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Lhamo D, Sun Q, Friesen TL, Karmacharya A, Li X, Fiedler JD, Faris JD, Xia G, Luo M, Gu YQ, Liu Z, Xu SS. Association mapping of tan spot and septoria nodorum blotch resistance in cultivated emmer wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:193. [PMID: 39073628 DOI: 10.1007/s00122-024-04700-2] [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: 03/10/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024]
Abstract
KEY MESSAGE A total of 65 SNPs associated with resistance to tan spot and septoria nodorum blotch were identified in a panel of 180 cultivated emmer accessions through association mapping Tan spot and septoria nodorum blotch (SNB) are foliar diseases caused by the respective fungal pathogens Pyrenophora tritici-repentis and Parastagonospora nodorum that affect global wheat production. To find new sources of resistance, we evaluated a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for reactions to four P. tritici-repentis isolates Pti2, 86-124, 331-9 and DW5, two P. nodorum isolate, Sn4 and Sn2000, and four necrotrophic effectors (NEs) produced by the pathogens. About 8-36% of the accessions exhibited resistance to the four P. tritici-repentis isolates, with five accessions demonstrating resistance to all isolates. For SNB, 64% accessions showed resistance to Sn4, 43% to Sn2000 and 36% to both isolates, with Spain (11% accessions) as the most common origin of resistance. To understand the genetic basis of resistance, association mapping was performed using SNP (single nucleotide polymorphism) markers generated by genotype-by-sequencing and the 9 K SNP Infinium array. A total of 46 SNPs were significantly associated with tan spot and 19 SNPs with SNB resistance or susceptibility. Six trait loci on chromosome arms 1BL, 3BL, 4AL (2), 6BL and 7AL conferred resistance to two or more isolates. Known NE sensitivity genes for disease development were undetected except Snn5 for Sn2000, suggesting novel genetic factors are controlling host-pathogen interaction in cultivated emmer. The emmer accessions with the highest levels of resistance to the six pathogen isolates (e.g., CItr 14133-1, PI 94634-1 and PI 377672) could serve as donors for tan spot and SNB resistance in wheat breeding programs.
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Affiliation(s)
- Dhondup Lhamo
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA
| | - Qun Sun
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Timothy L Friesen
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Anil Karmacharya
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jason D Fiedler
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation Biology, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yong-Qiang Gu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.
| | - Steven S Xu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA.
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Wang W, Jin P, Zhang J, Tang Y, Zhao B, Yue W, Cheng P, Li Q, Wang B. Favorable Loci Identified for Stripe Rust Resistance in Chinese Winter Wheat Accessions via Genome-Wide Association Study. PLANT DISEASE 2024; 108:71-81. [PMID: 37467133 DOI: 10.1094/pdis-12-22-2842-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Stripe rust (or yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Currently, the utilization of resistant cultivars is the most viable way to reduce yield losses. In this study, a panel of 188 wheat accessions from China was evaluated for stripe rust resistance, and genome-wide association studies were performed using high-quality Diversity Arrays Technology markers. According to the phenotype and genotype data, a total of 26 significant marker-trait associations were identified, representing 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3A, 3B, 5A, 5B, 6B, 7B, and 7D. Of the 18 QTLs, almost all were associated with adult plant resistance (APR) except QYr.nwsuaf-6B.2, which was associated with all-stage resistance (also known as seedling resistance). Three of the 18 QTLs were mapped far from previously identified Pst resistance genes and QTLs and were considered potentially new loci. The other 15 QTLs were mapped close to known resistance genes and QTLs. Subsequent haplotype analysis for QYr.nwsuaf-2A and QYr.nwsuaf-7B.3 revealed the degrees of resistance of the panel in the APR stage. In summary, the favorable alleles identified in this study may be useful in breeding for disease resistance to stripe rust.
