1
|
Spychała J, Tomkowiak A, Noweiska A, Bobrowska R, Bocianowski J, Sobiech A, Kwiatek MT. Diversity of Expression Patterns of Lr34, Lr67, and Candidate Genes towards Lr46 with Analysis of Associated miRNAs in Common Wheat Hybrids in Response to Puccinia triticina Fungus. Curr Issues Mol Biol 2024; 46:5511-5529. [PMID: 38921001 PMCID: PMC11201949 DOI: 10.3390/cimb46060329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Leaf rust caused by Puccinia triticina (Pt) is one of the most dangerous diseases causing significant losses in common wheat crops. In adult plants resistant to rust, a horizontal adult plant resistance (APR) type is observed, which protects the plant against multiple pathogen races and is distinguished by greater persistence under production conditions. Crucial pleiotropic slow-rust genes such as Lr34, Lr46, Lr67, and Lr68, in combination with other genes of lesser influence, continue to increase durable resistance to rust diseases. Based on our previous results, we selected four candidate genes for Lr46 out of ten candidates and analysed them for expression before and after inoculation by P. triticina. As part of our study, we also investigated the expression patterns of miRNA molecules complementary to Lr34 and the candidate genes. The aim of the study was to analyse the expression profiles of candidate genes for the Lr46 gene and the Lr34 and Lr67 genes responsible for the differential leaf-rust resistance of hybrid forms of the F1 generation resulting from crosses between the Glenlea cultivar and cultivars from Polish breeding companies. In addition, the expression of five miRNAs (tae-miR9653b, tae-miR5384-3p, tae-miR9780, tae-miR9775 and tae-miR164), complementary to Lr34, and selected candidate genes were analysed using stem-loop RT-PCR and ddPCR. Biotic stress was induced in adult plants by inoculation with Pt fungal spores, under controlled conditions. Plant material was collected before and 6, 12, 24, and 48 h after inoculation (hpi). Differences in expression patterns of Lr34, Lr67, and candidate genes (for Lr46) were analysed by qRT-PCR and showed that gene expression changed at the analysed time points. Identification of molecular markers coupled to the Lr genes studied was also carried out to confirm the presence of these genes in wheat hybrids. qRT-PCR was used to examine the expression levels of the resistance genes. The highest expression of Lr46/Yr29 genes (Lr46-Glu2, Lr46-RLK1, Lr46-RLK2, and Lr46-RLK3) occurred at 12 and 24 hpi, and such expression profiles were obtained for only one candidate gene among the four genes analysed (Lr46-Glu2), indicating that it may be involved in resistance mechanisms of response to Pt infection.
Collapse
Affiliation(s)
- Julia Spychała
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Aleksandra Noweiska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Roksana Bobrowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland
| | - Aleksandra Sobiech
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Michał Tomasz Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland
| |
Collapse
|
2
|
Lu Y, Burton IW, Ashe P, St-Jacques AD, Rajagopalan N, Monteil-Rivera F, Loewen MC. Characterization of a partially saturated and glycosylated apocarotenoid from wheat that is depleted upon leaf rust infection. Gene 2024; 893:147927. [PMID: 38374023 DOI: 10.1016/j.gene.2023.147927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 02/21/2024]
Abstract
Recent semi-targeted metabolomics studies have highlighted a number of metabolites in wheat that associate with leaf rust resistance genes and/or rust infection. Here, we report the structural characterization of a novel glycosylated and partially saturated apocarotenoid, reminiscent of a reduced form of mycorradicin, (6E,8E,10E)-4,9-dimethyl-12-oxo-12-((3,4,5-trihydroxy-6-(2-hydroxyethoxy)tetrahydro-2H-pyran-2-yl)methoxy)-3-((3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)dodeca-6,8,10-trienoic acid, isolated from Triticum aestivum L. (Poaceae) variety 'Thatcher' (Tc) flag leaves. While its accumulation was not associated with any of Lr34, Lr67 or Lr22a resistance genes, infection of Tc with leaf rust was found to deplete it, consistent with the idea of this metabolite being a glycosylated-storage form of an apocarotenoid of possible relevance to plant defense. A comparative analysis of wheat transcriptomic changes shows modulation of terpenoid, carotenoid, UDP-glycosyltransferase and glycosylase -related gene expression profiles, consistent with anticipated biosynthesis and degradation mechanisms. However, details of the exact nature of the relevant pathways remain to be validated in the future. Together these findings highlight another example of the breadth of unique metabolites underlying plant host-fungal pathogen interactions.
Collapse
Affiliation(s)
- Yuping Lu
- Aquatic and Crop Resources Development Research Centre, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Ian W Burton
- Aquatic and Crop Resources Development Research Centre, National Research Council of Canada, 1411 Oxford St., Halifax, NS B3H 3Z1, Canada.
| | - Paula Ashe
- Aquatic and Crop Resources Development Research Centre, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Antony D St-Jacques
- Aquatic and Crop Resources Development Research Centre, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada.
| | - Nandhakishore Rajagopalan
- Aquatic and Crop Resources Development Research Centre, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada; Department of Chemical and Biological Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada
| | - Fanny Monteil-Rivera
- Aquatic and Crop Resources Development Research Centre, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada.
| | - Michele C Loewen
- Aquatic and Crop Resources Development Research Centre, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada.
| |
Collapse
|
3
|
Gao P, Zhou Y, Gebrewahid TW, Zhang P, Wang S, Liu D, Li Z. QTL Mapping for Adult-Plant Resistance to Leaf Rust in Italian Wheat Cultivar Libellula. PLANT DISEASE 2024; 108:13-19. [PMID: 37526485 DOI: 10.1094/pdis-01-23-0105-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Wheat leaf rust (Lr), which is caused by Puccinia triticina Eriks. (Pt), is one of the most important wheat diseases affecting wheat production globally. Using resistant wheat cultivars is the most economical and environmentally friendly way to control leaf rust. The Italian wheat cultivar Libellula has demonstrated good resistance to Lr in field studies. To identify the genetic basis of Lr resistance in 'Libellula', 248 F6 recombinant inbred lines from the cross 'Libellula'/'Huixianhong' was phenotyped for Lr severity in seven environments: the 2014/2015, 2016/2017, 2017/2018, and 2018/2019 cropping seasons at Baoding, Hebei Province, and the 2016/2017, 2017/2018, and 2018/2019 crop seasons at Zhoukou, Henan Province. Bulked segregant analysis and simple sequence repeat markers were then used to identify the quantitative trait loci (QTLs) for Lr adult-plant resistance in the population. Six QTLs were consequently detected and designated as QLr.hebau-1AL and QLr.hebau-1AS that were presumed to be new and QLr.hebau-1BL, QLr.hebau-3AL, QLr.hebau-4BL, and QLr.hebau-7DS that were identified at similar physical positions as previously reported QTLs. Based on chromosome positions and molecular marker tests, QLr.hebau-1BL and QLr.hebau-7DS share similar flanking markers with Lr46 and Lr34, respectively. Lr46 and Lr34 are race nonspecific adult plant resistance (APR) genes for leaf rust and stripe rust and powdery mildew. QLr.hebau-4BL showed multiple disease resistance to leaf rust, stripe rust, Fusarium head blight, and powdery mildew. The QTL identified in this study, as well as their closely linked markers, may potentially be used in marker-assisted selection in wheat breeding.
