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Khan H, Krishnappa G, Kumar S, Devate NB, Rathan ND, Kumar S, Mishra CN, Ram S, Tiwari R, Parkash O, Ahlawat OP, Mamrutha HM, Singh GP, Singh G. Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:411. [PMID: 38760694 PMCID: PMC11100168 DOI: 10.1186/s12870-024-05124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR). RESULTS Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype. CONCLUSION The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.
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Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India.
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Narayana Bhat Devate
- International Centre for Agriculture Research in the Dry Area - Food Legume Research Platform, Amlaha, MP, 466113, India
| | | | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | | | - Sewa Ram
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Om Parkash Ahlawat
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | | | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
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Marone D, Laidò G, Saccomanno A, Petruzzino G, Giaretta Azevedo CV, De Vita P, Mastrangelo AM, Gadaleta A, Ammar K, Bassi FM, Wang M, Chen X, Rubiales D, Matny O, Steffenson BJ, Pecchioni N. Genome-wide association study of common resistance to rust species in tetraploid wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1290643. [PMID: 38235202 PMCID: PMC10792004 DOI: 10.3389/fpls.2023.1290643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.
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Affiliation(s)
- Daniela Marone
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Giovanni Laidò
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Antonietta Saccomanno
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Giuseppe Petruzzino
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Cleber V. Giaretta Azevedo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Pasquale De Vita
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Anna Maria Mastrangelo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Agata Gadaleta
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (Di.S.S.P.A.), Università di Bari “Aldo Moro”, Bari, Italy
| | - Karim Ammar
- International Maize and Wheat Improvement Centre (CIMMYT), Ciudad de México, Mexico
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Pullman, WA, United States
| | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Nicola Pecchioni
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
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Pradhan AK, Budhlakoti N, Chandra Mishra D, Prasad P, Bhardwaj SC, Sareen S, Sivasamy M, Jayaprakash P, Geetha M, Nisha R, Shajitha P, Peter J, Kaur A, Kaur S, Vikas VK, Singh K, Kumar S. Identification of Novel QTLs/Defense Genes in Spring Wheat Germplasm Panel for Seedling and Adult Plant Resistance to Stem Rust and Their Validation Through KASP Marker Assays. PLANT DISEASE 2023:PDIS09222242RE. [PMID: 37311158 DOI: 10.1094/pdis-09-22-2242-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stem rust is one of the major diseases threatening wheat production globally. To identify novel resistance quantitative trait loci (QTLs), we performed 35K Axiom Array SNP genotyping assays on an association mapping panel of 400 germplasm accessions, including Indian landraces, in conjunction with phenotyping for stem rust at seedling and adult plant stages. Association analyses using three genome wide association study (GWAS) models (CMLM, MLMM, and FarmCPU) revealed 20 reliable QTLs for seedling and adult plant resistance. Among these 20 QTLs, five QTLs were found consistent with three models, i.e., four QTLs on chromosome 2AL, 2BL, 2DL, and 3BL for seedling resistance and one QTL on chromosome 7DS for adult plant resistance. Further, we identified a total of 21 potential candidate genes underlying QTLs using gene ontology analysis, including a leucine rich repeat receptor (LRR) and P-loop nucleoside triphosphate hydrolase, which have a role in pathogen recognition and disease resistance. Furthermore, four QTLs (Qsr.nbpgr-3B_11, QSr.nbpgr-6AS_11, QSr.nbpgr-2AL_117-6, and QSr.nbpgr-7BS_APR) were validated through KASP located on chromosomes 3B, 6A, 2A, and 7B. Out of these QTLs, QSr.nbpgr-7BS_APR was identified as a novel QTL for stem rust resistance which has been found effective in both seedling as well as the adult plant stages. Identified novel genomic regions and validated QTLs have the potential to be deployed in wheat improvement programs to develop disease resistant varieties for stem rust and can diversify the genetic basis of resistance.
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Affiliation(s)
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | | | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - M Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Jayaprakash
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - M Geetha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - R Nisha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Shajitha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - John Peter
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - V K Vikas
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Kuldeep Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana 502324, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
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Mourad AM, Hamdy RM, Esmail SM. Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1160657. [PMID: 37235018 PMCID: PMC10208068 DOI: 10.3389/fpls.2023.1160657] [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: 02/07/2023] [Accepted: 03/27/2023] [Indexed: 05/28/2023]
Abstract
Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.
