51
|
Monitoring Wheat Leaf Rust and Stripe Rust in Winter Wheat Using High-Resolution UAV-Based Red-Green-Blue Imagery. REMOTE SENSING 2020. [DOI: 10.3390/rs12223696] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
During the past decade, imagery data acquired from unmanned aerial vehicles (UAVs), thanks to their high spatial, spectral, and temporal resolutions, have attracted increasing attention for discriminating healthy from diseased plants and monitoring the progress of such plant diseases in fields. Despite the well-documented usage of UAV-based hyperspectral remote sensing for discriminating healthy and diseased plant areas, employing red-green-blue (RGB) imagery for a similar purpose has yet to be fully investigated. This study aims at evaluating UAV-based RGB imagery to discriminate healthy plants from those infected by stripe and wheat leaf rusts in winter wheat (Triticum aestivum L.), with a focus on implementing an expert system to assist growers in improved disease management. RGB images were acquired at four representative wheat-producing sites in the Grand Duchy of Luxembourg. Diseased leaf areas were determined based on the digital numbers (DNs) of green and red spectral bands for wheat stripe rust (WSR), and the combination of DNs of green, red, and blue spectral bands for wheat leaf rust (WLR). WSR and WLR caused alterations in the typical reflectance spectra of wheat plants between the green and red spectral channels. Overall, good agreements between UAV-based estimates and observations were found for canopy cover, WSR, and WLR severities, with statistically significant correlations (p-value (Kendall) < 0.0001). Correlation coefficients were 0.92, 0.96, and 0.86 for WSR severity, WLR severity, and canopy cover, respectively. While the estimation of canopy cover was most often less accurate (correlation coefficients < 0.20), WSR and WLR infected leaf areas were identified satisfactorily using the RGB imagery-derived indices during the critical period (i.e., stem elongation and booting stages) for efficacious fungicide application, while disease severities were also quantified accurately over the same period. Using such a UAV-based RGB imagery method for monitoring fungal foliar diseases throughout the cropping season can help to identify any new disease outbreak and efficaciously control its spread.
Collapse
|
52
|
Carmona M, Sautua F, Pérez-Hérnandez O, Reis EM. Role of Fungicide Applications on the Integrated Management of Wheat Stripe Rust. FRONTIERS IN PLANT SCIENCE 2020; 11:733. [PMID: 32582257 PMCID: PMC7296138 DOI: 10.3389/fpls.2020.00733] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/07/2020] [Indexed: 05/14/2023]
Abstract
First described in Europe in 1777, stripe rust (SR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss (Pst) is one of the most important and destructive diseases of wheat worldwide. Until 2000, SR was mainly endemic to cooler regions, but since then, new aggressive strains have emerged, spread intercontinentally, and caused severe epidemics in warmer regions across the world. This has put SR as a disease that poses a threat to the world food security. At present, the preferred strategy for control of SR is the access to wheat cultivars with adequate levels of SR resistance. However, wheat breeding programs are not sufficiently advanced to cope with the recently emerged Pst strains. Under this scenario, foliar fungicide applications have become an important component of SR management, but information on the effects of fungicide applications on SR control and wheat cultivar yield response is scarce. This review seeks to provide an overview of the impact and role of fungicides on SR management. With focus on wheat management in the major wheat-growing regions of the world, the review addresses: (a) the efficacy of different fungicide active ingredients, optimal fungicide timing and number of applications in controlling SR, and (b) the impact of fungicide on wheat grain yield response. Inclusion of fungicides in an integrated crop management approach is discussed.
Collapse
Affiliation(s)
- Marcelo Carmona
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Francisco Sautua
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Oscar Pérez-Hérnandez
- School of Agricultural Sciences, Northwest Missouri State University, Maryville, MO, United States
| | - Erlei M. Reis
- Escuela Para Graduados “Alberto Soriano”, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
53
|
Atta BM, Saleem M, Ali H, Bilal M, Fayyaz M. Application of Fluorescence Spectroscopy in Wheat Crop: Early Disease Detection and Associated Molecular Changes. J Fluoresc 2020; 30:801-810. [PMID: 32430862 DOI: 10.1007/s10895-020-02561-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/14/2020] [Indexed: 11/24/2022]
Abstract
The application of fluorescence spectroscopy combined with chemometrics was explored in the current study for the detection of stripe rust in wheat. The healthy and stripe rust leaves were collected from the disease screening nursery. The variations in the blue-green region and chlorophyll fluorescence intensity in leaves provides the basis for the detection of stripe rust infection. With the progress of disease, the variations in the synchronous fluorescence spectroscopy (SFS) spectrum was witnessed. SFS is an excellent tool for the simultaneous measurement of multiple compound samples, in case of plants it generates evidence regarding the occurrence of leaf fluorophore bands thus revealing the biochemical variations going on at different infection stages. Based on the results of the current study, it is inferred that p-coumaric acid has the highest intensity in healthy samples followed by the asymptomatic leaf samples, whereas the band intensity of α-tocopherol, sinapic acid, chlorogenic acid, ferulic acid, tannins, flavonoid, carotenoids and anthocyanins increases in the diseased and the asymptomatic samples accordingly to the rust infection. Principal component analysis (PCA) beautifully differentiated the healthy and the infected leaf samples. It is evident that the asymptomatic samples are grouped with the diseased samples or independently; indicating the start of disease infection, the decision that is hard to make with the visual assessments. The results of the current study suggest that the fluorescence emission and the SFS spectral signatures acquired for stripe rust could be utilized as fingerprints for early disease detection.