Collapse
Affiliation(s)
- Pu Gao
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Yue Zhou
- Baoding University, Baoding 071001, Hebei, China
| | | | - Peipei Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Siman Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Daqun Liu
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Zaifeng Li
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| |
Collapse
|
4
|
Qureshi N, Singh RP, Gonzalez BM, Velazquez-Miranda H, Bhavani S. Genomic Regions Associated with Resistance to Three Rusts in CIMMYT Wheat Line "Mokue#1". Int J Mol Sci 2023; 24:12160. [PMID: 37569535 PMCID: PMC10418946 DOI: 10.3390/ijms241512160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Understanding the genetic basis of rust resistance in elite CIMMYT wheat germplasm enhances breeding and deployment of durable resistance globally. "Mokue#1", released in 2023 in Pakistan as TARNAB Gandum-1, has exhibited high levels of resistance to stripe rust, leaf rust, and stem rust pathotypes present at multiple environments in Mexico and Kenya at different times. To determine the genetic basis of resistance, a F5 recombinant inbred line (RIL) mapping population consisting of 261 lines was developed and phenotyped for multiple years at field sites in Mexico and Kenya under the conditions of artificially created rust epidemics. DArTSeq genotyping was performed, and a linkage map was constructed using 7892 informative polymorphic markers. Composite interval mapping identified three significant and consistent loci contributed by Mokue: QLrYr.cim-1BL and QLrYr.cim-2AS on chromosome 1BL and 2AS, respectively associated with stripe rust and leaf rust resistance, and QLrSr.cim-2DS on chromosome 2DS for leaf rust and stem rust resistance. The QTL on 1BL was confirmed to be the Lr46/Yr29 locus, whereas the QTL on 2AS represented the Yr17/Lr37 region on the 2NS/2AS translocation. The QTL on 2DS was a unique locus conferring leaf rust resistance in Mexico and stem rust resistance in Kenya. In addition to these pleiotropic loci, four minor QTLs were also identified on chromosomes 2DL and 6BS associated with stripe rust, and 3AL and 6AS for stem rust, respectively, using the Kenya disease severity data. Significant decreases in disease severities were also demonstrated due to additive effects of QTLs when present in combinations.
Collapse
Affiliation(s)
- Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Blanca Minerva Gonzalez
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Hedilberto Velazquez-Miranda
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, United Nations Avenue, Gigiri, Nairobi P.O. Box 1041-00621, Kenya
| |
Collapse
|
5
|
Hou W, Lu Q, Ma L, Sun X, Wang L, Nie J, Guo P, Liu T, Li Z, Sun C, Ren Y, Wang X, Yang J, Chen F. Mapping of quantitative trait loci for leaf rust resistance in the wheat population 'Xinmai 26/Zhoumai 22'. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3019-3032. [PMID: 36879436 DOI: 10.1093/jxb/erad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/02/2023] [Indexed: 05/21/2023]
Abstract
Leaf rust, caused by the fungal pathogen Puccinia triticina (Pt), is one of the major and dangerous diseases of wheat, and has caused serious yield loss of wheat worldwide. Here, we investigated adult-plant resistance (APR) to leaf rust in a recombinant inbred line (RIL) population derived from 'Xinmai 26' and 'Zhoumai 22' over 3 years. Linkage mapping for APR to leaf rust revealed four quantitative trait loci (QTL) in this RIL population. Two QTL, QLr.hnau-2BS and QLr.hnau-3BS were contributed by 'Zhoumai22', whereas QLr.hnau-2DS and QLr.hnau-5AL were contributed by 'Xinmai 26'. The QLr.hnau-2BS covering a race-specific resistance gene Lr13 showed the most stable APR to leaf rust. Overexpression of Lr13 significantly increased APR to leaf rust. Interestingly, we found that a CNL(coiled coil-nucleotide-binding site-leucine-rich repeat)-like gene, TaCN, in QLr.hnau-2BS completely co-segregated with leaf rust resistance. The resistant haplotype TaCN-R possessed half the sequence of the coiled-coil domain of TaCN protein. Lr13 strongly interacted with TaCN-R, but did not interact with the full-length TaCN (TaCN-S). In addition, TaCN-R was significantly induced after Pt inoculation and changed the sub-cellular localization of Lr13 after interaction. Therefore, we hypothesized that TaCN-R mediated leaf rust resistance possibly by interacting with Lr13. This study provides important QTL for APR to leaf rust, and new insights into understanding how a CNL gene modulates disease resistance in common wheat.
