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Golzar H, Shankar M, Sznajder B, Fox R, Reeves K, Mather DE. Genetic mapping of loci affecting seedling and adult-plant resistance to powdery mildew derived from two CIMMYT wheat lines. PLANTA 2024; 260:13. [PMID: 38809276 PMCID: PMC11136728 DOI: 10.1007/s00425-024-04444-9] [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: 12/12/2023] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
MAIN CONCLUSION PM3 and PM8 alleles carried by two CIMMYT wheat lines confer powdery mildew resistance in seedlings and/or adult plants. A stage-specific epistatic interaction was observed between PM3 and PM8. Powdery mildew is an important foliar disease of wheat. Major genes for resistance, which have been widely used in wheat breeding programs, are typically effective against only limited numbers of virulence genes of the pathogen. The main aim of this study was to map resistance loci in wheat lines 7HRWSN58 and ZWW09-149 from the International Maize and Wheat Improvement Center (CIMMYT). Doubled haploid populations (Magenta/7HRWSN58 and Emu Rock/ZWW09-149) were developed and grown in controlled environment experiments and inoculated with a composite of Blumeria graminis f.sp. tritici isolates that had been collected at various locations in Western Australia. Plants were assessed for powdery mildew symptoms (percentage leaf area diseased) on seedlings and adult plants. Populations were subjected to genotyping-by-sequencing and assayed for known SNPs in the resistance gene PM3. Linkage maps were constructed, and markers were anchored to the wheat reference genome sequence. In both populations, there were asymptomatic lines that exhibited no symptoms. Among symptomatic lines, disease severity varied widely. In the Magenta/7HRWSN58 population, most of the observed variation was attributed to the PM3 region of chromosome 1A, with the allele from 7HRWSN58 conferring resistance in seedlings and adult plants. In the Emu Rock/ZWW09-149 population, two interacting quantitative trait loci were mapped: one at PM3 and the other on chromosome 1B. The Emu Rock/ZWW09-149 population was confirmed to segregate for a 1BL·1RS translocation that carries the PM8 powdery mildew resistance gene from rye. Consistent with previous reports that PM8-derived resistance can be suppressed by PM3 alleles, the observed interaction between the quantitative trait loci on chromosomes 1A and 1B indicated that the PM3 allele carried by ZWW09-149 suppresses PM8-derived resistance from ZWW09-149, but only at the seedling stage. In adult plants, the PM8 region conferred resistance regardless of the PM3 genotype. The resistance sources and molecular markers that were investigated here could be useful in wheat breeding.
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Affiliation(s)
- Hossein Golzar
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA, 6151, Australia
| | - Manisha Shankar
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA, 6151, Australia.
- School of Agriculture and Environment, University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.
| | - Beata Sznajder
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Rebecca Fox
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Karyn Reeves
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA, 6151, Australia
| | - Diane E Mather
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
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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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3
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Heidari B, Nemie-Feyissa D, Lillo C. Distinct Clades of Protein Phosphatase 2A Regulatory B'/B56 Subunits Engage in Different Physiological Processes. Int J Mol Sci 2023; 24:12255. [PMID: 37569631 PMCID: PMC10418862 DOI: 10.3390/ijms241512255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is a strongly conserved and major protein phosphatase in all eukaryotes. The canonical PP2A complex consists of a catalytic (C), scaffolding (A), and regulatory (B) subunit. Plants have three groups of evolutionary distinct B subunits: B55, B' (B56), and B''. Here, the Arabidopsis B' group is reviewed and compared with other eukaryotes. Members of the B'α/B'β clade are especially important for chromatid cohesion, and dephosphorylation of transcription factors that mediate brassinosteroid (BR) signaling in the nucleus. Other B' subunits interact with proteins at the cell membrane to dampen BR signaling or harness immune responses. The transition from vegetative to reproductive phase is influenced differentially by distinct B' subunits; B'α and B'β being of little importance, whereas others (B'γ, B'ζ, B'η, B'θ, B'κ) promote transition to flowering. Interestingly, the latter B' subunits have three motifs in a conserved manner, i.e., two docking sites for protein phosphatase 1 (PP1), and a POLO consensus phosphorylation site between these motifs. This supports the view that a conserved PP1-PP2A dephosphorelay is important in a variety of signaling contexts throughout eukaryotes. A profound understanding of these regulators may help in designing future crops and understand environmental issues.
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Affiliation(s)
| | | | - Cathrine Lillo
- IKBM, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4036 Stavanger, Norway; (B.H.); (D.N.-F.)