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Affiliation(s)
- Amira M.I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Rania M. Hamdy
- Food Science and Technology Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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Talebi R, Mahboubi M, Naji AM, Mehrabi R. Physiological specialization of Puccinia triticina and genome-wide association mapping provide insights into the genetics of wheat leaf rust resistance in Iran. Sci Rep 2023; 13:4398. [PMID: 36927878 PMCID: PMC10020449 DOI: 10.1038/s41598-023-31559-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Leaf rust caused by Puccinia triticina Erikss. (Pt) is the most widely distributed and important wheat disease worldwide. The objective of the present study was to determine the frequency of Iranian Pt races, their virulence to key resistance genes and map quantitative trait loci (QTL) for resistance to different Pt races from 185 globally diverse wheat genotypes using a genome-wide association study (GWAS) approach. The virulence pattern of the 33 Pt isolates from various wheat-growing areas of Iran on 55 wheat differentials showed that the FKTPS and FKTTS were relatively frequent pathotypes among the 18 identified races. The weighted average frequency of virulence on the resistance genes Lrb, Lr3bg, Lr14b, Lr16, Lr24, Lr3ka, Lr11 and Lr20 were high (> 90%). However, low virulence on the resistant genes Lr2a, Lr9, Lr19, Lr25, Lr28 and Lr29 indicates that these genes are still effective against the pathogen population in Iran at present. GWAS on a panel of 185 wheat genotypes against 10 Pt races resulted into 62 significant marker-trait associations (MTAs) belonged to 34 quantitative trait loci (QTL) across 16 chromosomes. Among them, 10 QTLs on chromosomes 1A, 1B, 3B, 3D, 4A, 6D, 7A and 7D were identified as potential novel QTLs, of which four QTLs (QLr.iau-3B-2, QLr.iau-7A-2, QLr.iau-7A-3 and QLr.iau-7D-2) are more interesting, as they are associated with resistance to two or more Pt races. The known and novel QTLs associated with different Pt races found here, can be used in future wheat breeding programs to recombine different loci for durable resistance against leaf rust races.
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Affiliation(s)
- Reza Talebi
- Department of Plant Breeding, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran. .,Keygene N.V, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands.
| | - Mozghan Mahboubi
- Department of Plant Breeding, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
| | - Amir Mohammad Naji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahed University, Tehran, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, PO Box 8415683111, Isfahan, Iran. .,Keygene N.V, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands.
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Delfan S, Bihamta MR, Dadrezaei ST, Abbasi A, Alipoor H. Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis. BMC Genomics 2023; 24:83. [PMID: 36810004 PMCID: PMC9945389 DOI: 10.1186/s12864-022-09096-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/22/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Global wheat productivity is seriously challenged by a range of rust pathogens, especially leaf rust derived from Puccinia triticina. Since the most efficient approach to control leaf rust is genetic resistance, many efforts have been made to uncover resistance genes; however, it demands an ongoing exploration for effective resistance sources because of the advent of novel virulent races. Thus, the current study was focused on detecting leaf rust resistance-related genomic loci against the P. triticina prevalent races by GWAS in a set of Iranian cultivars and landraces. RESULTS Evaluation of 320 Iranian bread wheat cultivars and landraces against four prevalent rust pathotypes of P. triticina (LR-99-2, LR-98-12, LR-98-22, and LR-97-12) indicated the diversity in wheat accessions responses to P. triticina. From GWAS results, 80 leaf rust resistance QTLs were located in the surrounding known QTLs/genes on almost chromosomes, except for 1D, 3D, 4D, and 7D. Of these, six MTAs (rs20781/rs20782 associated with resistance to LR-97-12; rs49543/rs52026 for LR-98-22; rs44885/rs44886 for LR-98-22/LR-98-1/LR-99-2) were found on genomic regions where no resistance genes previously reported, suggesting new loci conferring resistance to leaf rust. The GBLUP genomic prediction model appeared better than RR-BLUP and BRR, reflecting that GBLUP is a potent model for genomic selection in wheat accessions. CONCLUSIONS Overall, the newly identified MTAs as well as the highly resistant accessions in the recent work provide an opportunity towards improving leaf rust resistance.