Collapse
Affiliation(s)
- Babar Manzoor Atta
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan.
| | - Muhammad Saleem
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - Hina Ali
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Bilal
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Fayyaz
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre (NARC), Park Road, Islamabad, 44000, Pakistan
| |
Collapse
|
54
|
Klymiuk V, Fatiukha A, Raats D, Bocharova V, Huang L, Feng L, Jaiwar S, Pozniak C, Coaker G, Dubcovsky J, Fahima T. Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2561-2572. [PMID: 31942623 PMCID: PMC7210774 DOI: 10.1093/jxb/eraa020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/12/2020] [Indexed: 05/21/2023]
Abstract
The wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303, and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and show here that these three resistance loci co-segregate in fine-mapping populations and share an identical full-length genomic sequence of functional Wtk1. Independent ethyl methanesulfonate (EMS)-mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303, and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303-, and YrH52-mediated resistances to yellow rust are encoded by a single locus, Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks.
Collapse
Affiliation(s)
- Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Dina Raats
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Valeria Bocharova
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lin Huang
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lihua Feng
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Samidha Jaiwar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Gitta Coaker
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Correspondence:
| |
Collapse
|
55
|
Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sørensen CK, Hovmøller MS, Rathjen JP, Justesen AF. Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. Genome Biol Evol 2020; 12:597-617. [PMID: 32271913 DOI: 10.1101/859728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 05/27/2023] Open
Abstract
Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
Collapse
Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Yan-Jun Chen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Richard Tien
- School of Dentistry, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Josef Korbinian Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Ramawatar Nagar
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, United Kingdom
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | | | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Annemarie Fejer Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| |
Collapse
|
56
|
Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sørensen CK, Hovmøller MS, Rathjen JP, Justesen AF. Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. Genome Biol Evol 2020; 12:597-617. [PMID: 32271913 PMCID: PMC7250506 DOI: 10.1093/gbe/evaa071] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
Collapse
Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Yan-Jun Chen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Richard Tien
- School of Dentistry, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Josef Korbinian Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Ramawatar Nagar
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, United Kingdom
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | | | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Annemarie Fejer Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| |
Collapse
|
57
|
Wang S, Li QP, Wang J, Yan Y, Zhang GL, Yan Y, Zhang H, Wu J, Chen F, Wang X, Kang Z, Dubcovsky J, Gou JY. YR36/WKS1-Mediated Phosphorylation of PsbO, an Extrinsic Member of Photosystem II, Inhibits Photosynthesis and Confers Stripe Rust Resistance in Wheat. MOLECULAR PLANT 2019; 12:1639-1650. [PMID: 31622682 DOI: 10.1016/j.molp.2019.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Wheat stripe rust, due to infection by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease that causes significant global grain yield losses. Yr36, which encodes Wheat Kinase START1 (WKS1), is an effective high-temperature adult-plant resistance gene and confers resistance to a broad spectrum of Pst races. We previously showed that WKS1 phosphorylates the thylakoid ascorbate peroxidase protein and reduces its ability to detoxify peroxides, which may contribute to the accumulation of reactive oxygen species (ROS). WKS1-mediated Pst resistance is accompanied by leaf chlorosis in Pst-infected regions, but the underlying mechanisms remain elusive. Here, we show that WKS1 interacts with and phosphorylates PsbO, an extrinsic member of photosystem II (PSII), to reduce photosynthesis, regulate leaf chlorosis, and confer Pst resistance. A point mutation in PsbO-A1 or reduction in its transcript levels by RNA interference resulted in chlorosis and reduced Pst sporulation. Biochemical analyses revealed that WKS1 phosphorylates PsbO at two conserved amino acids involved in physical interactions with PSII and reduces the binding affinity of PsbO with PSII. Presumably, phosphorylated PsbO proteins dissociate from the PSII complex and then undergo rapid degradation by cysteine and aspartic proteases. Taken together, these results demonstrate that perturbations of wheat PsbO by point mutation or phosphorylation by WKS1 reduce the rate of photosynthesis and delay the growth of Pst pathogen before the induction of ROS.
Collapse
Affiliation(s)
- Shuai Wang
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, MOE Engineering Research Center of Gene Technology, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiu-Ping Li
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, MOE Engineering Research Center of Gene Technology, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yan Yan
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, MOE Engineering Research Center of Gene Technology, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Guo-Liang Zhang
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, MOE Engineering Research Center of Gene Technology, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yan Yan
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, MOE Engineering Research Center of Gene Technology, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huifei Zhang
- State Key Laboratory of Crop Biology/College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology/College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Jin-Ying Gou
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, MOE Engineering Research Center of Gene Technology, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
58
|
Brar GS, Fetch T, McCallum BD, Hucl PJ, Kutcher HR. Virulence Dynamics and Breeding for Resistance to Stripe, Stem, and Leaf Rust in Canada Since 2000. PLANT DISEASE 2019; 103:2981-2995. [PMID: 31634033 DOI: 10.1094/pdis-04-19-0866-fe] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wheat (Triticum spp.) is a major field crop in Canada in terms of acreage, annual production, and export market value. There are nine classes of Canadian wheat based on growth habit (winter or spring), kernel hardness (hard or soft), seed coat color (red or white), and quality factors (grain protein content and gluten strength). Wheat was described by Newman in 1928 as "the economic fairy to the industrial and commercial life of Canada, having built practically the whole economic structure of the Prairie Provinces." Wheat production in Canada is affected by several biotic and abiotic stresses. The major abiotic stresses are frost damage, drought, and heat stress. Among biotic stresses, diseases caused by fungal pathogens are the most important although wheat streak mosaic virus (WSMV) has caused some localized outbreaks in some years. In context of cultivar registration in Canada, there are certain diseases that breeders have to take into account while developing resistant cultivars. The Prairie Recommending Committee for Wheat, Rye, and Triticale (PRCWRT) classify wheat diseases into priority one, priority two, and priority three depending on prevalence and potential damage they can cause. However, priority one diseases are more of a concern and a minimum level of resistance in commercial cultivars is recommended for those.