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Affiliation(s)
- Wenli Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengfei Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Chinese Jujube, School of Life Science, Yan'an University, Shaanxi 716000, China
| | - Jia Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaqi Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bingjie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weiyun Yue
- Tianshui Institute of Agricultural Science, Tianshui 741000, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Peters Haugrud AR, Shi G, Seneviratne S, Running KLD, Zhang Z, Singh G, Szabo-Hever A, Acharya K, Friesen TL, Liu Z, Faris JD. Genome-wide association mapping of resistance to the foliar diseases septoria nodorum blotch and tan spot in a global winter wheat collection. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:54. [PMID: 37337566 PMCID: PMC10276793 DOI: 10.1007/s11032-023-01400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Septoria nodorum blotch (SNB) and tan spot, caused by the necrotrophic fungal pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis, respectively, often occur together as a leaf spotting disease complex on wheat (Triticum aestivum L.). Both pathogens produce necrotrophic effectors (NEs) that contribute to the development of disease. Here, genome-wide association analysis of a diverse panel of 264 winter wheat lines revealed novel loci on chromosomes 5A and 5B associated with sensitivity to the NEs SnTox3 and SnTox5 in addition to the known sensitivity genes for NEs Ptr/SnToxA, SnTox1, SnTox3, and SnTox5. Sensitivity loci for SnTox267 and Ptr ToxB were not detected. Evaluation of the panel with five P. nodorum isolates for SNB development indicated the Snn3-SnTox3 and Tsn1-SnToxA interactions played significant roles in disease development along with additional QTL on chromosomes 2A and 2D, which may correspond to the Snn7-SnTox267 interaction. For tan spot, the Tsc1-Ptr ToxC interaction was associated with disease caused by two isolates, and a novel QTL on chromosome 7D was associated with a third isolate. The Tsn1-ToxA interaction was associated with SNB but not tan spot. Therefore some, but not all, of the previously characterized host gene-NE interactions in these pathosystems play significant roles in disease development in winter wheat. Based on these results, breeders should prioritize the selection of resistance alleles at the Tsc1, Tsn1, Snn3, and Snn7 loci as well as the 2A and 7D QTL to obtain good levels of resistance to SNB and tan spot in winter wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01400-5.
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Affiliation(s)
- Amanda R. Peters Haugrud
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102 USA
| | - Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | | | - Zengcui Zhang
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | - Agnes Szabo-Hever
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Krishna Acharya
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | - Timothy L. Friesen
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102 USA
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
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Gupta PK, Vasistha NK, Singh S, Joshi AK. Genetics and breeding for resistance against four leaf spot diseases in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1023824. [PMID: 37063191 PMCID: PMC10096043 DOI: 10.3389/fpls.2023.1023824] [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: 08/20/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Murdoch’s Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
| | - Neeraj Kumar Vasistha
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
| | - Sahadev Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
- The International Maize and Wheat Improvement Center (CIMMYT), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
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Taylor J, Jorgensen D, Moffat CS, Chalmers KJ, Fox R, Hollaway GJ, Cook MJ, Neate SM, See PT, Shankar M. An international wheat diversity panel reveals novel sources of genetic resistance to tan spot in Australia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:61. [PMID: 36912976 PMCID: PMC10011302 DOI: 10.1007/s00122-023-04332-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
KEY MESSAGE Novel sources of genetic resistance to tan spot in Australia have been discovered using one-step GWAS and genomic prediction models that accounts for additive and non-additive genetic variation. Tan spot is a foliar disease in wheat caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr) and has been reported to generate up to 50% yield losses under favourable disease conditions. Although farming management practices are available to reduce disease, the most economically sustainable approach is establishing genetic resistance through plant breeding. To further understand the genetic basis for disease resistance, we conducted a phenotypic and genetic analysis study using an international diversity panel of 192 wheat lines from the Maize and Wheat Improvement Centre (CIMMYT), the International Centre for Agriculture in the Dry Areas (ICARDA) and Australian (AUS) wheat research programmes. The panel was evaluated using Australian Ptr isolates in 12 experiments conducted in three Australian locations over two years, with assessment for tan spot symptoms at various plant development stages. Phenotypic modelling indicated high heritability for nearly all tan spot traits with ICARDA lines displaying the greatest average resistance. We then conducted a one-step whole-genome analysis of each trait using a high-density SNP array, revealing a large number of highly significant QTL exhibiting a distinct lack of repeatability across the traits. To better summarise the genetic resistance of the lines, a one-step genomic prediction of each tan spot trait was conducted by combining the additive and non-additive predicted genetic effects of the lines. This revealed multiple CIMMYT lines with broad genetic resistance across the developmental stages of the plant which can be utilised in Australian wheat breeding programmes to improve tan spot disease resistance.