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Affiliation(s)
- Saba Delfan
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran.
| | - Seyed Taha Dadrezaei
- grid.473705.20000 0001 0681 7351Department of Cereal Research, Seed and Plant Improvement Institute, Agricultural Research and Education Organization (AREEO), Karaj, Iran
| | - Alireza Abbasi
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Hadi Alipoor
- grid.412763.50000 0004 0442 8645Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
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Kaur S, Gill HS, Breiland M, Kolmer JA, Gupta R, Sehgal SK, Gill U. Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1090163. [PMID: 36818858 PMCID: PMC9929074 DOI: 10.3389/fpls.2023.1090163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.
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Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Matthew Breiland
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN, United States
| | - Rajeev Gupta
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fargo, ND, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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Mulugeta B, Tesfaye K, Ortiz R, Johansson E, Hailesilassie T, Hammenhag C, Hailu F, Geleta M. Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1009244. [PMID: 36777537 PMCID: PMC9909559 DOI: 10.3389/fpls.2022.1009244] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.
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Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Director General, Bio and Emerging Technology Institute (BETin), Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Shahinnia F, Geyer M, Schürmann F, Rudolphi S, Holzapfel J, Kempf H, Stadlmeier M, Löschenberger F, Morales L, Buerstmayr H, Sánchez JIY, Akdemir D, Mohler V, Lillemo M, Hartl L. Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3583-3595. [PMID: 36018343 PMCID: PMC9519682 DOI: 10.1007/s00122-022-04202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/17/2022] [Indexed: 05/03/2023]
Abstract
We found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat germplasm. Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13-0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.
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Affiliation(s)
- Fahimeh Shahinnia
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany.
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | | | - Sabine Rudolphi
- SECOBRA Saatzucht GmbH, Lagesche Str. 250, 32657, Lemgo, Germany
| | - Josef Holzapfel
- SECOBRA Saatzucht GmbH, Feldkirchen 3, 85368, Moosburg, Germany
| | - Hubert Kempf
- SECOBRA Saatzucht GmbH, Feldkirchen 3, 85368, Moosburg, Germany
| | | | | | - Laura Morales
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln an der Donau, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln an der Donau, Austria
| | - Julio Isidro Y Sánchez
- Centro de Biotecnologia y Genómica de Plantas, Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Deniz Akdemir
- Center for International Blood and Marrow Transplant Research (CIBMTR), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany.
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10
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Pal N, Jan I, Saini DK, Kumar K, Kumar A, Sharma PK, Kumar S, Balyan HS, Gupta PK. Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2385-2405. [PMID: 35699741 DOI: 10.1007/s00122-022-04119-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/28/2022] [Indexed: 05/20/2023]
Abstract
In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant cultivars. Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the 'Breeders' MQTLs'. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.
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Affiliation(s)
- Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
- Murdoch's Centre for Crop & Food Innovation, Murdoch University, Murdoch, Perth, WA 6150, Australia.
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11
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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.
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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
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12
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Wang P, Tian T, Ma J, Liu Y, Zhang P, Chen T, Shahinnia F, Yang D. Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:905660. [PMID: 35734257 PMCID: PMC9207461 DOI: 10.3389/fpls.2022.905660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Kernel size and weight are crucial components of grain yield in wheat. Deciphering their genetic basis is essential for improving yield potential in wheat breeding. In this study, five kernel traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), kernel perimeter (KP), and thousand-kernel weight (TKW), were evaluated in a panel consisting of 198 wheat accessions under six environments. Wheat accessions were genotyped using the 35K SNP iSelect chip array, resulting in a set of 13,228 polymorphic SNP markers that were used for genome-wide association study (GWAS). A total of 146 significant marker-trait associations (MTAs) were identified for five kernel traits on 21 chromosomes [-log10(P) ≥ 3], which explained 5.91-15.02% of the phenotypic variation. Of these, 12 stable MTAs were identified in multiple environments, and six superior alleles showed positive effects on KL, KP, and KDR. Four potential candidate genes underlying the associated SNP markers were predicted for encoding ML protein, F-box protein, ethylene-responsive transcription factor, and 1,4-α-glucan branching enzyme. These genes were strongly expressed in grain development at different growth stages. The results will provide new insights into the genetic basis of kernel traits in wheat. The associated SNP markers and predicted candidate genes will facilitate marker-assisted selection in wheat breeding.