Collapse
Affiliation(s)
- Gurcharn S Brar
- Crop Development Centre/Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Thomas Fetch
- Agriculture and Agri-Food Canada - Brandon Research and Development Centre, Brandon, MB R7A 5Y3, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada - Morden Research and Development Centre, Morden, MB R3T 2M9, Canada
| | - Pierre J Hucl
- Crop Development Centre/Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Hadley R Kutcher
- Crop Development Centre/Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| |
Collapse
|
59
|
Elbasyoni IS, El-Orabey WM, Morsy S, Baenziger PS, Al Ajlouni Z, Dowikat I. Evaluation of a global spring wheat panel for stripe rust: Resistance loci validation and novel resources identification. PLoS One 2019; 14:e0222755. [PMID: 31721783 PMCID: PMC6853611 DOI: 10.1371/journal.pone.0222755] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/07/2019] [Indexed: 12/27/2022] Open
Abstract
Stripe rust (incited by Puccinia striiformis f. sp. tritici) is airborne wheat (Triticum aestivum L.) disease with dynamic virulence evolution. Thus, anticipatory and continued screening in hotspot regions is crucial to identify new pathotypes and integrate new resistance resources to prevent potential disease epidemics. A global wheat panel consisting of 882 landraces and 912 improved accessions was evaluated in two locations in Egypt during 2016 and 2017. Five prevalent and aggressive pathotypes of stripe rust were used to inoculate the accessions during the two growing seasons and two locations under field conditions. The objectives were to evaluate the panel for stripe rust resistance at the adult plant stage, identify potentially novel QTLs associated with stripe rust resistance, and validate previously reported stripe rust QTLs under the Egyptian conditions. The results indicated that 42 landraces and 140 improved accessions were resistant to stripe rust. Moreover, 24 SNPs were associated with stripe rust resistance and were within 18 wheat functional genes. Four of these genes were involved in several plant defense mechanisms. The number of favorable alleles, based upon the associated SNPs, was significant and negatively correlated with stripe rust resistance score, i.e., as the number of resistances alleles increased the observed resistance increased. In conclusion, generating new stripe rust phenotypic information on this panel while using the publicly available molecular marker data, contributed to identifying potentially novel QTLs associated with stripe rust and validated 17 of the previously reported QTLs in one of the global hotspots for stripe rust.
Collapse
Affiliation(s)
- Ibrahim S. Elbasyoni
- Crop Science Department, Damanhur University, Damanhur, Egypt
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States of America
| | - Walid M. El-Orabey
- Wheat Diseases Res. Department, Plant Pathology Res. Institute, ARC, Giza, Egypt
| | - Sabah Morsy
- Crop Science Department, Damanhur University, Damanhur, Egypt
| | - P. S. Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States of America
| | - Zakaria Al Ajlouni
- Jordan University of Science and Technology, Department of Plant Pathology, Irbid, Jordan
| | - Ismail Dowikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States of America
| |
Collapse
|
60
|
Ledesma-Ramírez L, Solís-Moya E, Iturriaga G, Sehgal D, Reyes-Valdes MH, Montero-Tavera V, Sansaloni CP, Burgueño J, Ortiz C, Aguirre-Mancilla CL, Ramírez-Pimentel JG, Vikram P, Singh S. GWAS to Identify Genetic Loci for Resistance to Yellow Rust in Wheat Pre-Breeding Lines Derived From Diverse Exotic Crosses. FRONTIERS IN PLANT SCIENCE 2019; 10:1390. [PMID: 31781137 PMCID: PMC6831551 DOI: 10.3389/fpls.2019.01390] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/08/2019] [Indexed: 05/05/2023]
Abstract
Yellow rust (YR) or stripe rust, caused by Puccinia striformis f. sp tritici Eriks (Pst), is a major challenge to resistance breeding in wheat. A genome wide association study (GWAS) was performed using 22,415 single nucleotide polymorphism (SNP) markers and 591 haplotypes to identify genomic regions associated with resistance to YR in a subset panel of 419 pre-breeding lines (PBLs) developed at International Center for Maize and Wheat Improvement (CIMMYT). The 419 PBLs were derived from an initial set of 984 PBLs generated by a three-way crossing scheme (exotic/elite1//elite2) among 25 best elites and 244 exotics (synthetics, landraces) from CIMMYT's germplasm bank. For the study, 419 PBLs were characterized with 22,415 high-quality DArTseq-SNPs and phenotyped for severity of YR disease at five locations in Mexico. A population structure was evident in the panel with three distinct subpopulations, and a genome-wide linkage disequilibrium (LD) decay of 2.5 cM was obtained. Across all five locations, 14 SNPs and 7 haplotype blocks were significantly (P < 0.001) associated with the disease severity explaining 6.0 to 14.1% and 7.9 to 19.9% of variation, respectively. Based on average LD decay of 2.5 cM, identified 14 SNP-trait associations were delimited to seven quantitative trait loci in total. Seven SNPs were part of the two haplotype blocks on chromosome 2A identified in haplotypes-based GWAS. In silico analysis of the identified SNPs showed hits with interesting candidate genes, which are related to pathogenic process or known to regulate induction of genes related to pathogenesis such as those coding for glunolactone oxidase, quinate O-hydroxycinnamoyl transferase, or two-component histidine kinase. The two-component histidine kinase, for example, acts as a sensor in the perception of phytohormones ethylene and cytokinin. Ethylene plays a very important role in regulation of multiple metabolic processes of plants, including induction of defense mechanisms mediated by jasmonate. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.