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Affiliation(s)
- Julian Taylor
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia.
| | - Dorthe Jorgensen
- Department of Primary Industries and Regional Development, Agriculture and Food, 3 Baron Hay Ct, South Perth, WA, 6151, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Ken J Chalmers
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Rebecca Fox
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Grant J Hollaway
- Agriculture Victoria, Private Bag 260, Horsham, VIC, 3401, Australia
| | - Melissa J Cook
- Agriculture Victoria, Private Bag 260, Horsham, VIC, 3401, Australia
| | - Stephen M Neate
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Manisha Shankar
- Department of Primary Industries and Regional Development, Agriculture and Food, 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.
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Harnessing adult-plant resistance genes to deploy durable disease resistance in crops. Essays Biochem 2022; 66:571-580. [PMID: 35912968 PMCID: PMC9528086 DOI: 10.1042/ebc20210096] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022]
Abstract
Adult-plant resistance (APR) is a type of genetic resistance in cereals that is effective during the later growth stages and can protect plants from a range of disease-causing pathogens. Our understanding of the functions of APR-associated genes stems from the well-studied wheat-rust pathosystem. Genes conferring APR can offer pathogen-specific resistance or multi-pathogen resistance, whereby resistance is activated following a molecular recognition event. The breeding community prefers APR to other types of resistance because it offers broad-spectrum protection that has proven to be more durable. In practice, however, deployment of new cultivars incorporating APR is challenging because there is a lack of well-characterised APRs in elite germplasm and multiple loci must be combined to achieve high levels of resistance. Genebanks provide an excellent source of genetic diversity that can be used to diversify resistance factors, but introgression of novel alleles into elite germplasm is a lengthy and challenging process. To overcome this bottleneck, new tools in breeding for resistance must be integrated to fast-track the discovery, introgression and pyramiding of APR genes. This review highlights recent advances in understanding the functions of APR genes in the well-studied wheat-rust pathosystem, the opportunities to adopt APR genes in other crops and the technology that can speed up the utilisation of new sources of APR in genebank accessions.
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Jambuthenne DT, Riaz A, Athiyannan N, Alahmad S, Ng WL, Ziems L, Afanasenko O, Periyannan SK, Aitken E, Platz G, Godwin I, Voss-Fels KP, Dinglasan E, Hickey LT. Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1355-1373. [PMID: 35113190 PMCID: PMC9033734 DOI: 10.1007/s00122-022-04037-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.
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Affiliation(s)
- Dilani T Jambuthenne
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Naveenkumar Athiyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Wei Ling Ng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Laura Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Olga Afanasenko
- Department of Plant Resistance To Diseases, All Russian Research Institute for Plant Protection, St Petersburg, Russia, 196608
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Elizabeth Aitken
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
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Lozano-Ramírez N, Dreisigacker S, Sansaloni CP, He X, Islas SS, Pérez-Rodríguez P, Carballo AC, Nava-Díaz C, Kishii M, Singh PK. Genome-Wide Association Study for Resistance to Tan Spot in Synthetic Hexaploid Wheat. PLANTS (BASEL, SWITZERLAND) 2022; 11:433. [PMID: 35161413 PMCID: PMC8839754 DOI: 10.3390/plants11030433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Synthetic hexaploid wheat (SHW) has shown effective resistance to a diversity of diseases and insects, including tan spot, which is caused by Pyrenophora tritici-repentis, being an important foliar disease that can attack all types of wheat and several grasses. In this study, 443 SHW plants were evaluated for their resistance to tan spot under controlled environmental conditions. Additionally, a genome-wide association study was conducted by genotyping all entries with the DArTSeq technology to identify marker-trait associations for tan spot resistance. Of the 443 SHW plants, 233 showed resistant and 183 moderately resistant reactions, and only 27 were moderately susceptible or susceptible to tan spot. Durum wheat (DW) parents of the SHW showed moderately susceptible to susceptible reactions. A total of 30 significant marker-trait associations were found on chromosomes 1B (4 markers), 1D (1 marker), 2A (1 marker), 2D (2 markers), 3A (4 markers), 3D (3 markers), 4B (1 marker), 5A (4 markers), 6A (6 markers), 6B (1 marker) and 7D (3 markers). Increased resistance in the SHW in comparison to the DW parents, along with the significant association of resistance with the A and B genome, supported the concept of activating epistasis interaction across the three wheat genomes. Candidate genes coding for F-box and cytochrome P450 proteins that play significant roles in biotic stress resistance were identified for the significant markers. The identified resistant SHW lines can be deployed in wheat breeding for tan spot resistance.