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Affiliation(s)
- Peng Wang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Tian Tian
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yuan Liu
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fahimeh Shahinnia
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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13
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Genome-Wide Association Study Identifies Two Loci for Stripe Rust Resistance in a Durum Wheat Panel from Iran. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12104963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Stripe rust (Puccinia striiformis f. sp. tritici (Pst)) is one of the most devastating fungal diseases of durum wheat (Triticum turgidum L. var. durum Desf.). Races of Pst with new virulence combinations are emerging more regularly on wheat-growing continents, which challenges wheat breeding for resistance. This study aimed to identify and characterize resistance to Pst races based on a genome-wide association study. GWAS is an approach to analyze the associations between a genome-wide set of single-nucleotide polymorphisms (SNPs) and target phenotypic traits. A total of 139 durum wheat accessions from Iran were evaluated at the seedling stage against isolates Pstv-37 and Pstv-40 of Pst and then genotyped using a 15K SNP chip. In total, 230 significant associations were identified across 14 chromosomes, of which 30 were associated with resistance to both isolates. Furthermore, 17 durum wheat landraces showed an immune response against both Pst isolates. The SNP markers and resistant accessions identified in this study may be useful in programs breeding durum wheat for stripe rust resistance.
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14
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Kumar K, Jan I, Saripalli G, Sharma PK, Mir RR, Balyan HS, Gupta PK. An Update on Resistance Genes and Their Use in the Development of Leaf Rust Resistant Cultivars in Wheat. Front Genet 2022; 13:816057. [PMID: 35432483 PMCID: PMC9008719 DOI: 10.3389/fgene.2022.816057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Wheat is one of the most important cereal crops in the world. The production and productivity of wheat is adversely affected by several diseases including leaf rust, which can cause yield losses, sometimes approaching >50%. In the present mini-review, we provide updated information on (i) all Lr genes including those derived from alien sources and 14 other novel resistance genes; (ii) a list of QTLs identified using interval mapping and MTAs identified using GWAS (particular those reported recently i.e., after 2018) and their association with known Lr genes; (iii) introgression/pyramiding of individual Lr genes in commercial/prominent cultivars from 18 different countries including India. Challenges and future perspectives of breeding for leaf rust resistance are also provided at the end of this mini-review. We believe that the information in this review will prove useful for wheat geneticists/breeders, not only in the development of leaf rust-resistant wheat cultivars, but also in the study of molecular mechanism of leaf rust resistance in wheat.
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Affiliation(s)
- Kuldeep Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - P. K. Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura, India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- *Correspondence: P. K. Gupta, ,
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15
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Sidibé A, Charles MT, Lucier JF, Xu Y, Beaulieu C. Preharvest UV-C Hormesis Induces Key Genes Associated With Homeostasis, Growth and Defense in Lettuce Inoculated With Xanthomonas campestris pv. vitians. FRONTIERS IN PLANT SCIENCE 2022; 12:793989. [PMID: 35111177 PMCID: PMC8801786 DOI: 10.3389/fpls.2021.793989] [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: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Preharvest application of hormetic doses of ultraviolet-C (UV-C) generates beneficial effects in plants. In this study, within 1 week, four UV-C treatments of 0.4 kJ/m2 were applied to 3-week-old lettuce seedlings. The leaves were inoculated with a virulent strain of Xanthomonas campestris pv. vitians (Xcv) 48 h after the last UV-C application. The extent of the disease was tracked over time and a transcriptomic analysis was performed on lettuce leaf samples. Samples of lettuce leaves, from both control and treated groups, were taken at two different times corresponding to T2, 48 h after the last UV-C treatment and T3, 24 h after inoculation (i.e., 72 h after the last UV-C treatment). A significant decrease in disease severity between the UV-C treated lettuce and the control was observed on days 4, 8, and 14 after pathogen inoculation. Data from the transcriptomic study revealed, that in response to the effect of UV-C alone and/or UV-C + Xcv, a total of 3828 genes were differentially regulated with fold change (|log2-FC|) > 1.5 and false discovery rate (FDR) < 0.05. Among these, of the 2270 genes of known function 1556 were upregulated and 714 were downregulated. A total of 10 candidate genes were verified by qPCR and were generally consistent with the transcriptomic results. The differentially expressed genes observed in lettuce under the conditions of the present study were associated with 14 different biological processes in the plant. These genes are involved in a series of metabolic pathways associated with the ability of lettuce treated with hormetic doses of UV-C to resume normal growth and to defend themselves against potential stressors. The results indicate that the hormetic dose of UV-C applied preharvest on lettuce in this study, can be considered as an eustress that does not interfere with the ability of the treated plants to carry on a set of key physiological processes namely: homeostasis, growth and defense.