Collapse
Affiliation(s)
- Lourdes Ledesma-Ramírez
- Departamento de estudios e investigación de Posgrado, Tecnológico Nacional de México/Instituto Tecnológico de Roque, Celaya, Mexico
| | - Ernesto Solís-Moya
- Programa de mejoramiento genetico de trigo, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío, Celaya, Mexico
| | - Gabriel Iturriaga
- Departamento de estudios e investigación de Posgrado, Tecnológico Nacional de México/Instituto Tecnológico de Roque, Celaya, Mexico
| | - Deepmala Sehgal
- Department of Bioscience, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
| | | | - Víctor Montero-Tavera
- Programa de mejoramiento genetico de trigo, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío, Celaya, Mexico
| | - Carolina P. Sansaloni
- Department of Bioscience, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
| | - Juan Burgueño
- Department of Bioscience, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
| | - Cynthia Ortiz
- Department of Bioscience, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
| | - César L. Aguirre-Mancilla
- Departamento de estudios e investigación de Posgrado, Tecnológico Nacional de México/Instituto Tecnológico de Roque, Celaya, Mexico
| | - Juan G. Ramírez-Pimentel
- Departamento de estudios e investigación de Posgrado, Tecnológico Nacional de México/Instituto Tecnológico de Roque, Celaya, Mexico
| | - Prashant Vikram
- Department of Bioscience, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
| | - Sukhwinder Singh
- Department of Bioscience, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
- Department of Biotechnology, Geneshifters, Pullman, WA, United States
| |
Collapse
|
61
|
Khan MR, Rehman ZU, Nazir SN, Tshewang S, Baidya S, Hodson D, Imtiaz M, Ali S. Genetic Divergence and Diversity in Himalayan Puccinia striiformis Populations from Bhutan, Nepal, and Pakistan. PHYTOPATHOLOGY 2019; 109:1793-1800. [PMID: 31179857 DOI: 10.1094/phyto-01-19-0031-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The western Himalayan region in Pakistan has been shown to be the center of diversity of Puccinia striiformis; however, little is known about its genetic relations with the eastern part of the Himalayas. We studied the genetic structure of P. striiformis from Nepal (35 isolates) and Bhutan (31 isolates) in comparison with 81 Pakistani samples collected during 2015 and 2016, through microsatellite genotyping. Genetic analyses revealed a recombinant and highly diverse population structure in Pakistan, Bhutan, and Nepal. A high level of genotypic diversity (>0.90) was observed for the three countries of Pakistan (0.96), Bhutan (0.96), and Nepal (0.91) with the detection of 108 distinct multilocus genotypes (MLGs) in the overall population; 59 for Pakistan, 27 for Bhutan, and 26 for Nepal. Mean number of alleles per locus and gene diversity were higher in Nepal (3.19 and 0.458, respectively) than Bhutan (3.12 and 0.458, respectively). A nonsignificant difference between the observed and the expected heterozygosity in all populations further confirmed the recombinant structure. A clear population subdivision between the Himalayan region of Nepal, Bhutan, and Pakistan was evident, as revealed by FST values (ranging between 0.111 to 0.198), discriminant analysis of principal components, and resampling of MLGs. Limited gene flow could be present between Nepal and Bhutan, while the population from Pakistan was clearly distinct, and no divergence was present between two populations from Pakistan (Bajaur and Malakand). The overall high diversity and recombination signature suggested the potential role of recombination in the eastern Himalayan region (Nepal and Bhutan), which needs to be considered during host resistance deployment and in the context of aerial dispersal of the pathogen. Further surveillance should be made in the Himalayan region for disease management in the region and in the context of worldwide invasions.