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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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Zhao J, Sun L, Gao H, Hu M, Mu L, Cheng X, Wang J, Zhao Y, Li Q, Wang P, Li H, Zhang Y. Genome-wide association study of yield-related traits in common wheat ( Triticum aestivum L.) under normal and drought treatment conditions. FRONTIERS IN PLANT SCIENCE 2023; 13:1098560. [PMID: 36684753 PMCID: PMC9846334 DOI: 10.3389/fpls.2022.1098560] [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: 11/15/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The primary goal of modern wheat breeding is to develop new high-yielding and widely adaptable varieties. We analyzed four yield-related agronomic traits in 502 wheat accessions under normal conditions (NC) and drought treatment (DT) conditions over three years. The genome-wide association analysis identified 51 yield-related and nine drought-resistance-related QTL, including 13 for the thousand-grain weight (TGW), 30 for grain length (GL), three for grain width (GW), five for spike length (SL) and nine for stress tolerance index (STI) QTL in wheat. These QTL, containing 72 single nucleotide polymorphisms (SNPs), explained 2.23 - 7.35% of the phenotypic variation across multiple environments. Eight stable SNPs on chromosomes 2A, 2D, 3B, 4A, 5B, 5D, and 7D were associated with phenotypic stability under NC and DT conditions. Two of these stable SNPs had association with TGW and STI. Several novel QTL for TGW, GL and SL were identified on different chromosomes. Three linked SNPs were transformed into kompetitive allele-specific PCR (KASP) markers. These results will facilitate the discovery of promising SNPs for yield-related traits and/or drought stress tolerance and will accelerate the development of new wheat varieties with desirable alleles.
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Affiliation(s)
- Jie Zhao
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Lijing Sun
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Huimin Gao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Mengyun Hu
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Liming Mu
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Xiaohu Cheng
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Jianbing Wang
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Yun Zhao
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Qianying Li
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Peinan Wang
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Hui Li
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yingjun Zhang
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
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Xu L, Zhao C, Pang J, Niu Y, Liu H, Zhang W, Zhou M. Genome-wide association study reveals quantitative trait loci for waterlogging-triggered adventitious roots and aerenchyma formation in common wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1066752. [PMID: 36507408 PMCID: PMC9727299 DOI: 10.3389/fpls.2022.1066752] [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: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Waterlogging severely affects wheat growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of plants. The formation of adventitious roots (ARs) and root cortical aerenchyma (RCA) are the most important adaptive trait contributing to plants' ability to survive in waterlogged soil conditions. This study used a genome-wide association study (GWAS) approach with 90K single nucleotide polymorphisms (SNPs) in a panel of 329 wheat genotypes, to reveal quantitative trait loci (QTL) conferring ARs and RCA. The wheat genotypes exposed to waterlogging were evaluated for ARs and RCA in both field and glasshouse over two consecutive years. Six and five significant marker-trait associations (MTAs) were identified for ARs and RCA formation under waterlogging, respectively. The most significant MTA for AR and RCA was found on chromosome 4B. Two wheat cultivars with contrasting waterlogging tolerance (tolerant: H-242, sensitive: H-195) were chosen to compare the development and regulation of aerenchyma in waterlogged conditions using staining methods. Results showed that under waterlogging conditions, H2O2 signal generated before aerenchyma formation in both sensitive and tolerant varieties with the tolerant variety accumulating more H2O2 and in a quicker manner compared to the sensitive one. Several genotypes which performed consistently well under different conditions can be used in breeding programs to develop waterlogging-tolerant wheat varieties.
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Affiliation(s)
- Le Xu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS, Australia
| | - Jiayin Pang
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Yanan Niu
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS, Australia
| | - Huaqiong Liu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Wenying Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS, Australia
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7
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Zia MAB, Yousaf MF, Asim A, Naeem M. An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice). Mol Biol Rep 2022; 49:12077-12090. [DOI: 10.1007/s11033-022-08036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
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8
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Dong Y, Xu D, Xu X, Ren Y, Gao F, Song J, Jia A, Hao Y, He Z, Xia X. Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1083-1099. [PMID: 35006334 DOI: 10.1007/s00122-021-04019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
A stable QTL QPm.caas-3BS for adult-plant resistance to powdery mildew was mapped in an interval of 431 kb, and candidate genes were predicted based on gene sequences and expression profiles. Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91 Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3 cM interval flanked by KASP14800 and snp_50465, corresponding to a 431 kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene.