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Affiliation(s)
- Nerida Lozano-Ramírez
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, El Batán, Texcoco 56237, Mexico; (N.L.-R.); (C.P.S.); (X.H.); (M.K.)
- Colegio de Postgraduados (COLPOS), Montecillo 56264, Mexico; (S.S.I.); (P.P.-R.); (A.C.C.); (C.N.-D.)
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, El Batán, Texcoco 56237, Mexico; (N.L.-R.); (C.P.S.); (X.H.); (M.K.)
| | - Carolina P. Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, El Batán, Texcoco 56237, Mexico; (N.L.-R.); (C.P.S.); (X.H.); (M.K.)
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, El Batán, Texcoco 56237, Mexico; (N.L.-R.); (C.P.S.); (X.H.); (M.K.)
| | - Sergio Sandoval Islas
- Colegio de Postgraduados (COLPOS), Montecillo 56264, Mexico; (S.S.I.); (P.P.-R.); (A.C.C.); (C.N.-D.)
| | - Paulino Pérez-Rodríguez
- Colegio de Postgraduados (COLPOS), Montecillo 56264, Mexico; (S.S.I.); (P.P.-R.); (A.C.C.); (C.N.-D.)
| | - Aquiles Carballo Carballo
- Colegio de Postgraduados (COLPOS), Montecillo 56264, Mexico; (S.S.I.); (P.P.-R.); (A.C.C.); (C.N.-D.)
| | - Cristian Nava-Díaz
- Colegio de Postgraduados (COLPOS), Montecillo 56264, Mexico; (S.S.I.); (P.P.-R.); (A.C.C.); (C.N.-D.)
| | - Masahiro Kishii
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, El Batán, Texcoco 56237, Mexico; (N.L.-R.); (C.P.S.); (X.H.); (M.K.)
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, El Batán, Texcoco 56237, Mexico; (N.L.-R.); (C.P.S.); (X.H.); (M.K.)
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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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10
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Dinglasan EG, Peressini T, Marathamuthu KA, See PT, Snyman L, Platz G, Godwin I, Voss-Fels KP, Moffat CS, Hickey LT. Genetic characterization of adult-plant resistance to tan spot (syn, yellow spot) in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2823-2839. [PMID: 34061222 DOI: 10.1007/s00122-021-03861-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
QTL mapping identified key genomic regions associated with adult-plant resistance to tan spot, which are effective even in the presence of the sensitivity gene Tsn1, thus serving as a new genetic solution to develop disease-resistant wheat cultivars. Improving resistance to tan spot (Pyrenophora tritici-repentis; Ptr) in wheat by eliminating race-specific susceptibility genes is a common breeding approach worldwide. The potential to exploit variation in quantitative forms of resistance, such as adult-plant resistance (APR), offers an alternative approach that could lead to broad-spectrum protection. We previously identified wheat landraces in the Vavilov diversity panel that exhibited high levels of APR despite carrying the sensitivity gene Tsn1. In this study, we characterised the genetic control of APR by developing a recombinant inbred line population fixed for Tsn1, but segregating for the APR trait. Linkage mapping using DArTseq markers and disease response phenotypes identified a QTL associated with APR to Ptr race 1 (producing Ptr ToxA- and Ptr ToxC) on chromosome 2B (Qts.313-2B), which was consistently detected in multiple adult-plant experiments. Additional loci were also detected on chromosomes 2A, 3D, 5A, 5D, 6A, 6B and 7A at the seedling stage, and on chromosomes 1A and 5B at the adult stage. We demonstrate that Qts.313-2B can be combined with other adult-plant QTL (i.e. Qts.313-1A and Qts.313-5B) to strengthen resistance levels. The APR QTL reported in this study provide a new genetic solution to tan spot in Australia and could be deployed in wheat cultivars, even in the presence of Tsn1, to decrease production losses and reduce the application of fungicides.