Collapse
Affiliation(s)
- Muhammad Rameez Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Zia-Ur Rehman
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Sidra Noreen Nazir
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Sangay Tshewang
- Department of Agriculture, Ministry of Agriculture and Forests, Tsirang, Bhutan
| | - Suraj Baidya
- Plant Pathology Division, Nepal Agriculture Research Council, Nepal
| | - David Hodson
- International Maize and Wheat Improvement Center, CIMMYT, Mexico
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center, CIMMYT, Islamabad, Pakistan
| | - Sajid Ali
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| |
Collapse
|
62
|
Zhang C, Huang L, Zhang H, Hao Q, Lyu B, Wang M, Epstein L, Liu M, Kou C, Qi J, Chen F, Li M, Gao G, Ni F, Zhang L, Hao M, Wang J, Chen X, Luo MC, Zheng Y, Wu J, Liu D, Fu D. An ancestral NB-LRR with duplicated 3'UTRs confers stripe rust resistance in wheat and barley. Nat Commun 2019; 10:4023. [PMID: 31492844 PMCID: PMC6731223 DOI: 10.1038/s41467-019-11872-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/05/2019] [Indexed: 11/25/2022] Open
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a global threat to wheat production. Aegilops tauschii, one of the wheat progenitors, carries the YrAS2388 locus for resistance to Pst on chromosome 4DS. We reveal that YrAS2388 encodes a typical nucleotide oligomerization domain-like receptor (NLR). The Pst-resistant allele YrAS2388R has duplicated 3’ untranslated regions and is characterized by alternative splicing in the nucleotide-binding domain. Mutation of the YrAS2388R allele disrupts its resistance to Pst in synthetic hexaploid wheat; transgenic plants with YrAS2388R show resistance to eleven Pst races in common wheat and one race of P. striiformis f. sp. hordei in barley. The YrAS2388R allele occurs only in Ae. tauschii and the Ae. tauschii-derived synthetic wheat; it is absent in 100% (n = 461) of common wheat lines tested. The cloning of YrAS2388R will facilitate breeding for stripe rust resistance in wheat and other Triticeae species. Stripe rust is a serious threat to wheat production. Here, the authors reveal that the resistance gene, only present in the wheat progenitor Aegilops tauschii and its derived synthetic wheat, encodes a nucleotide oligomerization domain-like receptor and confers resistance in common wheat and barley.
Collapse
Affiliation(s)
- Chaozhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 271018, Tai'an, Shandong, China.,Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Huifei Zhang
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Qunqun Hao
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Bo Lyu
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Miao Liu
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Chunlan Kou
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Juan Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 271018, Tai'an, Shandong, China
| | - Fengjuan Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 271018, Tai'an, Shandong, China
| | - Mengkai Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 271018, Tai'an, Shandong, China
| | - Ge Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 271018, Tai'an, Shandong, China
| | - Fei Ni
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 271018, Tai'an, Shandong, China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 271018, Tai'an, Shandong, China.
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China. .,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.
| | - Daolin Fu
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA.
| |
Collapse
|
63
|
Cowger C, Brown JKM. Durability of Quantitative Resistance in Crops: Greater Than We Know? ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:253-277. [PMID: 31206351 DOI: 10.1146/annurev-phyto-082718-100016] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Quantitative resistance (QR) to crop diseases has usually been much more durable than major-gene, effector-triggered resistance. It has been observed that the effectiveness of some QR has eroded as pathogens adapt to it, especially when deployment is extensive and epidemics occur regularly, but it generally declines more slowly than effector-triggered resistance. Changes in aggressiveness and specificity of diverse pathogens on cultivars with QR have been recorded, along with experimental data on fitness costs of pathogen adaptation to QR, but there is little information about molecular mechanisms of adaptation. Some QR has correlated or antagonistic effects on multiple diseases. Longitudinal data on cultivars' disease ratings in trials over several years can be used to assess the significance of QR for durable resistance in crops. It is argued that published data likely underreport the durability of QR, owing to publication bias. The implications of research on QR for plant breeding are discussed.
Collapse
Affiliation(s)
- Christina Cowger
- USDA-ARS and North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - James K M Brown
- Department of Crop Genetics, John Innes Centre, Colney, Norwich NR4 7UK, United Kingdom;
| |
Collapse
|
64
|
Radhakrishnan GV, Cook NM, Bueno-Sancho V, Lewis CM, Persoons A, Mitiku AD, Heaton M, Davey PE, Abeyo B, Alemayehu Y, Badebo A, Barnett M, Bryant R, Chatelain J, Chen X, Dong S, Henriksson T, Holdgate S, Justesen AF, Kalous J, Kang Z, Laczny S, Legoff JP, Lesch D, Richards T, Randhawa HS, Thach T, Wang M, Hovmøller MS, Hodson DP, Saunders DGO. MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens. BMC Biol 2019; 17:65. [PMID: 31405370 PMCID: PMC6691556 DOI: 10.1186/s12915-019-0684-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/23/2019] [Indexed: 01/06/2023] Open
Abstract
Background Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. Results Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (Pst), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. Conclusions MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats. Electronic supplementary material The online version of this article (10.1186/s12915-019-0684-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Nicola M Cook
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Clare M Lewis
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | | | - Bekele Abeyo
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Yoseph Alemayehu
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Ayele Badebo
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Marla Barnett
- Limagrain Cereal Seeds, 2040 SE Frontage Road, Fort Collins, CO, 80525, USA
| | | | - Jeron Chatelain
- Limagrain Cereal Seeds, 2040 SE Frontage Road, Fort Collins, CO, 80525, USA
| | - Xianming Chen
- USDA-ARS and Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | | | | | | | | | - Jay Kalous
- Limagrain Cereal Seeds, 2040 SE Frontage Road, Fort Collins, CO, 80525, USA