Collapse
Affiliation(s)
- Weixiu Hou
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Qisen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Lin Ma
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaonan Sun
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Liyan Wang
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Jingyun Nie
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Peng Guo
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Ti Liu
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Zaifeng Li
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Congwei Sun
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaodong Wang
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/ CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou 450046, China
| |
Collapse
|
6
|
Bokore FE, Cuthbert RD, Knox RE, Hiebert CW, Pozniak CJ, Berraies S, Ruan Y, Meyer B, Hucl P, McCallum BD. Genetic mapping of leaf rust ( Puccinia triticina Eriks) resistance genes in six Canadian spring wheat cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1130768. [PMID: 37021307 PMCID: PMC10067638 DOI: 10.3389/fpls.2023.1130768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
The Canada Western Red Spring wheat (Triticum aestivum L.) cultivars AAC Concord, AAC Prevail, CDC Hughes, Lillian, Glenlea, and elite line BW961 express a spectrum of resistance to leaf rust caused by Puccinia triticina Eriks. This study aimed to identify and map the leaf rust resistance of the cultivars using three doubled haploid populations, AAC Prevail/BW961 (PB), CDC Hughes/AAC Concord (HC), and Lillian/Glenlea (LG). The populations were evaluated for seedling resistance in the greenhouse and adult plant disease response in the field at Morden, MB for 3 years and genotyped with the 90K wheat Infinium iSelect SNP array. Genetic maps were constructed to perform QTL analysis on the seedling and field leaf rust data. A total of three field leaf rust resistance QTL segregated in the PB population, five in the HC, and six in the LG population. In the PB population, BW961 contributed two QTL on chromosomes 2DS and 7DS, and AAC Prevail contributed a QTL on 4AL consistent across trials. Of the five QTL in HC, AAC Concord contributed two QTL on 4AL and 7AL consistent across trials and a QTL on 3DL.1 that provided seedling resistance only. CDC Hughes contributed two QTL on 1DS and 3DL.2. Lillian contributed four QTL significant in at least two of the three trials on 2BS, 4AL, 5AL, and 7AL, and Glenlea two QTL on 4BL and 7BL. The 1DS QTL from CDC Hughes, the 2DS from BW961, the 4AL from the AAC Prevail, AAC Concord, and Lillian, and the 7AL from AAC Concord and Lillian conferred seedling leaf rust resistance. The QTL on 4AL corresponded with Lr30 and was the same across cultivars AAC Prevail, AAC Concord, and Lillian, whereas the 7AL corresponding with LrCen was coincident between AAC Concord and Lillian. The 7DS and 2DS QTL in BW961 corresponded with Lr34 and Lr2a, respectively, and the 1DS QTL in CDC Hughes with Lr21. The QTL identified on 5AL could represent a novel gene. The results of this study will widen our knowledge of leaf rust resistance genes in Canadian wheat and their utilization in resistance breeding.
Collapse
Affiliation(s)
- Firdissa E. Bokore
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard D. Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron E. Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Samia Berraies
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Pierre Hucl
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| |
Collapse
|
7
|
Kaur S, Pennington T, Conley EJ, Green A, Kolmer J, Anderson J, Gupta R, Gill U. High-Resolution Melting-Based Marker Development for Wheat Leaf Rust Resistance Gene Lr34. PHYTOPATHOLOGY 2023; 113:508-515. [PMID: 36346374 DOI: 10.1094/phyto-08-22-0313-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Deploying adult plant resistance (APR) against rust diseases is an important breeding objective of most wheat-breeding programs. The gene Lr34 is an effective and widely deployed broad-spectrum APR gene in wheat against leaf rust fungus Puccinia triticina. Various molecular markers have been developed for Lr34, but they either require post-PCR handling processes or are not economical. Herein, we developed a high-resolution melting (HRM)-based diagnostic assay for Lr34 based on a 3-bp 'TTC' deletion in exon 11 of the resistant allele. The susceptible cultivar Thatcher (Tc) and the near-isogenic Thatcher line (RL6058) with Lr34 yielded distinct melting profiles and were differentiated with high reproducibility. For further validation, all three copies of Lr34 were cloned in plasmid vectors, and HRM analysis using individual and combination (equimolar mixture of three copies) homoeologs yielded distinct melting profiles. An additional layer of genotyping was provided by a LunaProbe assay. The allele-specific probes successfully distinguished the homoeologs but not Tc and RL6058. Furthermore, the practical deployment of the HRM assay was tested by running the marker on a set of breeding lines. When compared with a kompetitive allele-specific PCR (KASP) Lr34 assay, the HRM assay had similar genotyping results and was able to accurately differentiate the resistant and susceptible breeding lines. However, our HRM assay was unable to detect the heterozygote. To our knowledge, this is the first report of an HRM assay for genotyping a wheat rust resistance gene.
Collapse
Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Taylor Pennington
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Emily J Conley
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Andrew Green
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108
| | - James Kolmer
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108
| | - James Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Rajeev Gupta
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| |
Collapse
|
8
|
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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 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] [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.
Collapse
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.
| |
Collapse
|
9
|
Saleem K, Shokat S, Waheed MQ, Arshad HMI, Arif MAR. A GBS-Based GWAS Analysis of Leaf and Stripe Rust Resistance in Diverse Pre-Breeding Germplasm of Bread Wheat (Triticum aestivum L.). PLANTS 2022; 11:plants11182363. [PMID: 36145764 PMCID: PMC9504680 DOI: 10.3390/plants11182363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
Yellow (YR) and leaf (LR) rusts caused by Puccinia striiformis f. sp. tritici (Pst) and Puccinia triticina, respectively, are of utmost importance to wheat producers because of their qualitative and quantitative effect on yield. The search for new loci resistant to both rusts is an ongoing challenge faced by plant breeders and pathologists. Our investigation was conducted on a subset of 168 pre-breeding lines (PBLs) to identify the resistant germplasm against the prevalent local races of LR and YR under field conditions followed by its genetic mapping. Our analysis revealed a range of phenotypic responses towards both rusts. We identified 28 wheat lines with immune response and 85 resistant wheat genotypes against LR, whereas there were only eight immune and 52 resistant genotypes against YR. A GWAS (genome-wide association study) identified 190 marker-trait associations (MTAs), where 120 were specific to LR and 70 were specific to YR. These MTAs were confined to 86 quantitative trait loci (QTLs), where 50 QTLs carried MTAs associated with only LR, 29 QTLs carried MTAs associated with YR, and seven QTLs carried MTAs associated with both LR and YR. Possible candidate genes at the site of these QTLs are discussed. Overall, 70 PBLs carried all seven LR/YR QTLs. Furthermore, there were five PBLs with less than five scores for both LR and YR carrying positive alleles of all seven YR/LR QTLs, which are fit to be included in a breeding program for rust resistance induction.