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Affiliation(s)
- Eric G Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Tamaya Peressini
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | | | - Pao Theen See
- Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia
| | - Lisle Snyman
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
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11
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Muqaddasi QH, Kamal R, Mirdita V, Rodemann B, Ganal MW, Reif JC, Röder MS. Genome-Wide Association Studies and Prediction of Tan Spot ( Pyrenophora tritici-repentis) Infection in European Winter Wheat via Different Marker Platforms. Genes (Basel) 2021; 12:genes12040490. [PMID: 33801723 PMCID: PMC8103242 DOI: 10.3390/genes12040490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/17/2021] [Accepted: 03/25/2021] [Indexed: 11/22/2022] Open
Abstract
Tan spot, caused by the fungus Pyrenophoratritici-repentis (Ptr), is a severe foliar disease of wheat (Triticumaestivum L.). Improving genetic resistance is a durable strategy to reduce Ptr-related losses. Here, we dissected Ptr-infection’s genetic basis in 372 European wheat varieties via simple sequence repeats (SSRs) plus 35k and 90k single nucleotide polymorphism (SNP) marker platforms. In our phenotypic data analyses, Ptr infection showed a significant genotypic variance and a significant negative correlation with plant height. Genome-wide association studies revealed a highly quantitative nature of Ptr infection and identified two quantitative trait loci (QTL), viz., QTs.ipk-7A and QTs.ipk-7B, which imparted 21.23 and 5.84% of the genotypic variance, respectively. Besides, the Rht-D1 gene showed a strong allelic influence on the infection scores. Due to the complex genetic nature of the Ptr infection, the potential of genome-wide prediction (GP) was assessed via three different genetic models on individual and combined marker platforms. The GP results indicated that the marker density and marker platforms do not considerably impact prediction accuracy (~40–42%) and that higher-order epistatic interactions may not be highly pervasive. Our results provide a further understanding of Ptr-infection’s genetic nature, serve as a resource for marker-assisted breeding, and highlight the potential of genome-wide selection for improved Ptr resistance.