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Affiliation(s)
- Amadou Sidibé
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Marie Thérèse Charles
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | | | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, Hangzhou, China
| | - Carole Beaulieu
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
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16
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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17
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Draz IS, Serfling A, Muqaddasi QH, Röder MS. Quantitative trait loci for yellow rust resistance in spring wheat doubled haploid populations developed from the German Federal ex situ genebank genetic resources. THE PLANT GENOME 2021; 14:e20142. [PMID: 34498808 DOI: 10.1002/tpg2.20142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Novel resistance sources to the pathogen Puccinia striiformis f. sp. tritici, which causes yellow rust (stripe rust), a widespread devastating foliar disease in wheat (Triticum aestivum L.), are in demand. Here, we tested two doubled haploid (DH) spring wheat populations derived from the genetic resources for resistance to yellow rust in field trials in Germany and Egypt. Additionally, we performed tests for all-stage resistance (seedling resistance). We performed linkage mapping based on 15k Infinium SNP chip genotyping data that resulted in 3,567 and 3,457 polymorphic markers for DH Population 1 (103 genotypes) and DH Population 2 (148 genotypes), respectively. In DH Population 1, we identified a major and consistent quantitative trait locus (QTL) on chromosome 1B that explained up to 28 and 39% of the phenotypic variation in the field and seedling tests, respectively. The favorable allele was contributed by the line 'TRI-5645', a landrace from Iran, and is most probably the yellow rust resistance (Yr) gene Yr10. In DH Population 2, the favorable allele of a major QTL on chromosome 6B was contributed by the line 'TRI-5310', representing the variety 'Eureke' from France. This QTL was mainly effective in the German environments and explained up to 36% of the phenotypic variation. In Egypt, however, only a moderate resistance QTL was identified in the field tests and no resistance QTL was observed in the seedling tests. Our results demonstrate the usefulness of genetic resources to identify novel sources of resistance to yellow rust, including the "Warrior" race PstS10.
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Affiliation(s)
- Ibrahim S Draz
- Wheat Disease Research Dep., Plant Pathology Research Institute, Agricultural Research Center, 9 Gamaa Street, Giza, 12619, Egypt
| | - Albrecht Serfling
- Julius Kühn Institute-Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin Baur Straße 27, Quedlinburg, 06484, Germany
| | - Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland OT, Gatersleben, Germany
- Present address: European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT, Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland OT, Gatersleben, Germany
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18
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Volante A, Barabaschi D, Marino R, Brandolini A. Genome-wide association study for morphological, phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum). G3 (BETHESDA, MD.) 2021; 11:jkab281. [PMID: 34849796 PMCID: PMC8527505 DOI: 10.1093/g3journal/jkab281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/27/2021] [Indexed: 11/12/2022]
Abstract
Einkorn (Triticum monococcum L. subsp. monococcum, 2n = 2× = 14, AmAm) is a diploid wheat whose cultivation was widespread in the Mediterranean and European area till the Bronze Age, before it was replaced by the more productive durum and bread wheats. Although scarcely cultivated nowadays, it has gained renewed interest due to its relevant nutritional properties and as source of genetic diversity for crop breeding. However, the molecular basis of many traits of interest in einkorn remain still unknown. A panel of 160 einkorn landraces, from different parts of the distribution area, was characterized for several phenotypic traits related to morphology, phenology, quality, and yield for 4 years in two locations. An approach based on co-linearity with the A genome of bread wheat, supported also by that with Triticum urartu genome, was exploited to perform association mapping, even without an einkorn anchored genome. The association mapping approach uncovered numerous marker-trait associations; for 37 of these, a physical position was inferred by homology with the bread wheat genome. Moreover, numerous associated regions were also assigned to the available T. monococcum contigs. Among the intervals detected in this work, three overlapped with regions previously described as involved in the same trait, while four other regions were localized in proximity of loci previously described and presumably refer to the same gene/QTL. The remaining associated regions identified in this work could represent a novel and useful starting point for breeding approaches to improve the investigated traits in this neglected species.