Collapse
Affiliation(s)
- Kamran Saleem
- Molecular Phytopathology Group, Plant Protection Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad P.O. Box 128, Pakistan
- Correspondence: (K.S.); (M.A.R.A.); Tel.: +92-345-588-2908 (K.S.); +92-333-552-1394 (M.A.R.A.)
| | - Sajid Shokat
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad P.O. Box 128, Pakistan
| | - Muhammad Qandeel Waheed
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad P.O. Box 128, Pakistan
| | - Hafiz Muhammad Imran Arshad
- Molecular Phytopathology Group, Plant Protection Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad P.O. Box 128, Pakistan
| | - Mian Abdur Rehman Arif
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad P.O. Box 128, Pakistan
- Correspondence: (K.S.); (M.A.R.A.); Tel.: +92-345-588-2908 (K.S.); +92-333-552-1394 (M.A.R.A.)
| |
Collapse
|
10
|
Zhang P, Lan C, Singh RP, Huerta-Espino J, Li Z, Lagudah E, Bhavani S. Identification and Characterization of Resistance Loci to Wheat Leaf Rust and Stripe Rust in Afghan Landrace "KU3067". FRONTIERS IN PLANT SCIENCE 2022; 13:894528. [PMID: 35837449 PMCID: PMC9274257 DOI: 10.3389/fpls.2022.894528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust and stripe rust are important wheat diseases worldwide causing significant losses where susceptible varieties are grown. Resistant cultivars offer long-term control and reduce the use of hazardous chemicals, which can be detrimental to both human health and the environment. Land races have been a valuable resource for mining new genes for various abiotic and biotic stresses including wheat rusts. Afghan wheat landrace "KU3067" displayed high seedling infection type (IT) for leaf rust and low IT for stripe rust; however, it displayed high levels of field resistance for both rusts when tested for multiple seasons against the Mexican rust isolates. This study focused on identifying loci-conferring seedling resistance to stripe rust, and also loci-conferring adult plant resistance (APR) against the Mexican races of leaf rust and stripe rust. A backcrossed inbred line (BIL) population advanced to the BC1F5 generation derived from the cross of KU3067 and Apav (triple rust susceptible line) was used for both, inheritance and QTL mapping studies. The population and parents were genotyped with Diversity Arrays Technology-genotyping-by-sequencing (DArT-Seq) and phenotyped for leaf rust and stripe rust response at both seedling and adult plant stages during multiple seasons in Mexico with relevant pathotypes. Mapping results identified an all-stage resistance gene for stripe rust, temporarily designated as YrKU, on chromosome 7BL. In total, six QTL-conferring APR to leaf rust on 1AS, 2AL, 4DL, 6BL, 7AL, and 7BL, and four QTL for stripe rust resistance on 1BS, 2AL, 4DL, and 7BL were detected in the analyses. Among these, pleiotropic gene Lr67/Yr46 on 4DL with a significantly large effect is the first report in an Afghan landrace-conferring resistance to both leaf and stripe rusts. QLr.cim-7BL/YrKU showed pleiotropic resistance to both rusts and explained 7.5-17.2 and 12.6-19.3% of the phenotypic variance for leaf and stripe rusts, respectively. QYr.cim-1BS and QYr.cim-2AL detected in all stripe environments with phenotypic variance explained (PVE) 12.9-20.5 and 5.4-12.5%, and QLr.cim-6BL are likely to be new. These QTL and their closely linked markers will be useful for fine mapping and marker-assisted selection (MAS) in breeding for durable resistance to multiple rust diseases.
Collapse
Affiliation(s)
- Peipei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Caixia Lan
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México the National Institute of Forestry, Agricultural and Livestock Research (INIFAP), Texcoco, Mexico
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, ACT, Australia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| |
Collapse
|
11
|
Mourad AMI, Draz IS, Omar GE, Börner A, Esmail SM. Genome-Wide Screening of Broad-Spectrum Resistance to Leaf Rust ( Puccinia triticina Eriks) in Spring Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:921230. [PMID: 35812968 PMCID: PMC9258335 DOI: 10.3389/fpls.2022.921230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/30/2022] [Indexed: 06/01/2023]
Abstract
Wheat leaf rust (LR) causes significant yield losses worldwide. In Egypt, resistant cultivars began to lose their efficiency in leaf rust resistance. Therefore, a diverse spring wheat panel was evaluated at the seedling stage to identify new sources of broad-spectrum seedling resistance against the Egyptian Puccinia triticina (Pt) races. In three different experiments, seedling evaluation was done using Pt spores collected from different fields and growing seasons. Highly significant differences were found among experiments confirming the presence of different races population in each experiment. Highly significant differences were found among the tested genotypes confirming the ability to select superior genotypes. Genome-wide association study (GWAS) was conducted for each experiment and a set of 87 markers located within 48 gene models were identified. The identified gene models were associated with disease resistance in wheat. Five gene models were identified to resist all Pt races in at least two experiments and could be identified as stable genes under Egyptian conditions. Ten genotypes from five different countries were stable against all the tested Pt races but showed different degrees of resistance.
Collapse
Affiliation(s)
- Amira M. I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ibrahim S. Draz
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ghady E. Omar
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| |
Collapse
|
12
|
Identification of Three Novel QTLs Associated with Yellow Rust Resistance in Wheat (Triticum aestivum L.) Anong-179/Khaista-17 F2 Population. SUSTAINABILITY 2022. [DOI: 10.3390/su14127454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Wheat yellow rust (YR) caused by Puccinia striiformis is lethal for the leaf photosynthetic process, which substantially affects yield components and ultimately causes drastic yield reduction. The current study aimed to identify all-stage YR resistance linked QTLs in the best cross-combination. Experimental materials were phenotyped for disease severity in YR-hot spot area at Cereal Crops Research Institute, Pirsabak Pakistan in Khyber Pakhtunkhwa province in 2019 and 2020 and 2020 and 2021 Rabi seasons. The AN179 × KS17 was found to be the best cross combination, which showed high resistance to YR, whereas crosses AN179 × PK15 and PR129 × PK15 demonstrated susceptibility to YR with high disease severity. The recombinant inbred lines (RIL) F2 wheat population Annong-179/Khaista-17 demonstrated highly desirable YR resistance and yield component traits. Simple sequence repeat (SSR) markers were used to genotype the RIL population and their parents. Three novel QTLs linked to all-stage YR resistance were found on chromosomes 2BS, 3BS and 6BS, which explained 1.24, 0.54, and 0.75 phenotypic variance, respectively. Incorporation of the newly identified novel YR-resistance associated QTLs into hybridization wheat breeding program could be effective for marker-assisted selection of the improved and sustainable resistance.