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Affiliation(s)
- Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xiaowan Xu
- College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yan Ren
- College of Agronomy, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, 450002, Henan, China
| | - Fengmei Gao
- Institute of Crop Germplasm Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Aolin Jia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Quamruzzaman M, Manik SMN, Shabala S, Cao F, Zhou M. Genome-wide association study reveals a genomic region on 5AL for salinity tolerance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:709-721. [PMID: 34797396 DOI: 10.1007/s00122-021-03996-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Soil salinity is a major threat to crop productivity and quality worldwide. In order to reduce the negative effects of salinity stress, it is important to understand the genetic basis of salinity tolerance. Identifying new salinity tolerance QTL or genes is crucial for breeders to pyramid different tolerance mechanisms to improve crop adaptability to salinity. Being one of the major cereal crops, wheat is known as a salt-sensitive glycophyte and subject to substantial yield losses when grown in the presence of salt. In this study, both pot and tank experiments were conducted to investigate the genotypic variation present in 328 wheat varieties in their salinity tolerance at the vegetative stage. A Genome-Wide Association Studies (GWAS) were carried out to identify QTL conferring salinity tolerance through a mixed linear model. Six, five and eight significant marker-trait associations (MTAs) were identified from pot experiments, tank experiments and average damage scores, respectively. These markers are located on the wheat chromosomes 1B, 2B, 2D, 3A, 4B, and 5A. These tolerance alleles were additive in their effects and, when combined, increased tolerance to salinity. Candidate genes identified in these QTL regions encoded a diverse class of proteins involved in salinity tolerance in plants. A Na+/H+ exchanger and a potassium transporter on chromosome 5A (IWB30519) will be of a potential value for improvement of salt tolerance of wheat cultivars using marker assisted selection programs. Some useful genotypes, which showed consistent tolerance in different trials, can also be effectively used in breeding programs.
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Affiliation(s)
- Md Quamruzzaman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | | | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Chancheng, China
| | - Fangbin Cao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia.
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China.
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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: 49] [Impact Index Per Article: 24.5] [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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Hyten DL. Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations. Methods Mol Biol 2022; 2481:29-42. [PMID: 35641757 DOI: 10.1007/978-1-0716-2237-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genome-wide association studies (GWAS) in crops requires genotyping platforms that are capable of producing accurate high density genotyping data on hundreds of plants in a cost-effective manner. Currently there are multiple commercial platforms available that are being effectively used across crops. These platforms include genotyping arrays such as the Illumina Infinium arrays and the Applied Biosystems Axiom Arrays along with a variety of resequencing methods. These methods are being used to genotype tens of thousands of markers up to millions of markers on GWAS panels. They are being used on crops with simple genomes to crops with very complex, large, polyploid genomes. Depending on the crop and the goal of the GWAS, there are several options and practical considerations to take into account when selecting a genotyping technology to ensure that the right coverage, accuracy, and cost for the study is achieved.
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Affiliation(s)
- David L Hyten
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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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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Mapping Powdery Mildew ( Blumeria graminis f. sp. tritici) Resistance in Wild and Cultivated Tetraploid Wheats. Int J Mol Sci 2020; 21:ijms21217910. [PMID: 33114422 PMCID: PMC7662567 DOI: 10.3390/ijms21217910] [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: 10/05/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/22/2023] Open
Abstract
Wheat is the most widely grown crop and represents the staple food for one third of the world’s population. Wheat is attacked by a large variety of pathogens and the use of resistant cultivars is an effective and environmentally safe strategy for controlling diseases and eliminating the use of fungicides. In this study, a collection of wild and cultivated tetraploid wheats (Triticum turgidum) were evaluated for seedling resistance (SR) and adult plant resistance (APR) to powdery mildew (Blumeria graminis) and genotyped with a 90K single nucleotide polymorphism (SNP) array to identify new sources of resistance genes. The genome-wide association mapping detected 18 quantitative trait loci (QTL) for APR and 8 QTL for SR, four of which were identical or at least closely linked to four QTL for APR. Thirteen candidate genes, containing nucleotide binding sites and leucine-rich repeats, were localized in the confidence intervals of the QTL-tagging SNPs. The marker IWB6155, associated to QPm.mgb-1AS, was located within the gene TRITD1Av1G004560 coding for a disease resistance protein. While most of the identified QTL were described previously, five QTL for APR (QPm.mgb-1AS, QPm.mgb-2BS, QPm.mgb-3BL.1, QPm.mgb-4BL, QPm.mgb-7BS.1) and three QTL for SR (QPm.mgb-3BL.3, QPm.mgb-5AL.2, QPm.mgb-7BS.2) were mapped on chromosome regions where no resistance gene was reported before. The novel QTL/genes can contribute to enriching the resistance sources available to breeders.
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Muhammad A, Hu W, Li Z, Li J, Xie G, Wang J, Wang L. Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS. Int J Mol Sci 2020; 21:ijms21165649. [PMID: 32781752 PMCID: PMC7460857 DOI: 10.3390/ijms21165649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.
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Affiliation(s)
- Ali Muhammad
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Weicheng Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Zhaoyang Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
| | - Lingqiang Wang
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
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