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Szymon Laczny
- BASF Poland, Al. Jerozolimskie 142b, 02-305, Warsaw, Poland
| | | | | | - Tracy Richards
- Limagrain Cereal Seeds, 2040 SE Frontage Road, Fort Collins, CO, 80525, USA
| | - Harpinder S Randhawa
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Tine Thach
- Aarhus University Flakkebjerg, Slagelse, Denmark
| | - Meinan Wang
- USDA-ARS and Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | | | - David P Hodson
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | | |
Collapse
|
65
|
Smallholders' coping mechanisms with wheat rust epidemics: Lessons from Ethiopia. PLoS One 2019; 14:e0219327. [PMID: 31365535 PMCID: PMC6668782 DOI: 10.1371/journal.pone.0219327] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/20/2019] [Indexed: 11/19/2022] Open
Abstract
Crops are variously susceptible to biotic stresses-something expected to increase under climate change. In the case of staple crops, this potentially undermines household and national food security. We examine recent wheat rust epidemics and smallholders' coping mechanisms in Ethiopia as a case study. Wheat is a major food crop in Ethiopia widely grown by smallholders. In 2010/11 a yellow rust epidemic affected over one-third of the national wheat area. Two waves of nationally representative household level panel data collected for the preceding wheat season (2009/10) and three years after (2013/14) the occurrence of the epidemic allow us to analyze the different coping mechanisms farmers used in response. Apart from using fungicides as ex-post coping mechanism, increasing wheat area under yellow rust resistant varieties, increasing diversity of wheat varieties grown, or a combination of these strategies were the main ex-ante coping mechanisms farmers had taken in reducing the potential effects of rust re-occurrence. Large-scale dis-adoption of highly susceptible varieties and replacement with new, rust resistant varieties was observed subsequent to the 2010/11 epidemic. Multinomial logistic regression models were used to identify the key factors associated with smallholder ex-ante coping strategies. Household characteristics, level of specialization in wheat and access to improved wheat seed were the major factors that explained observed choices. There was 29-41% yield advantage in increasing wheat area to the new, resistant varieties even under normal seasons with minimum rust occurrence in the field. Continuous varietal development in responding to emerging new rust races and supporting the deployment of newly released resistant varieties could help smallholders in dealing with rust challenges and maintaining improved yields in the rust-prone environments of Ethiopia. Given the global importance of both wheat and yellow rust and climate change dynamics study findings have relevance to other regions.
Collapse
|
66
|
Genome-Wide Association Study for Multiple Biotic Stress Resistance in Synthetic Hexaploid Wheat. Int J Mol Sci 2019; 20:ijms20153667. [PMID: 31357467 PMCID: PMC6696463 DOI: 10.3390/ijms20153667] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/22/2022] Open
Abstract
Genetic resistance against biotic stress is a major goal in many wheat breeding programs. However, modern wheat cultivars have a limited genetic variation for disease and pest resistance and there is always a possibility of the evolution of new diseases and pests to overcome previously identified resistance genes. A total of 125 synthetic hexaploid wheats (SHWs; 2n = 6x = 42, AABBDD, Triticum aestivum L.) were characterized for resistance to fungal pathogens that cause wheat rusts (leaf; Puccinia triticina, stem; P. graminis f.sp. tritici, and stripe; P. striiformis f.sp. tritici) and crown rot (Fusarium spp.); cereal cyst nematode (Heterodera spp.); and Hessian fly (Mayetiola destructor). A wide range of genetic variation was observed among SHWs for multiple (two to five) biotic stresses and 17 SHWs that were resistant to more than two stresses. The genomic regions and potential candidate genes conferring resistance to these biotic stresses were identified from a genome-wide association study (GWAS). This GWAS study identified 124 significant marker-trait associations (MTAs) for multiple biotic stresses and 33 of these were found within genes. Furthermore, 16 of the 33 MTAs present within genes had annotations suggesting their potential role in disease resistance. These results will be valuable for pyramiding novel genes/genomic regions conferring resistance to multiple biotic stresses from SHWs into elite bread wheat cultivars and providing further insights on a wide range of stress resistance in wheat.
Collapse
|
67
|
Pretorius ZA, Booysen GJ, Boshoff WHP, Joubert JH, Maree GJ, Els J. Additive Manufacturing of Devices Used for Collection and Application of Cereal Rust Urediniospores. FRONTIERS IN PLANT SCIENCE 2019; 10:639. [PMID: 31156688 PMCID: PMC6530045 DOI: 10.3389/fpls.2019.00639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/29/2019] [Indexed: 06/01/2023]
Abstract
Optimized inoculation procedures are an important consideration in achieving repeatable plant infection when working with biotrophic rust fungi. Several plant pathology laboratories specializing in rust research employ a system where the collection and application of fungal spores are accomplished using an exchangeable gelatin capsule. Urediniospores are collected from erumpent pustules on plant surfaces into a capsule fitted to a cyclone collector controlled by a vacuum pump. By adding light mineral oil to the same capsule, the spore suspension is then sprayed onto plants by means of a dedicated atomizer (inoculator) connected to an air pressure source. Although devices are not commercially available, modern day technologies provide an opportunity to efficiently design and manufacture collectors and inoculators. Using a process called Additive Manufacturing (AM), also known as "3D printing," the bodies of a collector and inoculator were digitally designed and then laser-sintered in nylon. Depending on availability, copper or aluminum tubes were fitted to the bodies of both devices afterward to either facilitate directed collection of spores from rust pustules on plant surfaces or act as a siphon tube to deliver the spore suspension contained in the capsule. No statistical differences were found between AM and metal inoculators for spray delivery time or spore deposition per unit area. In replicated collection and inoculation tests of wheat seedlings with urediniospore bulks or single pustule collections of Puccinia triticina and P. graminis f. sp. tritici, the causal organisms of leaf rust and stem rust, consistent and satisfactory infection levels were achieved. Immersing used devices in acetone for 60 s followed by a 2 h heat treatment at 75°C produced no contaminant infection in follow-up tests.