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Affiliation(s)
- Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, D-06466 Stadt Seeland OT Gatersleben, Germany;
- Correspondence:
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
| | - Vilson Mirdita
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, D-06466 Stadt Seeland OT Gatersleben, Germany;
| | - Bernd Rodemann
- Julius-Kühn-Institute (JKI), D-38104 Braunschweig, Germany;
| | - Martin W. Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, D-06466 Stadt Seeland OT Gatersleben, Germany;
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
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12
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Yao F, Long L, Wang Y, Duan L, Zhao X, Jiang Y, Li H, Pu Z, Li W, Jiang Q, Wang J, Wei Y, Ma J, Kang H, Dai S, Qi P, Zheng Y, Chen X, Chen G. Population structure and genetic basis of the stripe rust resistance of 140 Chinese wheat landraces revealed by a genome-wide association study. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110688. [PMID: 33218646 DOI: 10.1016/j.plantsci.2020.110688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most devastating foliar diseases in wheat. Host resistance is the most effective strategy for the management of the disease. To screen for accessions with stable resistance and identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using a panel of 140 Chinese wheat landraces. The panel was evaluated for stripe rust response at the adult-plant stage at six field-year environments with mixed races and at the seedling stage with two separate predominant races of the pathogen, and genotyped with the genome-wide Diversity Arrays Technology markers. The panel displayed abundant phenotypic variation in stripe rust responses, with 9 landraces showing stable resistance to the mixture of Pst races at the adult-plant stage in the field and 10 landraces showing resistance to individual races at the seedling stage in the greenhouse. GWAS identified 12 quantitative trait loci (QTL) significantly (P ≤ 0.001) associated to stripe rust resistance using the field data of at least two environments and 18 QTL using the seedling data with two races. Among these QTL, 10 were presumably novel, including 4 for adult-plant resistance mapped to chromosomes 1B (QYrcl.sicau-1B.3), 4A (QYrcl.sicau-4A.3), 6A (QYrcl.sicau-6A.2) and 7B (QYrcl.sicau-7B.2) and 6 for all-stage resistance mapped to chromosomes 2D (QYrcl.sicau-2D.1), 3B (QYrcl.sicau-3B.3), 3D (QYrcl.sicau-3D), 4B (QYrcl.sicau-4B), 6A (QYrcl.sicau-6A.1) and 6D (QYrcl.sicau-6D). The landraces with stable resistance can be used for developing wheat cultivars with effective resistance to stripe rust.
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Affiliation(s)
- Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Luyao Duan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Xuyang Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Hao Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China.
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13
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Liu Y, Salsman E, Wang R, Galagedara N, Zhang Q, Fiedler JD, Liu Z, Xu S, Faris JD, Li X. Meta-QTL analysis of tan spot resistance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2363-2375. [PMID: 32436020 DOI: 10.1007/s00122-020-03604-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/09/2020] [Indexed: 05/20/2023]
Abstract
A total of 19 meta-QTL conferring resistance to tan spot were identified from 104 initial QTL detected in 15 previous QTL mapping studies. Tan spot, caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr), is a major foliar disease worldwide in both bread wheat and durum wheat and can reduce grain yield due to reduction in photosynthetic area of leaves. Developing and growing resistant cultivars is a cost-effective and environmentally friendly approach to mitigate negative effects of the disease. Understanding the genetic basis of tan spot resistance can enhance the development of resistant cultivars. With that goal, over 100 QTL associated with resistance to tan spot induced by a variety of Ptr races and isolates have been identified from previous QTL mapping studies. Meta-QTL analysis can identify redundant QTL among various studies and reveal major QTL for targeting in marker-assisted selection applications. In this study, we performed a meta-QTL analysis of tan spot resistance using the reported QTL from 15 previous QTL mapping studies. An integrated linkage map with a total length of 4080.5 cM containing 47,309 markers was assembled from 21 individual linkage maps and three previously published consensus maps. Nineteen meta-QTL were clustered from 104 initial QTL projected on the integrated map. Three of the 19 meta-QTL located on chromosomes 2A, 3B, and 5A show large genetic effects and confer resistance to multiple races in multiple bread wheat and durum wheat mapping populations. The integration of those race-nonspecific QTL is a promising strategy to provide high and stable resistance to tan spot in wheat.
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Affiliation(s)
- Yuan Liu
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Evan Salsman
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Runhao Wang
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Nelomie Galagedara
- Department of Plant Pathology, North Dakota State University, Fargo, 58108, USA
| | - Qijun Zhang
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Jason D Fiedler
- Biosciences Research Laboratory, USDA-ARS Genotyping Laboratory, Fargo, ND, 58102, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, 58108, USA
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Xuehui Li
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA.
