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Mohammadi M, Mohammadi R. Potential of tetraploid wheats in plant breeding: A review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112155. [PMID: 38885883 DOI: 10.1016/j.plantsci.2024.112155] [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: 03/22/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Domestication syndrome, selection pressure, and modern plant breeding programs have reduced the genetic diversity of the wheat germplasm. For the genetic gains of breeding programs to be sustainable, plant breeders require a diverse gene pool to select genes for resistance to biotic stress factors, tolerance to abiotic stress factors, and improved quality and yield components. Thus, old landraces, subspecies and wild ancestors are rich sources of genetic diversity that have not yet been fully exploited, and it is possible to utilize this diversity. Compared with durum wheat, tetraploid wheat subspecies have retained much greater genetic diversity despite genetic drift and various environmental influences, and the identification and utilization of this diversity can make a greater contribution to the genetic enrichment of wheat. In addition, using the pre-breeding method, the valuable left-behind alleles in the wheat gene pool can be re-introduced through hybridization and introgressive gene flow to create a sustainable opportunity for the genetic gain of wheat. This review provides some insights about the potential of tetraploid wheats in plant breeding and the genetic gains made by them in plant breeding across past decades, and gathers the known functional information on genes/QTLs, metabolites, traits and their direct involvement in wheat resistance/tolerance to biotic/abiotic stresses.
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Affiliation(s)
- Majid Mohammadi
- Dryland Agricultural Research Institute (DARI), Sararood branch, AREEO, Kermanshah, Iran.
| | - Reza Mohammadi
- Dryland Agricultural Research Institute (DARI), Sararood branch, AREEO, Kermanshah, Iran.
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Sharma D, Budhlakoti N, Kumari A, Saini DK, Sharma A, Yadav A, Mir RR, Singh AK, Vikas VK, Singh GP, Kumar S. Exploring the genetic architecture of powdery mildew resistance in wheat through QTL meta-analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1386494. [PMID: 39022610 PMCID: PMC11251950 DOI: 10.3389/fpls.2024.1386494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/11/2024] [Indexed: 07/20/2024]
Abstract
Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, poses a significant threat to wheat production, necessitating the development of genetically resistant varieties for long-term control. Therefore, exploring genetic architecture of PM in wheat to uncover important genomic regions is an important area of wheat research. In recent years, the utilization of meta-QTL (MQTL) analysis has gained prominence as an essential tool for unraveling the complex genetic architecture underlying complex quantitative traits. The aim of this research was to conduct a QTL meta-analysis to pinpoint the specific genomic regions in wheat responsible for governing PM resistance. This study integrated 222 QTLs from 33 linkage-based studies using a consensus map with 54,672 markers. The analysis revealed 39 MQTLs, refined to 9 high-confidence MQTLs (hcMQTLs) with confidence intervals of 0.49 to 12.94 cM. The MQTLs had an average physical interval of 41.00 Mb, ranging from 0.000048 Mb to 380.71 Mb per MQTL. Importantly, 18 MQTLs co-localized with known resistance genes like Pm2, Pm3, Pm8, Pm21, Pm38, and Pm41. The study identified 256 gene models within hcMQTLs, providing potential targets for marker-assisted breeding and genomic prediction programs to enhance PM resistance. These MQTLs would serve as a foundation for fine mapping, gene isolation, and functional genomics studies, facilitating a deeper understanding of molecular mechanisms. The identification of candidate genes opens up exciting possibilities for the development of PM-resistant wheat varieties after validation.
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Affiliation(s)
- Divya Sharma
- Divison of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Neeraj Budhlakoti
- Centre for Agriculture Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, Ludhiana, India
| | - Anshu Sharma
- Divison of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aakash Yadav
- Divison of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Reyazul Rouf Mir
- Department of Genetics and Plant Breeding , Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Amit Kumar Singh
- Divison of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - V. K. Vikas
- Divison of Crop Improvement, ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, Tamilnadu, India
| | - Gyanendra Pratap Singh
- Divison of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- Divison of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Kaur R, Vasistha NK, Ravat VK, Mishra VK, Sharma S, Joshi AK, Dhariwal R. Genome-Wide Association Study Reveals Novel Powdery Mildew Resistance Loci in Bread Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:3864. [PMID: 38005757 PMCID: PMC10675159 DOI: 10.3390/plants12223864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023]
Abstract
Powdery mildew (PM), caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), significantly threatens global bread wheat production. Although the use of resistant cultivars is an effective strategy for managing PM, currently available wheat cultivars lack sufficient levels of resistance. To tackle this challenge, we conducted a comprehensive genome-wide association study (GWAS) using a diverse panel of 286 bread wheat genotypes. Over three consecutive years (2020-2021, 2021-2022, and 2022-2023), these genotypes were extensively evaluated for PM severity under field conditions following inoculation with virulent Bgt isolates. The panel was previously genotyped using the Illumina 90K Infinium iSelect assay to obtain genome-wide single-nucleotide polymorphism (SNP) marker coverage. By applying FarmCPU, a multilocus mixed model, we identified a total of 113 marker-trait associations (MTAs) located on chromosomes 1A, 1B, 2B, 3A, 3B, 4A, 4B, 5A, 5B, 6B, 7A, and 7B at a significance level of p ≤ 0.001. Notably, four novel MTAs on chromosome 6B were consistently detected in 2020-2021 and 2021-2022. Furthermore, within the confidence intervals of the identified SNPs, we identified 96 candidate genes belonging to different proteins including 12 disease resistance/host-pathogen interaction-related protein families. Among these, protein kinases, leucine-rich repeats, and zinc finger proteins were of particular interest due to their potential roles in PM resistance. These identified loci can serve as targets for breeding programs aimed at developing disease-resistant wheat cultivars.