Collapse
Affiliation(s)
| | - Gerrie J. Booysen
- Centre for Rapid Prototyping and Manufacturing, Central University of Technology, Bloemfontein, South Africa
| | - Willem H. P. Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Jozua H. Joubert
- Product Development Technology Station, Central University of Technology, Bloemfontein, South Africa
| | - Gerrie J. Maree
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Johan Els
- Centre for Rapid Prototyping and Manufacturing, Central University of Technology, Bloemfontein, South Africa
| |
Collapse
|
68
|
Knorr K, Jørgensen LN, Nicolaisen M. Fungicides have complex effects on the wheat phyllosphere mycobiome. PLoS One 2019; 14:e0213176. [PMID: 30893325 PMCID: PMC6426229 DOI: 10.1371/journal.pone.0213176] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/15/2019] [Indexed: 11/21/2022] Open
Abstract
Effects of fungicide treatments on non-target fungi in the phyllosphere are not well known. We studied community composition and dynamics of target (Puccinia striiformis) and non-target fungi in wheat that was heavily infected with yellow rust. Mycobiotas in bulk leaf samples and individual leaves were studied by metabarcoding targeting the internal transcribed spacer-1 (ITS1) region of the ribosomal DNA. The amount of yellow rust in individual samples was quantified by qPCR (quantitative PCR). In addition, septoria tritici blotch (Zymoseptoria tritici), powdery mildew (Blumeria graminis), tan spot (Pyrenophora tritici-repentis), and yellow rust (P. striiformis) were visually evaluated. We showed how fungal communities were affected by three different broad-spectrum fungicides that had been applied at different timings and doses to control Puccinia striiformis. We showed that fungal content was relatively constant even after fungicide treatments. Principal component analysis demonstrated that communities from fungicide-treated plots could be separated from the communities in non-treated plots. We observed effects of fungicide treatments on fungal communities using different dose, timing and products. Some fungi, including the target organism P. striiformis were effectively controlled by most of the fungicide applications whereas some yeasts and also P. tritici-repentis increased after treatments. We demonstrated the feasibility of using metabarcoding as a supplement to visual assessments of fungicide effects on target as well as non-target fungi.
Collapse
Affiliation(s)
- Kamilla Knorr
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
- * E-mail:
| |
Collapse
|
69
|
Zhang R, Singh RP, Lillemo M, He X, Randhawa MS, Huerta-Espino J, Singh PK, Li Z, Lan C. Two Main Stripe Rust Resistance Genes Identified in Synthetic-Derived Wheat Line Soru#1. PHYTOPATHOLOGY 2019; 109:120-126. [PMID: 30070970 DOI: 10.1094/phyto-04-18-0141-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Stripe rust is a major disease constraint of wheat production worldwide. Resistance to stripe rust was analyzed using 131 F6 recombinant inbred lines (RILs) derived from a cross between synthetic derived wheat line Soru#1 and wheat cultivar Naxos. The phenotype was evaluated in Mexico and Norway at both seedling and adult plant stages. Linkage groups were constructed based on 90K single-nucleotide polymorphism (SNP), sequence-tagged site, and simple sequence repeat markers. Two major resistance loci conferred by Soru#1 were detected and located on chromosomes 1BL and 4DS. The 1BL quantitative trait loci explained 15.8 to 40.2 and 51.1% of the phenotypic variation at adult plant and seedling stages, respectively. This locus was identified as Yr24/Yr26 based on the flanking markers and infection types. Locus 4DS was flanked by molecular markers D_GB5Y7FA02JMPQ0_238 and BS00108770_51. It explained 8.4 to 27.8 and 5.5% of stripe rust variation at the adult plant and seedling stages, respectively. The 4DS locus may correspond to known resistance gene Yr28 based on the resistance source. All RILs that combine Yr24/Yr26 and Yr28 showed significantly reduced stripe rust severity in all four environments compared with the lines with only one of the genes. SNP marker BS00108770_51 was converted into a breeder-friendly kompetitive allele-specific polymerase chain reaction marker that will be useful to accelerate Yr28 deployment in wheat breeding programs.