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Affiliation(s)
- Andrea Volante
- CREA—Research Centre for Cereal and Industrial Crops, 13100 Vercelli, Italy
| | - Delfina Barabaschi
- CREA—Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy and
| | - Rosanna Marino
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
| | - Andrea Brandolini
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
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19
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Eltaher S, Mourad AMI, Baenziger PS, Wegulo S, Belamkar V, Sallam A. Identification and Validation of High LD Hotspot Genomic Regions Harboring Stem Rust Resistant Genes on 1B, 2A ( Sr38), and 7B Chromosomes in Wheat. Front Genet 2021; 12:749675. [PMID: 34659366 PMCID: PMC8517078 DOI: 10.3389/fgene.2021.749675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/13/2021] [Indexed: 12/02/2022] Open
Abstract
Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is an important disease of common wheat globally. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F3:6 lines. The results indicated that 184 genotypes (86.8%) had different degrees of resistance to this common race. While 28 genotypes (13.2%) were susceptible to stem rust. A set of 11,911 single-nucleotide polymorphism (SNP) markers was used to perform GWAS which detected 84 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1B, 2A, 2B, 7B and an unknown chromosome. Promising high linkage disequilibrium (LD) genomic regions were found in all chromosomes except 2B which suggested they include candidate genes controlling stem rust resistance. Highly significant LD was found among these 59 significant SNPs on chromosome 2A and 12 significant SNPs with an unknown chromosomal position. The LD analysis between SNPs located on 2A and Sr38 gene reveal high significant LD genomic regions which was previously reported. To select the most promising stem rust resistant genotypes, a new approach was suggested based on four criteria including, phenotypic selection, number of resistant allele(s), the genetic distance among the selected parents, and number of the different resistant allele(s) in the candidate crosses. As a result, 23 genotypes were considered as the most suitable parents for crossing to produce highly resistant stem rust genotypes against the QFCSC.
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Affiliation(s)
- Shamseldeen Eltaher
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), Sadat, Egypt
| | - Amira M I Mourad
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Stephen Wegulo
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
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20
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Atia MAM, El-Khateeb EA, Abd El-Maksoud RM, Abou-Zeid MA, Salah A, Abdel-Hamid AME. Mining of Leaf Rust Resistance Genes Content in Egyptian Bread Wheat Collection. PLANTS (BASEL, SWITZERLAND) 2021; 10:1378. [PMID: 34371581 PMCID: PMC8309345 DOI: 10.3390/plants10071378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/15/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Wheat is a major nutritional cereal crop that has economic and strategic value worldwide. The sustainability of this extraordinary crop is facing critical challenges globally, particularly leaf rust disease, which causes endless problems for wheat farmers and countries and negatively affects humanity's food security. Developing effective marker-assisted selection programs for leaf rust resistance in wheat mainly depends on the availability of deep mining of resistance genes within the germplasm collections. This is the first study that evaluated the leaf rust resistance of 50 Egyptian wheat varieties at the adult plant stage for two successive seasons and identified the absence/presence of 28 leaf rust resistance (Lr) genes within the studied wheat collection. The field evaluation results indicated that most of these varieties demonstrated high to moderate leaf rust resistance levels except Gemmeiza 1, Gemmeiza 9, Giza162, Giza 163, Giza 164, Giza 165, Sids 1, Sids 2, Sids 3, Sakha 62, Sakha 69, Sohag 3 and Bany Swif 4, which showed fast rusting behavior. On the other hand, out of these 28 Lr genes tested against the wheat collection, 21 Lr genes were successfully identified. Out of 15 Lr genes reported conferring the adult plant resistant or slow rusting behavior in wheat, only five genes (Lr13, Lr22a, Lr34, Lr37, and Lr67) were detected within the Egyptian collection. Remarkedly, the genes Lr13, Lr19, Lr20, Lr22a, Lr28, Lr29, Lr32, Lr34, Lr36, Lr47, and Lr60, were found to be the most predominant Lr genes across the 50 Egyptian wheat varieties. The molecular phylogeny results also inferred the same classification of field evaluation, through grouping genotypes characterized by high to moderate leaf rust resistance in one cluster while being highly susceptible in a separate cluster, with few exceptions.