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Affiliation(s)
- Ramandeep Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Sigh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Sigh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Rono Hills, Itanagar 791112, India
| | - Vikas Kumar Ravat
- Department of Plant Pathology, Rajiv Gandhi University, Rono Hills, Itanagar 791112, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), NASC Complex, DPS Marg, New Delhi 110012, India
- International Maize and Wheat Improvement Center (CIMMYT) Regional Office, NASC Complex, DPS Marg, New Delhi 110012, India
| | - Raman Dhariwal
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, 5403 1 Avenue South, Lethbridge, AB T1J 4B1, Canada
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Singh J, Chhabra B, Raza A, Yang SH, Sandhu KS. Important wheat diseases in the US and their management in the 21st century. FRONTIERS IN PLANT SCIENCE 2023; 13:1010191. [PMID: 36714765 PMCID: PMC9877539 DOI: 10.3389/fpls.2022.1010191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/28/2022] [Indexed: 05/27/2023]
Abstract
Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.
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Affiliation(s)
- Jagdeep Singh
- Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Bhavit Chhabra
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Ali Raza
- College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Seung Hwan Yang
- Department of Integrative Biotechnology, Chonnam National University, Yeosu, Republic of Korea
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Nigro D, Blanco A, Piarulli L, Signorile MA, Colasuonno P, Blanco E, Simeone R. Fine Mapping and Candidate Gene Analysis of Pm36, a Wild Emmer-Derived Powdery Mildew Resistance Locus in Durum Wheat. Int J Mol Sci 2022; 23:ijms232113659. [PMID: 36362444 PMCID: PMC9657016 DOI: 10.3390/ijms232113659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region harboring the wild emmer PM resistance locus Pm36 and to identify candidate genes by exploiting the improved tetraploid wheat genomic resources. A set of backcross inbred lines (BILs) of durum wheat were genotyped with the SNP 25K chip array and comparison of the PM-resistant and susceptible lines defined a 1.5 cM region (physical interval of 1.08 Mb) harboring Pm36. The genetic map constructed with F2:3 progenies derived by crossing the PM resistant line 5BIL-42 and the durum parent Latino, restricted to 0.3 cM the genetic distance between Pm36 and the SNP marker IWB22904 (physical distance 0.515 Mb). The distribution of the marker interval including Pm36 in a tetraploid wheat collection indicated that the positive allele was largely present in the domesticated and wild emmer Triticum turgidum spp. dicoccum and ssp. dicoccoides. Ten high-confidence protein coding genes were identified in the Pm36 region of the emmer, durum and bread wheat reference genomes, while three added genes showed no homologous in the emmer genome. The tightly linked markers can be used for marker-assisted selection in wheat breeding programs, and as starting point for the Pm36 map-based cloning.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Correspondence: ; Tel.: +39-080-5442993
| | - Luciana Piarulli
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Massimo Antonio Signorile
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Pasqualina Colasuonno
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
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Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-Genomic Era. Int J Mol Sci 2022; 23:ijms23063273. [PMID: 35328694 PMCID: PMC8949510 DOI: 10.3390/ijms23063273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
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Hinterberger V, Douchkov D, Lück S, Kale S, Mascher M, Stein N, Reif JC, Schulthess AW. Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:836723. [PMID: 35300015 PMCID: PMC8922026 DOI: 10.3389/fpls.2022.836723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 05/02/2023]
Abstract
Genetic pathogen control is an economical and sustainable alternative to the use of chemicals. In order to breed resistant varieties, information about potentially unused genetic resistance mechanisms is of high value. We phenotyped 8,316 genotypes of the winter wheat collection of the German Federal ex situ gene bank for Agricultural and Horticultural Crops, Germany, for resistance to powdery mildew (PM), Blumeria graminis f. sp. tritici, one of the most important biotrophic pathogens in wheat. To achieve this, we used a semi-automatic phenotyping facility to perform high-throughput detached leaf assays. This data set, combined with genotyping-by-sequencing (GBS) marker data, was used to perform a genome-wide association study (GWAS). Alleles of significantly associated markers were compared with SNP profiles of 171 widely grown wheat varieties in Germany to identify currently unexploited resistance conferring genes. We also used the Chinese Spring reference genome annotation and various domain prediction algorithms to perform a domain enrichment analysis and produced a list of candidate genes for further investigation. We identified 51 significantly associated regions. In most of these, the susceptible allele was fixed in the tested commonly grown wheat varieties. Eleven of these were located on chromosomes for which no resistance conferring genes have been previously reported. In addition to enrichment of leucine-rich repeats (LRR), we saw enrichment of several domain types so far not reported as relevant to PM resistance, thus, indicating potentially novel candidate genes for the disease resistance research and prebreeding in wheat.
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Affiliation(s)
| | - Dimitar Douchkov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stefanie Lück
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sandip Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- *Correspondence: Albert W. Schulthess
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Alemu A, Brazauskas G, Gaikpa DS, Henriksson T, Islamov B, Jørgensen LN, Koppel M, Koppel R, Liatukas Ž, Svensson JT, Chawade A. Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat. Front Genet 2021; 12:661742. [PMID: 34054924 PMCID: PMC8149967 DOI: 10.3389/fgene.2021.661742] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/06/2021] [Indexed: 11/29/2022] Open
Abstract
Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53–0.75 and 0.36–0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Gintaras Brazauskas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kėdainiai, Lithuania
| | - David S Gaikpa
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | | | | | - Mati Koppel
- Estonian University of Life Sciences, Tartu, Estonia
| | - Reine Koppel
- Estonian Crop Research Institute, Jõgeva, Estonia
| | - Žilvinas Liatukas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kėdainiai, Lithuania
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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