Collapse
|
13
|
Wang Z, Jiang X, Zhang Y, Du Z, Feng J, Quan W, Ren J, Che M, Zhang Z. Identification and Validation of a Major Quantitative Trait Locus for Adult Plant Resistance Against Leaf Rust From the Chinese Wheat Landrace Bai Qimai. FRONTIERS IN PLANT SCIENCE 2022; 13:812002. [PMID: 35665144 PMCID: PMC9158542 DOI: 10.3389/fpls.2022.812002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/21/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust caused by Puccinia triticina Eriks. (Pt) is a common disease of wheat worldwide. The Chinese wheat landrace Bai Qimai (BQM) has shown high resistance to leaf rust for a prolonged period of time; the infected leaves of BQM displayed high infection types (ITs), but they showed low disease severities at the adult plant stage. To find quantitative trait loci (QTL) for resistance to leaf rust, 186 recombinant inbred lines from the cross Nugaines × BQM were phenotyped for leaf rust response in multiple field environments under natural Pt infections and genotyped using the 90K wheat single nucleotide polymorphism (SNP) chip and simple sequence repeat (SSR) markers. A total of 2,397 polymorphic markers were used for QTL mapping, and a novel major QTL (QLr.cau-6DL) was detected on chromosome 6DL from BQM. The effectiveness of QLr.cau-6DL was validated using the three additional wheat populations (RL6058 × BQM, Aikang58 × BQM, and Jimai22 × BQM). QLr.cau-6DL could significantly reduce leaf rust severities across all tested environments and different genetic backgrounds, and its resistance was more effective than that of Lr34. Moreover, QLr.cau-6DL acted synergistically with Lr34 to confer strong resistance to leaf rust. We believe that QLr.cau-6DL should have high potential value in the breeding of wheat cultivars with leaf rust resistance.
Collapse
Affiliation(s)
- Zhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xu Jiang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Yuzhu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Ziyi Du
- School of Agroforestry & Medicine, Open University of China, Beijing, China
| | - Jing Feng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Quan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Junda Ren
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
| | - Mingzhe Che
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| |
Collapse
|
14
|
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.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 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] [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.
Collapse
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
| |
Collapse
|
15
|
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] [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.
Collapse
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, ,
| |
Collapse
|
16
|
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: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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.
Collapse
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,
| |
Collapse
|
17
|
Bokore FE, Knox RE, Hiebert CW, Cuthbert RD, DePauw RM, Meyer B, N’Diaye A, Pozniak CJ, McCallum BD. A Combination of Leaf Rust Resistance Genes, Including Lr34 and Lr46, Is the Key to the Durable Resistance of the Canadian Wheat Cultivar, Carberry. FRONTIERS IN PLANT SCIENCE 2022; 12:775383. [PMID: 35069630 PMCID: PMC8770329 DOI: 10.3389/fpls.2021.775383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
The hexaploid spring wheat cultivar, Carberry, was registered in Canada in 2009, and has since been grown over an extensive area on the Canadian Prairies. Carberry has maintained a very high level of leaf rust (Puccinia triticina Eriks.) resistance since its release. To understand the genetic basis of Carberry's leaf rust resistance, Carberry was crossed with the susceptible cultivar, Thatcher, and a doubled haploid (DH) population of 297 lines was generated. The DH population was evaluated for leaf rust in seven field environments at the adult plant stage. Seedling and adult plant resistance (APR) to multiple virulence phenotypes of P. triticina was evaluated on the parents and the progeny population in controlled greenhouse studies. The population was genotyped with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, and quantitative trait loci (QTL) analysis was performed. The analysis using field leaf rust response indicated that Carberry contributed nine QTL located on chromosomes 1B, 2B (2 loci), 2D, 4A, 4B, 5A, 5B, and 7D. The QTL located on 1B, 2B, 5B, and 7D chromosomes were observed in two or more environments, whereas the remainder were detected in single environments. The resistance on 1B, detected in five environments, was attributed to Lr46 and on 7D, detected in seven environments to Lr34. The first 2B QTL corresponded with the adult plant gene, Lr13, while the second QTL corresponded with Lr16. The seedling analysis showed that Carberry carries Lr2a, Lr16, and Lr23. Five epistatic effects were identified in the population, with synergistic interactions being observed for Lr34 with Lr46, Lr16, and Lr2a. The durable rust resistance of Carberry is attributed to Lr34 and Lr46 in combination with these other resistance genes, because the resistance has remained effective even though the P. triticina population has evolved virulent to Lr2a, Lr13, Lr16, and Lr23.
Collapse
Affiliation(s)
- Firdissa E. Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Swift Current, SK, Canada
| | - Ron E. Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Swift Current, SK, Canada
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Richard D. Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Swift Current, SK, Canada
| | - Ron M. DePauw
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Swift Current, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Swift Current, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| |
Collapse
|
18
|
Discovery of a Novel Leaf Rust ( Puccinia recondita) Resistance Gene in Rye ( Secale cereale L.) Using Association Genomics. Cells 2021; 11:cells11010064. [PMID: 35011626 PMCID: PMC8750363 DOI: 10.3390/cells11010064] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/22/2022] Open
Abstract
Leaf rust constitutes one of the most important foliar diseases in rye (Secale cereale L.). To discover new sources of resistance, we phenotyped 180 lines belonging to a less well-characterized Gülzow germplasm at three field trial locations in Denmark and Northern Germany in 2018 and 2019. We observed lines with high leaf rust resistance efficacy at all locations in both years. A genome-wide association study using 261,406 informative single-nucleotide polymorphisms revealed two genomic regions associated with resistance on chromosome arms 1RS and 7RS, respectively. The most resistance-associated marker on chromosome arm 1RS physically co-localized with molecular markers delimiting Pr3. In the reference genomes Lo7 and Weining, the genomic region associated with resistance on chromosome arm 7RS contained a large number of nucleotide-binding leucine-rich repeat (NLR) genes. Residing in close proximity to the most resistance-associated marker, we identified a cluster of NLRs exhibiting close protein sequence similarity with the wheat leaf rust Lr1 gene situated on chromosome arm 5DL in wheat, which is syntenic to chromosome arm 7RS in rye. Due to the close proximity to the most resistance-associated marker, our findings suggest that the considered leaf rust R gene, provisionally denoted Pr6, could be a Lr1 ortholog in rye.
Collapse
|
19
|
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 DISEASE 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] [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.