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14
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Galagedara N, Liu Y, Fiedler J, Shi G, Chiao S, Xu SS, Faris JD, Li X, Liu Z. Genome-wide association mapping of tan spot resistance in a worldwide collection of durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2227-2237. [PMID: 32300825 DOI: 10.1007/s00122-020-03593-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Resistance to tan spot in durum wheat involves race-nonspecific QTL and necrotrophic insensitivity gene. Tan spot, caused by the necrotrophic fungus Pyrenophoratritici-repentis, is a major foliar disease on all cultivated wheat crops worldwide. Compared to common wheat, much less work has been done to investigate the genetic basis of tan spot resistance in durum. Here, we conducted disease evaluations, necrotrophic effector (NE) sensitivity assays and a genome-wide association study using a collection of durum accessions. The durum panel segregated for the reaction to disease inoculations and NE infiltrations with eighteen accessions being highly resistant to all races and most of them insensitive to both PtrToxA and PtrToxB. Over 65,000SNP markers were developed from genotyping-by-sequencing for the association mapping. As expected, sensitivity to PtrToxA and PtrToxB was mapped to the chromosome arms 5BL and 2BS, respectively. For the fungal inoculations, a quantitative trait locus (QTL) on chromosome 3B was associated with resistance to all races and likely corresponds to the race-nonspecific resistance QTL previously identified in common wheat. The Tsn1locus was not significantly associated with tan spot caused by the PtrToxA-producing isolates Pti2 and 86-124, but the Tsc2 locus was significantly associated with tan spot caused by the PtrToxB-producing isolate DW5. Another QTL on chromosome arm 1AS was associated with tan spot caused by the PtrToxC-producing isolate Pti2 and likely corresponds to the Tsc1 locus. Additional QTL for specific races was identified on chromosome 1B and 3B. Our work highlights the complexity of genetic resistance to tan spot and further confirms that the Ptr ToxA-Tsn1 interaction plays no significant role in disease development in tetraploid wheat.
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Affiliation(s)
- Nelomie Galagedara
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Yuan Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jason Fiedler
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Shiaoman Chiao
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Steven S Xu
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.
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15
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Liu Y, Zhang Q, Salsman E, Fiedler JD, Hegstad JB, Liu Z, Faris JD, Xu SS, Li X. QTL mapping of resistance to tan spot induced by race 2 of Pyrenophora tritici-repentis in tetraploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:433-442. [PMID: 31720702 DOI: 10.1007/s00122-019-03474-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/05/2019] [Indexed: 05/24/2023]
Abstract
A total of 12 QTL conferring resistance to tan spot induced by a race 2 isolate, 86-124, were identified in three tetraploid wheat mapping populations. Durum is a tetraploid species of wheat and an important food crop. Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is a major foliar disease of both tetraploid durum wheat and hexaploid bread wheat. Understanding the Ptr-wheat interaction and identifying major QTL can facilitate the development of resistant cultivars and effectively mitigate the negative effect of this disease. Over 100 QTL have already been discovered in hexaploid bread wheat, whereas few mapping studies have been conducted in durum wheat. Utilizing resistant resources and identifying novel resistant loci in tetraploid wheat will be beneficial for the development of tan spot-resistant durum varieties. In this study, we evaluated four interconnected tetraploid wheat populations for their reactions to the race 2 isolate 86-124, which produces Ptr ToxA. Tsn1, the wheat gene that confers sensitivity to Ptr ToxA, was not associated with tan spot severity in any of the four populations. We found a total of 12 tan spot-resistant QTL among the three mapping populations. The QTL located on chromosomes 3A and 5A were detected in multiple populations and co-localized with race-nonspecific QTL identified in other mapping studies. Together, these QTL can confer high levels of resistance and can be used for the improvement in tan spot resistance in both hexaploid bread and durum wheat breeding. Two QTL on chromosomes 1B and 7A, respectively, were found in one population when inoculated with a ToxA knockout strain 86-124ΔToxA only, indicating that their association with tan spot was induced by other unidentified necrotrophic effectors, but under the absence of Ptr ToxA. In addition to removal of the known dominant susceptibility genes, integrating major race-nonspecific resistance loci like the QTL identified on chromosome 3A and 5A in this study could confer high and stable tan spot resistance in durum wheat.
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Affiliation(s)
- Yuan Liu
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Qijun Zhang
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Evan Salsman
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Jason D Fiedler
- Biosciences Research Laboratory, USDA-ARS Genotyping Laboratory, Fargo, ND, 58102, USA
| | - Justin B Hegstad
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, 58108, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Northern Crop Science Laboratory, Fargo, ND, 58102, USA
| | - Steven S Xu
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Northern Crop Science Laboratory, Fargo, ND, 58102, USA
| | - Xuehui Li
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA.
