adult-plant resistance to leaf rust in the Chinese landraces Pingyuan 50/Mingxian 169 using the wheat 55K SNP array. Mol Breeding 2019. [PMID: 0 DOI: 10.1007/s11032-019-1004-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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Gill HS, Li C, Sidhu JS, Liu W, Wilson D, Bai G, Gill BS, Sehgal SK. Fine Mapping of the Wheat Leaf Rust Resistance Gene Lr42. Int J Mol Sci 2019; 20:ijms20102445. [PMID: 31108903 PMCID: PMC6567072 DOI: 10.3390/ijms20102445] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/06/2019] [Accepted: 05/14/2019] [Indexed: 11/30/2022] Open
Abstract
Leaf rust caused by Puccinia triticina Eriks is one of the most problematic diseases of wheat throughout the world. The gene Lr42 confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported Lr42 to be both recessive and dominant in hexaploid wheat; however, in diploid Aegilops tauschii (TA2450), we found Lr42 to be dominant by studying segregation in two independent F2 and their F2:3 populations. We further fine-mapped Lr42 in hexaploid wheat using a KS93U50/Morocco F5 recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers TC387992 and WMC432. The 3.7 cM Lr42 region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the Ae. tauschii reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in Ae. tauschii, respectively, and these are the likely candidates for Lr42. Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers (SNP113325 and TC387992) flanking Lr42 to facilitate marker-assisted selection for rust resistance in wheat breeding programs.
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Affiliation(s)
- Harsimardeep S Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| | - Chunxin Li
- National Engineering Laboratory of Wheat, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
| | - Jagdeep S Sidhu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| | - Wenxuan Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Duane Wilson
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetic Research Unit, Manhattan, KS 66506, USA.
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.
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Ye X, Li J, Cheng Y, Yao F, Long L, Yu C, Wang Y, Wu Y, Li J, Wang J, Jiang Q, Li W, Ma J, Wei Y, Zheng Y, Chen G. Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat. BMC Plant Biol 2019; 19:147. [PMID: 30991940 PMCID: PMC6469213 DOI: 10.1186/s12870-019-1764-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 09/02/2018] [Accepted: 04/08/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Stripe rust (also called yellow rust) is a common and serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici. The narrow genetic basis of modern wheat cultivars and rapid evolution of the rust pathogen have been responsible for periodic and devastating epidemics of wheat rust diseases. In this study, we conducted a genome-wide association study with 44,059 single nucleotide polymorphism markers to identify loci associated with resistance to stripe rust in 244 Sichuan wheat accessions, including 79 landraces and 165 cultivars, in six environments. RESULTS In all the field assessments, 24 accessions displayed stable high resistance to stripe rust. Significant correlations among environments were observed for both infection (IT) and disease severity (DS), and high heritability levels were found for both IT and DS. Using mixed linear models, 12 quantitative trait loci (QTLs) significantly associated with IT and/or DS were identified. Two QTLs were mapped on chromosomes 5AS and 5AL and were distant from previously identified stripe rust resistance genes or QTL regions, indicating that they may be novel resistance loci. CONCLUSIONS Our results revealed that resistance alleles to stripe rust were accumulated in Sichuan wheat germplasm, implying direct or indirect selection for improved stripe rust resistance in elite wheat breeding programs. The identified stable QTLs or favorable alleles could be important chromosome regions in Sichuan wheat that controlled the resistance to stripe rust. These markers can be used molecular marker-assisted breeding of Sichuan wheat cultivars, and will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.
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Affiliation(s)
- Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
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Kthiri D, Loladze A, N’Diaye A, Nilsen KT, Walkowiak S, Dreisigacker S, Ammar K, Pozniak CJ. Mapping of Genetic Loci Conferring Resistance to Leaf Rust From Three Globally Resistant Durum Wheat Sources. Front Plant Sci 2019; 10:1247. [PMID: 31649708 PMCID: PMC6792298 DOI: 10.3389/fpls.2019.01247] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/06/2019] [Indexed: 05/21/2023]
Abstract
Genetic resistance in the host plant is the most economical and environmentally friendly strategy for controlling wheat leaf rust, caused by Puccinia triticina Eriks. The durum wheat lines Gaza (Middle East), Arnacoris (France) and Saragolla (Italy) express high levels of resistance to the Mexican races of P. triticina. Three recombinant inbred line (RIL) populations, derived from crosses of each of these resistance sources to the susceptible line ATRED #2, were evaluated for leaf rust reactions at CIMMYT's leaf rust nurseries in Mexico. Genetic analyses of host reactions suggested oligogenic control of resistance in all populations. The F8 RILs from each cross were genotyped using the Illumina iSelect 90K array, and high-density genetic maps were constructed for each population. Using composite interval mapping, a total of seven quantitative trait loci (QTL) that provide resistance to leaf rust were identified. Two QTL designated as QLr.usw-6BS and QLr.usw-6BL were identified on chromosome 6B in Gaza, which explained up to 78.5% and 21.3% of the observed leaf rust severity variance, respectively. A major QTL designated as QLr.usw-7BL was detected on the long arm of chromosome 7B in Arnacoris, which accounted for up to 65.9% of the disease severity variance. Arnacoris also carried a minor QTL on chromosome 1BL, designated as QLr.usw-1BL.1 that explained up to 17.7% of the phenotypic variance. Three QTL conferred leaf rust resistance in Saragolla, namely QLr.usw-2BS, QLr.usw-3B, and QLr.usw-1BL.2, which accounted for up to 42.3, 9.4, and 7.1% of the phenotypic variance, respectively. Markers flanking each QTL were physically mapped against the durum wheat reference sequence and candidate genes involved in disease resistance were identified within the QTL intervals. The QTL identified in this study and their closely linked markers are useful resources for gene pyramiding and breeding for durable leaf rust resistance in durum wheat.
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Affiliation(s)
- Dhouha Kthiri
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alexander Loladze
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Curtis J. Pozniak,
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