Collapse
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
| |
Collapse
|
20
|
Pang Y, Wu Y, Liu C, Li W, St Amand P, Bernardo A, Wang D, Dong L, Yuan X, Zhang H, Zhao M, Li L, Wang L, He F, Liang Y, Yan Q, Lu Y, Su Y, Jiang H, Wu J, Li A, Kong L, Bai G, Liu S. High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2857-2873. [PMID: 34075443 DOI: 10.1007/s00122-021-03863-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
High-resolution genome-wide association study (GWAS) facilitated QTL fine mapping and candidate gene identification, and the GWAS based genomic prediction models were highly predictive and valuable in wheat genomic breeding. Wheat is a major staple food crop and provides more than one-fifth of the daily calories and dietary proteins for humans. Genome-wide association study (GWAS) and genomic selection (GS) for wheat stress resistance and tolerance related traits are critical to understanding their genetic architecture for improvement of breeding selection efficiency. However, the insufficient marker density in previous studies limited the utility of GWAS and GS in wheat genomic breeding. Here, we conducted a high-resolution GWAS for wheat leaf rust (LR), yellow rust (YR), powdery mildew (PM), and cold tolerance (CT) by genotyping a panel of 768 wheat cultivars using genotyping-by-sequencing. Among 153 quantitative trait loci (QTLs) identified, 81 QTLs were delimited to ≤ 1.0 Mb intervals with three validated using bi-parental populations. Furthermore, 837 stress resistance-related genes were identified in the QTL regions with 12 showing induced expression by YR and PM pathogens. Genomic prediction using 2608, 4064, 3907, and 2136 pre-selected SNPs based on GWAS and genotypic correlations between the SNPs showed high prediction accuracies of 0.76, 0.73, and 0.78 for resistance to LR, YR, and PM, respectively, and 0.83 for resistance to cold damage. Our study laid a solid foundation for large-scale QTL fine mapping, candidate gene validation and GS in wheat.
Collapse
Affiliation(s)
- Yunlong Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yuye Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Chunxia Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Wenhui Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Paul St Amand
- Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Amy Bernardo
- Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Danfeng Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lei Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Xiufang Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Huirui Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Meng Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Linzhi Li
- Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Liming Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, China
| | - Fang He
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yunlong Liang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Qiang Yan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yue Lu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yu Su
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongming Jiang
- Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Anfei Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
| |
Collapse
|
21
|
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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 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] [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.
Collapse
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.
| |
Collapse
|
22
|
Rollar S, Serfling A, Geyer M, Hartl L, Mohler V, Ordon F. QTL mapping of adult plant and seedling resistance to leaf rust (Puccinia triticina Eriks.) in a multiparent advanced generation intercross (MAGIC) wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:37-51. [PMID: 33201290 PMCID: PMC7813716 DOI: 10.1007/s00122-020-03657-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 05/22/2023]
Abstract
The Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines was phenotyped for Puccinia triticina resistance in multi-years' field trials at three locations and in a controlled environment seedling test. Simple intervall mapping revealed 19 QTL, corresponding to 11 distinct chromosomal regions. The biotrophic rust fungus Puccinia triticina is one of the most important wheat pathogens with the potential to cause yield losses up to 70%. Growing resistant cultivars is the most cost-effective and environmentally friendly way to encounter this problem. The emergence of leaf rust races being virulent against common resistance genes increases the demand for wheat varieties with novel resistances. In the past decade, the use of complex experimental populations, like multiparent advanced generation intercross (MAGIC) populations, has risen and offers great advantages for mapping resistances. The genetic diversity of multiple parents, which has been recombined over several generations, leads to a broad phenotypic diversity, suitable for high-resolution mapping of quantitative traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for leaf rust resistance in the Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs for adult plant resistance was carried out in field trials at three locations and two years, as well as in a controlled-environment seedling inoculation test. In total, interval mapping revealed 19 QTL, which corresponded to 11 distinct chromosomal regions controlling leaf rust resistance. Six of these regions may represent putative new QTL. Due to the elite parental material, RILs identified to be resistant to leaf rust can be easily introduced in breeding programs.
Collapse
Affiliation(s)
- Sandra Rollar
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| |
Collapse
|
23
|
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. THE 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] [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.
Collapse
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
| |
Collapse
|
24
|
Leonova IN, Skolotneva ES, Salina EA. Genome-wide association study of leaf rust resistance in Russian spring wheat varieties. BMC PLANT BIOLOGY 2020; 20:135. [PMID: 33050873 PMCID: PMC7557001 DOI: 10.1186/s12870-020-02333-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/06/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND Leaf rust (Puccinia triticina Eriks.) is one of the most dangerous diseases of common wheat worldwide. Three approaches: genome-wide association study (GWAS), marker-assisted selection (MAS) and phytopathological evaluation in field, were used for assessment of the genetic diversity of Russian spring wheat varieties on leaf rust resistance loci and for identification of associated molecular markers. RESULTS The collection, consisting of 100 Russian varieties of spring wheat, was evaluated over three seasons for resistance to the native population of leaf rust specific to the West Siberian region of Russia. The results indicated that most cultivars showed high susceptibility to P. triticina, with severity ratings (SR) of 60S-90S, however some cultivars showed a high level of leaf rust resistance (SR < 20MR-R). Based on the results of genome-wide association studies (GWAS) performed using the wheat 15 K genotyping array, 20 SNPs located on chromosomes 6D, 6A, 6B, 5A, 1B, 2A, 2B and 7A were revealed to be associated with leaf rust resistance. Genotyping with markers developed for known leaf rust resistance genes showed that most of the varieties contain genes Lr1, Lr3a, Lr9, Lr10, Lr17a, Lr20, Lr26 and Lr34, which are not currently effective against the pathogen. In the genome of three wheat varieties, gene Lr6Ai = 2 inherited from Th. intermedium was detected, which provides complete protection against the rust pathogen. It has been suggested that the QTL mapped to the chromosome 5AS of wheat cultivar Tulaikovskaya-zolotistaya, Tulaikovskaya-10, Samsar, and Volgouralskaya may be a new, previously undescribed locus conferring resistance to leaf rust. Obtained results also indicate that chromosome 1BL of the varieties Sonata, Otrada-Sibiri, Tertsiya, Omskaya-23, Tulaikovskaya-1, Obskaya-14, and Sirena may contain an unknown locus that provides a resistance response to local population. CONCLUSIONS This study provides new insights into the genetic basis of resistance to leaf rust in Russian spring wheat varieties. The SNPs significantly associated with leaf rust resistance can be used for the development and application of diagnostic markers in marker-assisted selection schemes.