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16
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Cheng Y, Li J, Yao F, Long L, Wang Y, Wu Y, Li J, Ye X, Wang J, Jiang Q, Kang H, Li W, Qi P, Liu Y, Deng M, Ma J, Jiang Y, Chen X, Zheng Y, Wei Y, Chen G. Dissection of loci conferring resistance to stripe rust in Chinese wheat landraces from the middle and lower reaches of the Yangtze River via genome-wide association study. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110204. [PMID: 31481207 DOI: 10.1016/j.plantsci.2019.110204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 05/13/2023]
Abstract
Stripe rust (Yr), caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a devastating foliar disease of wheat in China. Chinese wheat landraces originating from the middle and lower reaches of the Yangtze River are potential stripe-rust resistance resources. To identify APR genes for stripe-rust resistance, a panel of 188 accessions derived from the middle and lower reaches of the Yangtze River were inoculated with a mixture of Chinese P. striiformis f. sp. tritici races and resistance evaluated under field conditions in five environments at adult-plant stages. Seventy-three accessions showed degrees of stable resistance. Combining phenotypic datasets from multiple field experiments with high-quality Diversity Arrays Technology and simple sequence repeat markers, we detected 21 marker-trait associations spanning 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3B, 4A, 5A, 5B, 6B, and 6D, respectively. Single QTLs explained 9.67% to 16.14% of the observed phenotypic variation. Nine QTLs co-localized with previously reported Yr genes or genomic regions. The remaining QTLs were potential novel loci associated with adult-stage stripe-rust resistance. Two novel QTLs, QYr.sicau-3B.2 and QYr.sicau-5B.3, located on chromosomes 3B and 5B significantly explained 16.14% and 11.16% of the phenotypic variation, respectively. Haplotype analysis revealed that accessions carrying APR variants or their combinations showed enhanced degrees of resistance. The potentially novel loci or genomic regions associated with adult-stage resistance may be useful to improve stripe-rust resistance in current wheat cultivars and for future isolation of stripe-rust resistance genes.
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Affiliation(s)
- Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, USA; Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China.
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Parmley K, Nagasubramanian K, Sarkar S, Ganapathysubramanian B, Singh AK. Development of Optimized Phenomic Predictors for Efficient Plant Breeding Decisions Using Phenomic-Assisted Selection in Soybean. PLANT PHENOMICS (WASHINGTON, D.C.) 2019; 2019:5809404. [PMID: 33313530 PMCID: PMC7706298 DOI: 10.34133/2019/5809404] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/06/2019] [Indexed: 05/19/2023]
Abstract
The rate of advancement made in phenomic-assisted breeding methodologies has lagged those of genomic-assisted techniques, which is now a critical component of mainstream cultivar development pipelines. However, advancements made in phenotyping technologies have empowered plant scientists with affordable high-dimensional datasets to optimize the operational efficiencies of breeding programs. Phenomic and seed yield data was collected across six environments for a panel of 292 soybean accessions with varying genetic improvements. Random forest, a machine learning (ML) algorithm, was used to map complex relationships between phenomic traits and seed yield and prediction performance assessed using two cross-validation (CV) scenarios consistent with breeding challenges. To develop a prescriptive sensor package for future high-throughput phenotyping deployment to meet breeding objectives, feature importance in tandem with a genetic algorithm (GA) technique allowed selection of a subset of phenotypic traits, specifically optimal wavebands. The results illuminated the capability of fusing ML and optimization techniques to identify a suite of in-season phenomic traits that will allow breeding programs to decrease the dependence on resource-intensive end-season phenotyping (e.g., seed yield harvest). While we illustrate with soybean, this study establishes a template for deploying multitrait phenomic prediction that is easily amendable to any crop species and any breeding objective.
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Affiliation(s)
- Kyle Parmley
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
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