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Affiliation(s)
- Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Eman A. El-Khateeb
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt;
| | - Reem M. Abd El-Maksoud
- Department of Nucleic Acid & Protein Structure, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Mohamed A. Abou-Zeid
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Arwa Salah
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Amal M. E. Abdel-Hamid
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Roxy, Cairo 11341, Egypt;
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21
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Sharma A, Srivastava P, Mavi GS, Kaur S, Kaur J, Bala R, Singh TP, Sohu VS, Chhuneja P, Bains NS, Singh GP. Resurrection of Wheat Cultivar PBW343 Using Marker-Assisted Gene Pyramiding for Rust Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:570408. [PMID: 33643338 PMCID: PMC7905314 DOI: 10.3389/fpls.2021.570408] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 01/07/2021] [Indexed: 05/29/2023]
Abstract
Wheat variety PBW343, released in India in 1995, became the most widely grown cultivar in the country by the year 2000 owing to its wide adaptability and yield potential. It initially succumbed to leaf rust, and resistance genes Lr24 and Lr28 were transferred to PBW343. After an unbroken reign of about 10 years, the virulence against gene Yr27 made PBW343 susceptible to stripe rust. Owing to its wide adaptability and yield potential, PBW343 became the prime target for marker-assisted introgression of stripe rust resistance genes. The leaf rust-resistant versions formed the base for pyramiding stripe rust resistance genes Yr5, Yr10, Yr15, Yr17, and Yr70, in different introgression programs. Advanced breeding lines with different gene combinations, PBW665, PBW683, PBW698, and PBW703 were tested in national trials but could not be released as varieties. The genes from alien segments, Aegilops ventricosa (Lr37/Yr17/Sr38) and Aegilops umbellulata (Lr76/Yr70), were later pyramided in PBW343. Modified marker-assisted backcross breeding was performed, and 81.57% of the genetic background was recovered in one of the selected derivative lines, PBW723. This line was evaluated in coordinated national trials and was released for cultivation under timely sown irrigated conditions in the North Western Plain Zone of India. PBW723 yields an average of 58.0 qtl/ha in Punjab with high potential yields. The genes incorporated are susceptible to stripe rust individually, but PBW723 with both genes showed enhanced resistance. Three years post-release, PBW723 occupies approximately 8-9% of the cultivated area in the Punjab state. A regular inflow of diverse resistant genes, their rapid mobilization to most productive backgrounds, and keeping a close eye on pathogen evolution is essential to protect the overall progress for productivity and resistance in wheat breeding, thus helping breeders to keep pace with pathogen evolution.
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Affiliation(s)
- Achla Sharma
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Puja Srivastava
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - G. S. Mavi
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Jaspal Kaur
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Ritu Bala
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - V. S. Sohu
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Navtej S. Bains
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - G. P. Singh
- Indian Institute of Wheat & Barley Research, Karnal, India
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22
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Abou-Zeid MA, Mourad AMI. Genomic regions associated with stripe rust resistance against the Egyptian race revealed by genome-wide association study. BMC PLANT BIOLOGY 2021; 21:42. [PMID: 33446120 PMCID: PMC7809828 DOI: 10.1186/s12870-020-02813-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/22/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Wheat stripe rust (caused by Puccinia striiformis f. sp. Tritici), is a major disease that causes huge yield damage. New pathogen races appeared in the last few years and caused a broke down in the resistant genotypes. In Egypt, some of the resistant genotypes began to be susceptible to stripe rust in recent years. This situation increases the need to produce new genotypes with durable resistance. Besides, looking for a new resistant source from the available wheat genotypes all over the world help in enhancing the breeding programs. RESULTS In the recent study, a set of 103-spring wheat genotypes from different fourteen countries were evaluated to their field resistant to stripe rust for two years. These genotypes included 17 Egyptian genotypes from the old and new cultivars. The 103-spring wheat genotypes were reported to be well adapted to the Egyptian environmental conditions. Out of the tested genotypes, eight genotypes from four different countries were found to be resistant in both years. Genotyping was carried out using genotyping-by-sequencing and a set of 26,703 SNPs were used in the genome-wide association study. Five SNP markers, located on chromosomes 2A and 4A, were found to be significantly associated with the resistance in both years. Three gene models associated with disease resistance and underlying these significant SNPs were identified. One immune Iranian genotype, with the highest number of different alleles from the most resistant Egyptian genotypes, was detected. CONCLUSION the high variation among the tested genotypes in their resistance to the Egyptian stripe rust race confirming the possible improvement of stripe rust resistance in the Egyptian wheat genotypes. The identified five SNP markers are stable and could be used in marker-assisted selection after validation in different genetic backgrounds. Crossing between the immune Iranian genotype and the Egyptian genotypes will improve stripe rust resistance in Egypt.