Collapse
Affiliation(s)
- Irina N. Leonova
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - Ekaterina S. Skolotneva
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - Elena A. Salina
- Kurchatov Genomics Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090 Russia
| |
Collapse
|
25
|
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. FRONTIERS IN PLANT SCIENCE 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] [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.
Collapse
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
| |
Collapse
|
26
|
Liu F, Zhao Y, Beier S, Jiang Y, Thorwarth P, H. Longin CF, Ganal M, Himmelbach A, Reif JC, Schulthess AW. Exome association analysis sheds light onto leaf rust (Puccinia triticina) resistance genes currently used in wheat breeding (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1396-1408. [PMID: 31782598 PMCID: PMC7207002 DOI: 10.1111/pbi.13303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/06/2019] [Accepted: 11/17/2019] [Indexed: 05/18/2023]
Abstract
Resistance breeding is crucial for a sustainable control of leaf rust (Puccinia triticina) in wheat (Triticum aestivum L.) while directly targeting functional variants is the Holy Grail for efficient marker-assisted selection and map-based cloning. We assessed the limits and prospects of exome association analysis for severity of leaf rust in a large hybrid wheat population of 1574 single-crosses plus their 133 parents. After imputation and quality control, exome sequencing revealed 202 875 single-nucleotide polymorphisms (SNPs) covering 19.7% of the high-confidence annotated gene space. We performed intensive data mining and found significant associations for 2171 SNPs corresponding to 50 different loci. Some of these associations mapped in the proximity of the already known resistance genes Lr21, Lr34-B, Lr1 and Lr10, while other associated genomic regions, such as those on chromosomes 1A and 3D, harboured several annotated genes putatively involved in resistance. Validation with an independent population helped to narrow down the list of putative resistance genes that should be targeted by fine-mapping. We expect that the proposed strategy of intensive data mining coupled with validation will significantly influence research in plant genetics and breeding.
Collapse
Affiliation(s)
- Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Patrick Thorwarth
- State Plant Breeding InstituteUniversity of HohenheimStuttgartGermany
| | | | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| |
Collapse
|
27
|
Yuan C, Singh RP, Liu D, Randhawa MS, Huerta-Espino J, Lan C. Genome-Wide Mapping of Adult Plant Resistance to Leaf Rust and Stripe Rust in CIMMYT Wheat Line Arableu#1. PLANT DISEASE 2020; 104:1455-1464. [PMID: 32196419 DOI: 10.1094/pdis-10-19-2198-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Leaf (brown) rust (LR) and stripe (yellow) rust (YR), caused by Puccinia triticina and P. striiformis f. sp. tritici, respectively, significantly reduce wheat production worldwide. Disease-resistant wheat varieties offer farmers one of the most effective ways to manage these diseases. The common wheat (Triticum aestivum L.) Arableu#1, developed by the International Maize and Wheat Improvement Center and released as Deka in Ethiopia, shows susceptibility to both LR and YR at the seedling stage but a high level of adult plant resistance (APR) to the diseases in the field. We used 142 F5 recombinant inbred lines (RILs) derived from Apav#1 × Arableu#1 to identify quantitative trait loci (QTLs) for APR to LR and YR. A total of 4,298 genotyping-by-sequencing markers were used to construct a genetic linkage map. The study identified four LR resistance QTLs and six YR resistance QTLs in the population. Among these, QLr.cim-1BL.1/QYr.cim-1BL.1 was located in the same location as Lr46/Yr29, a known pleiotropic resistance gene. QLr.cim-1BL.2 and QYr.cim-1BL.2 were also located on wheat chromosome 1BL at 37 cM from Lr46/Yr29 and may represent a new segment for pleiotropic resistance to both rusts. QLr.cim-7BL is likely Lr68 given its association with the tightly linked molecular marker cs7BLNLRR. In addition, QLr.cim-3DS, QYr.cim-2AL, QYr.cim-4BL, QYr.cim-5AL, and QYr.cim-7DS are probably new resistance loci based on comparisons with published QTLs for resistance to LR and YR. Our results showed the diversity of minor resistance QTLs in Arableu#1 and their role in conferring near-immune levels of APR to both LR and YR, when combined with the pleiotropic APR gene Lr46/Yr29.
Collapse
Affiliation(s)
- Chan Yuan
- Huazhong Agricultural University, College of Plant Science & Technology, Hongshan District, Wuhan, Hubei Province 430070, People's Republic of China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico D.F., Mexico
| | - Demei Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, People's Republic of China
| | - Mandeep S Randhawa
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico D.F., Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico INIFAP, 56230 Chapingo, Edo. de Mexico, Mexico
| | - Caixia Lan
- Huazhong Agricultural University, College of Plant Science & Technology, Hongshan District, Wuhan, Hubei Province 430070, People's Republic of China
| |
Collapse
|
28
|
Bokore FE, Knox RE, Cuthbert RD, Pozniak CJ, McCallum BD, N’Diaye A, DePauw RM, Campbell HL, Munro C, Singh A, Hiebert CW, McCartney CA, Sharpe AG, Singh AK, Spaner D, Fowler DB, Ruan Y, Berraies S, Meyer B. Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers. PLoS One 2020; 15:e0230855. [PMID: 32267842 PMCID: PMC7141615 DOI: 10.1371/journal.pone.0230855] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/10/2020] [Indexed: 01/27/2023] Open
Abstract
Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New Zealand near Lincoln in 2014. The populations were genotyped with the 90K Infinium iSelect assay and quantitative trait loci (QTL) analysis was performed. A high density consensus map generated based on 14 doubled haploid populations and integrating SNP and SSR markers was used to compare QTL identified in different populations. AC Cadillac contributed QTL on chromosomes 2A, 3B and 7B (2 loci), Carberry on 1A, 2B (2 loci), 2D, 4B (2 loci), 5A, 6A, 7A and 7D, Lillian on 4A and 7D, Stettler on 2D and 6B, Vesper on 1B, 1D, 2A, 6B and 7B (2 loci), and Red Fife on 7A and 7B. Lillian contributed to a novel locus QLr.spa-4A, and similarly Carberry at QLr.spa-5A. The discovery of novel leaf rust resistance QTL QLr.spa-4A and QLr.spa-5A, and several others in contemporary Canada Western Red Spring wheat varieties is a tremendous addition to our present knowledge of resistance gene deployment in breeding. Carberry demonstrated substantial stacking of genes which could be supplemented with the genes identified in other cultivars with the expectation of increasing efficacy of resistance to leaf rust and longevity with little risk of linkage drag.