Collapse
Affiliation(s)
- Ruiqi Zhang
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Ravi P Singh
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Morten Lillemo
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Xinyao He
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Mandeep S Randhawa
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Julio Huerta-Espino
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Pawan K Singh
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Zhikang Li
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Caixia Lan
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| |
Collapse
|
70
|
Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T. Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun 2018; 9:3735. [PMID: 30282993 PMCID: PMC6170490 DOI: 10.1038/s41467-018-06138-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/26/2018] [Indexed: 01/11/2023] Open
Abstract
Yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease threatening much of global wheat production. Race-specific resistance (R)-genes are used to control rust diseases, but the rapid emergence of virulent Pst races has prompted the search for a more durable resistance. Here, we report the cloning of Yr15, a broad-spectrum R-gene derived from wild emmer wheat, which encodes a putative kinase-pseudokinase protein, designated as wheat tandem kinase 1, comprising a unique R-gene structure in wheat. The existence of a similar gene architecture in 92 putative proteins across the plant kingdom, including the barley RPG1 and a candidate for Ug8, suggests that they are members of a distinct family of plant proteins, termed here tandem kinase-pseudokinases (TKPs). The presence of kinase-pseudokinase structure in both plant TKPs and the animal Janus kinases sheds light on the molecular evolution of immune responses across these two kingdoms.
Collapse
Affiliation(s)
- Valentina Klymiuk
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Elitsur Yaniv
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Lin Huang
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Dina Raats
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Andrii Fatiukha
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Shisheng Chen
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Lihua Feng
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Gabriel Lidzbarsky
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Wei Chang
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Marko J Jääskeläinen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Christian Schudoma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Harbans Bariana
- The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Hanan Sela
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- The Institute for Cereal Crops Improvement, Tel Aviv University, P.O. Box 39040, 6139001, Tel Aviv, Israel
| | - Kamran Saleem
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | | | - Mogens S Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Assaf Distelfeld
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- School of Plant Sciences and Food Security, Tel Aviv University, P.O. Box 39040, 6139001, Tel Aviv, Israel
| | - Boulos Chalhoub
- Institute of System and Synthetic Biology-Organization and Evolution of Complex Genomes, 2 rue Gaston Crémieux CP 5708, 91057, Evry Cedex, France
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, 20815, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Alan H Schulman
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790, Helsinki, Finland
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.
| |
Collapse
|
71
|
Brar GS, Ali S, Qutob D, Ambrose S, Lou K, Maclachlan R, Pozniak CJ, Fu YB, Sharpe AG, Kutcher HR. Genome re-sequencing and simple sequence repeat markers reveal the existence of divergent lineages in the Canadian Puccinia striiformis
f. sp. tritici
population with extensive DNA methylation. Environ Microbiol 2018; 20:1498-1515. [DOI: 10.1111/1462-2920.14067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Gurcharn S. Brar
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Sajid Ali
- Institute of Biotechnology and Genetic Engineering; University of Agriculture; Peshawar Pakistan
| | - Dinah Qutob
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Stephen Ambrose
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Kun Lou
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Ron Maclachlan
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Curtis J. Pozniak
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Agriculture & Agri-Food Canada- Saskatoon Research and Development Centre, 107 Science Place; Saskatoon SK S7N 0X2 Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Hadley R. Kutcher
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| |
Collapse
|
72
|
Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. mBio 2018; 9:e02275-17. [PMID: 29463659 PMCID: PMC5821087 DOI: 10.1128/mbio.02275-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
Collapse
Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - William S Cuddy
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Diana P Garnica
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
| | - John P Rathjen
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| |
Collapse
|
73
|
Ali S, Hodson D. Wheat Rust Surveillance: Field Disease Scoring and Sample Collection for Phenotyping and Molecular Genotyping. Methods Mol Biol 2017; 1659:3-11. [PMID: 28856636 DOI: 10.1007/978-1-4939-7249-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Long-distance migration capacity, emergence of invasive lineages, and variability in adaptation to a wide range of climatic conditions make wheat rusts the most important threat to wheat production worldwide. Efficient and coordinated efforts are required for surveillance of the pathogen population at different geographical levels to enable tracking of rust pathogen populations at local, regional, continental, and ultimately worldwide scale. Here we describe a standard procedure for rust surveillance to enable comparison across various research groups for a final compilation. The procedure described would enable tracking of disease severity, field level expression of host resistance, and collection of samples for further virulence phenotyping and molecular genotyping.
Collapse
Affiliation(s)
- Sajid Ali
- Institute of Biotechnology & Genetic Engineering, University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.
| | - David Hodson
- ILRI/CIMMYT, P.O. Box 5689, Addis Ababa, Ethiopia.
| |
Collapse
|
74
|
Ali S, Khan MR, Gautier A, Swati ZA, Walter S. Microsatellite Genotyping of the Wheat Yellow Rust Pathogen Puccinia striiformis. Methods Mol Biol 2017; 1659:59-70. [PMID: 28856641 DOI: 10.1007/978-1-4939-7249-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To combat the ever-increasing threat of wheat yellow rust worldwide, understanding of the pathogen (Puccinia striiformis) population biology is indispensable. Molecular markers, particularly microsatellites, have been reported to be important tools for deciphering pathogen population structure, invasion sources, and migration history. The utility of these DNA-based markers and sequencing has been increased by the direct DNA extraction from infected leaves with subsequent multiplex-based SSR genotyping. In this chapter we describe the protocol for direct DNA extraction and its genotyping with microsatellite markers in multiplex reactions. We describe the procedure for allele scoring, and various troubles faced during microsatellite scoring and potential solutions for them.
Collapse
Affiliation(s)
- Sajid Ali
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.
| | - Muhammad R Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Angelique Gautier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Zahoor A Swati
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | | |
Collapse
|