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Affiliation(s)
- Mohamed A. Abou-Zeid
- Wheat Disease Research Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Amira M. I. Mourad
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
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23
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Pradhan AK, Kumar S, Singh AK, Budhlakoti N, Mishra DC, Chauhan D, Mittal S, Grover M, Kumar S, Gangwar OP, Kumar S, Gupta A, Bhardwaj SC, Rai A, Singh K. Identification of QTLs/Defense Genes Effective at Seedling Stage Against Prevailing Races of Wheat Stripe Rust in India. Front Genet 2020; 11:572975. [PMID: 33329711 PMCID: PMC7728992 DOI: 10.3389/fgene.2020.572975] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
Resistance in modern wheat cultivars for stripe rust is not long lasting due to the narrow genetic base and periodical evolution of new pathogenic races. Though nearly 83 Yr genes conferring resistance to stripe rust have been cataloged so far, few of them have been mapped and utilized in breeding programs. Characterization of wheat germplasm for novel sources of resistance and their incorporation into elite cultivars is required to achieve durable resistance and thus to minimize the yield losses. Here, a genome-wide association study (GWAS) was performed on a set of 391 germplasm lines with the aim to identify quantitative trait loci (QTL) using 35K Axiom® array. Phenotypic evaluation disease severity against four stripe rust pathotypes, i.e., 46S119, 110S119, 238S119, and 47S103 (T) at the seedling stage in a greenhouse providing optimal conditions was carried out consecutively for 2 years (2018 and 2019 winter season). We identified, a total of 17 promising QTl which passed FDR criteria. Moreover these 17 QTL identified in the current study were mapped at different genomic locations i.e. 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5B and 6B. These 17 QTLs identified in the present study might play a key role in marker-assisted breeding for developing stripe rust resistant wheat cultivars.
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Affiliation(s)
- Anjan Kumar Pradhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Amit Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Neeraj Budhlakoti
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dwijesh C Mishra
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Divya Chauhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shikha Mittal
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Monendra Grover
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Suneel Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Om P Gangwar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Subodh Kumar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Arun Gupta
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Subhash C Bhardwaj
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Anil Rai
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kuldeep Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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24
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Jamil S, Shahzad R, Ahmad S, Fatima R, Zahid R, Anwar M, Iqbal MZ, Wang X. Role of Genetics, Genomics, and Breeding Approaches to Combat Stripe Rust of Wheat. Front Nutr 2020; 7:580715. [PMID: 33123549 PMCID: PMC7573350 DOI: 10.3389/fnut.2020.580715] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/19/2020] [Indexed: 02/01/2023] Open
Abstract
Puccinia striiformis (Pst) is a devastating biotrophic fungal pathogen that causes wheat stripe rust. It usually loves cool and moist places and can cause 100% crop yield losses in a single field when ideal conditions for disease incidence prevails. Billions of dollars are lost due to fungicide application to reduce stripe rust damage worldwide. Pst is a macrocyclic, heteroecious fungus that requires primary (wheat or grasses) as well as secondary host (Berberis or Mahonia spp.) for completion of life cycle. In this review, we have summarized the knowledge about pathogen life cycle, genes responsible for stripe rust resistance, and susceptibility in wheat. In the end, we discussed the importance of conventional and modern breeding tools for the development of Pst-resistant wheat varieties. According to our findings, genetic engineering and genome editing are less explored tools for the development of Pst-resistant wheat varieties; hence, we highlighted the putative use of advanced genome-modifying tools, i.e., base editing and prime editing, for the development of Pst-resistant wheat.
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Affiliation(s)
- Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Rida Fatima
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Rameesha Zahid
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Madiha Anwar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zaffar Iqbal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, China
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25
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Jia M, Yang L, Zhang W, Rosewarne G, Li J, Yang E, Chen L, Wang W, Liu Y, Tong H, He W, Zhang Y, Zhu Z, Gao C. Genome-wide association analysis of stripe rust resistance in modern Chinese wheat. BMC PLANT BIOLOGY 2020; 20:491. [PMID: 33109074 PMCID: PMC7590722 DOI: 10.1186/s12870-020-02693-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/12/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm. RESULTS Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation. CONCLUSION The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.
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Affiliation(s)
- Mengjie Jia
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lijun Yang
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58108-6050, USA
| | - Garry Rosewarne
- Department of Jobs, Precincts and Regions, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria, 3400, Australia
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico D.F., Mexico
| | - Junhui Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Enian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Ling Chen
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Wenxue Wang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Yike Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Hanwen Tong
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Weijie He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Yuqing Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Zhanwang Zhu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
| | - Chunbao Gao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze university, Jingzhou, 434025, China.
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