Collapse
Affiliation(s)
- Firdissa E Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Ron E. Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
- * E-mail: (REK); (RDC); (CJP)
| | - Richard D. Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
- * E-mail: (REK); (RDC); (CJP)
| | - Curtis J. Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
- * E-mail: (REK); (RDC); (CJP)
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | | | - Heather L. Campbell
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Catherine Munro
- Plant and Food Research, Canterbury Agriculture and Science Centre, Lincoln, New Zealand
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Curt A. McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4–10N Agriculture-Forestry Centre, University of Alberta, Edmonton, Canada
| | - D. B. Fowler
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| |
Collapse
|
29
|
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] [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.
Collapse
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.
| |
Collapse
|
30
|
Dmochowska-Boguta M, Kloc Y, Zielezinski A, Werecki P, Nadolska-Orczyk A, Karlowski WM, Orczyk W. TaWAK6 encoding wall-associated kinase is involved in wheat resistance to leaf rust similar to adult plant resistance. PLoS One 2020; 15:e0227713. [PMID: 31929605 PMCID: PMC6957155 DOI: 10.1371/journal.pone.0227713] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/25/2019] [Indexed: 11/19/2022] Open
Abstract
In wheat, adult plant resistance (APR) to leaf rust (Puccinia triticina), is effective in restricting pathogen growth and provides durable resistance against a wide range of virulent forms of P. triticina. Despite the importance, there is limited knowledge on the molecular basis of this type of resistance. We isolated and characterized the wall-associated kinase encoding gene in wheat, and assigned it as TaWAK6. Localization of TaWAK6 homeologs in A and B wheat subgenomes was consistent with the presence of the gene's orthologs in T. urartu (AA) and T. dicoccoides (AABB) and with the absence of its orthologs in Aegilops tauschii (DD). Overexpression of TaWAK6 did not change the wheat phenotype, nor did it affect seedling resistance. However, the adult plants overexpressing TaWAK6 showed that important parameters of APR were significantly elevated. Infection types scored on the first (flag), second and third leaves indicated elevated resistance, which significantly correlated with expression of TaWAK6. Analysis of plant-pathogen interactions showed a lower number of uredinia and higher rates of necrosis at the infection sites and this was associated with smaller size of uredinia and a longer latent period. The results indicated a role of TaWAK6 in quantitative partial resistance similar to APR in wheat. It is proposed that TaWAK6, which is a non-arginine-aspartate (non-RD) kinase, represents a novel class of quantitative immune receptors in monocots.
Collapse
Affiliation(s)
- Marta Dmochowska-Boguta
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Yuliya Kloc
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Przemysław Werecki
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Wacław Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| |
Collapse
|
31
|
Rosa SB, Zanella CM, Hiebert CW, Brûlé-Babel AL, Randhawa HS, Shorter S, Boyd LA, McCallum BD. Genetic Characterization of Leaf and Stripe Rust Resistance in the Brazilian Wheat Cultivar Toropi. PHYTOPATHOLOGY 2019; 109:1760-1768. [PMID: 31282829 DOI: 10.1094/phyto-05-19-0159-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Leaf and stripe rust are major threats to wheat production worldwide. The effective, multiple rust resistances present in the Brazilian cultivar Toropi makes it an excellent choice for a genetic study of rust resistance. Testing of DNA from different seed lots of Toropi with 2,194 polymorphic 90K iSelect single nucleotide polymorphism markers identified significant genetic divergence, with as much as 35% dissimilarity between seed lots. As a result, further work was conducted with a single plant line derived from Toropi variant Toropi-6.4. A double haploid population with 168 lines derived from the cross Toropi-6.4 × Thatcher was phenotyped over multiple years and locations in Canada, New Zealand, and Kenya, with a total of seven field trials undertaken for leaf rust and nine for stripe rust. Genotyping with the 90K iSelect array, simple sequence repeat and Kompetitive allele-specific polymerase chain reaction markers resulted in a genetic map of 3,043 cM, containing 1,208 nonredundant markers. Significant quantitative trait loci (QTL) derived from Toropi-6.4 were identified in multiple environments on chromosomes 1B (QLr.crc-1BL/QYr.crc-1BL), 3B (QLr.crc-3BS), 4B (QYr.crc-4BL), 5A (QLr.crc-5AL and QYr.crc-5AL), and 5D (QLr.crc-5DS). The QTL QLr.crc-1BL/QYr.crc-1BL colocated with the multi-rust resistance locus Lr46/Yr29, while the QTL QLr.crc-5DS located to the Lr78 locus previously found in a wheat backcross population derived from Toropi. Comparisons of QTL combinations showed QLr.crc-1BL to contribute a significantly enhanced leaf rust resistance when combined with QLr.crc-5AL or QLr.crc-5DS, more so than when QLr.crc-5AL and QLr.crc-5DS were combined. A strong additive effect was also seen when the stripe rust resistance QTL QYr.crc-1BL and QYr.crc-5AL were combined.
Collapse
Affiliation(s)
- Silvia B Rosa
- CÉROM, Centre de recherché sur les grains, 740 Chemin Trudeau, Saint-Mathieu-de-Beloeil, QC, J3G 0E2, Canada
| | | | - Colin W Hiebert
- Agriculture and Agri-Food Canada, Morden Research Centre, Morden, MB, R6M 1Y5, Canada
| | | | - Harpinder S Randhawa
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, 5403-1 Avenue South, Lethbridge, AB, T1J 4P4, Canada
| | - Stephen Shorter
- Plant and Food Research, Canterbury Agriculture & Science Centre, Gerald Street, Lincoln, New Zealand
| | | | - Brent D McCallum
- Agriculture and Agri-Food Canada, Morden Research Centre, Morden, MB, R6M 1Y5, Canada
| |
Collapse
|
32
|
El-Orabey WM, Hamwieh A, Ahmed SM. Molecular markers and phenotypic characterization of adult plant resistance genes Lr 34, Lr 46, Lr 67 and Lr 68 and their association with partial resistance to leaf rust in wheat. J Genet 2019. [DOI: 10.1007/s12041-019-1122-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
33
|
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. MOLECULAR 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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
|