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Starosta E, Jamruszka T, Szwarc J, Bocianowski J, Jędryczka M, Grynia M, Niemann J. DArTseq-Based, High-Throughput Identification of Novel Molecular Markers for the Detection of Blackleg ( Leptosphaeria Spp.) Resistance in Rapeseed. Int J Mol Sci 2024; 25:8415. [PMID: 39125985 PMCID: PMC11313370 DOI: 10.3390/ijms25158415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/19/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Blackleg disease, caused by Leptosphaeria spp. fungi, is one of the most important diseases of Brassica napus, responsible for severe yield losses worldwide. Blackleg resistance is controlled by major R genes and minor quantitative trait loci (QTL). Due to the high adaptation ability of the pathogen, R-mediated resistance can be easily broken, while the resistance mediated via QTL is believed to be more durable. Thus, the identification of novel molecular markers linked to blackleg resistance for B. napus breeding programs is essential. In this study, 183 doubled haploid (DH) rapeseed lines were assessed in field conditions for resistance to Leptosphaeria spp. Subsequently, DArTseq-based Genome-Wide Association Study (GWAS) was performed to identify molecular markers linked to blackleg resistance. A total of 133,764 markers (96,121 SilicoDArT and 37,643 SNP) were obtained. Finally, nine SilicoDArT and six SNP molecular markers were associated with plant resistance to Leptosphaeria spp. at the highest significance level, p < 0.001. Importantly, eleven of these fifteen markers were found within ten genes located on chromosomes A06, A07, A08, C02, C03, C06 and C08. Given the immune-related functions of the orthologues of these genes in Arabidopsis thaliana, the identified markers hold great promise for application in rapeseed breeding programs.
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Affiliation(s)
- Ewa Starosta
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (E.S.); (T.J.); (J.S.)
| | - Tomasz Jamruszka
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (E.S.); (T.J.); (J.S.)
| | - Justyna Szwarc
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (E.S.); (T.J.); (J.S.)
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-627 Poznań, Poland;
| | - Małgorzata Jędryczka
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | - Magdalena Grynia
- IHAR Group, Borowo Department, Strzelce Plant Breeding Ltd., Borowo 35, 64-020 Czempiń, Poland;
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (E.S.); (T.J.); (J.S.)
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Vasquez-Teuber P, Rouxel T, Mason AS, Soyer JL. Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:192. [PMID: 39052130 PMCID: PMC11272824 DOI: 10.1007/s00122-024-04641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/29/2024] [Indexed: 07/27/2024]
Abstract
Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.
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Affiliation(s)
- Paula Vasquez-Teuber
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez 595, Chillán, Chile
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France.
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Cantila AY, Thomas WJ, Saad NSM, Severn-Ellis AA, Anderson R, Bayer PE, Edwards D, Van de Wouw AP, Batley J. Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1051994. [PMID: 36866377 PMCID: PMC9971972 DOI: 10.3389/fpls.2023.1051994] [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: 09/23/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Utilising resistance (R) genes, such as LepR1, against Leptosphaeria maculans, the causal agent of blackleg in canola (Brassica napus), could help manage the disease in the field and increase crop yield. Here we present a genome wide association study (GWAS) in B. napus to identify LepR1 candidate genes. Disease phenotyping of 104 B. napus genotypes revealed 30 resistant and 74 susceptible lines. Whole genome re-sequencing of these cultivars yielded over 3 million high quality single nucleotide polymorphisms (SNPs). GWAS in mixed linear model (MLM) revealed a total of 2,166 significant SNPs associated with LepR1 resistance. Of these SNPs, 2108 (97%) were found on chromosome A02 of B. napus cv. Darmor bzh v9 with a delineated LepR1_mlm1 QTL at 15.11-26.08 Mb. In LepR1_mlm1, there are 30 resistance gene analogs (RGAs) (13 nucleotide-binding site-leucine rich repeats (NLRs), 12 receptor-like kinases (RLKs), and 5 transmembrane-coiled-coil (TM-CCs)). Sequence analysis of alleles in resistant and susceptible lines was undertaken to identify candidate genes. This research provides insights into blackleg resistance in B. napus and assists identification of the functional LepR1 blackleg resistance gene.
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Affiliation(s)
- Aldrin Y. Cantila
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - William J.W. Thomas
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Nur Shuhadah Mohd Saad
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Anita A. Severn-Ellis
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Robyn Anderson
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Philipp E. Bayer
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | | | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
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Borhan MH, Van de Wouw AP, Larkan NJ. Molecular Interactions Between Leptosphaeria maculans and Brassica Species. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:237-257. [PMID: 35576591 DOI: 10.1146/annurev-phyto-021621-120602] [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: 06/15/2023]
Abstract
Canola is an important oilseed crop, providing food, feed, and fuel around the world. However, blackleg disease, caused by the ascomycete Leptosphaeria maculans, causes significant yield losses annually. With the recent advances in genomic technologies, the understanding of the Brassica napus-L. maculans interaction has rapidly increased, with numerous Avr and R genes cloned, setting this system up as a model organism for studying plant-pathogen associations. Although the B. napus-L. maculans interaction follows Flor's gene-for-gene hypothesis for qualitative resistance, it also puts some unique spins on the interaction. This review discusses the current status of the host-pathogen interaction and highlights some of the future gaps that need addressing moving forward.
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Affiliation(s)
- M Hossein Borhan
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada;
| | | | - Nicholas J Larkan
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada;
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Jiquel A, Gay EJ, Mas J, George P, Wagner A, Fior A, Faure S, Balesdent M, Rouxel T. "Late" effectors from Leptosphaeria maculans as tools for identifying novel sources of resistance in Brassica napus. PLANT DIRECT 2022; 6:e435. [PMID: 35949954 PMCID: PMC9356234 DOI: 10.1002/pld3.435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The Dothideomycete Leptosphaeria maculans, causing stem canker (blackleg) of Brassica napus, secretes different cocktails of effectors at specific infection stages. Some effectors ("Late" effectors) are specifically produced during the long asymptomatic phase of stem colonization. By manipulating their expression so that they are overexpressed during cotyledon infection (OEC transformants of the fungus), we previously postulated that resistance genes operating in the stem may be involved in gene-for-gene relationship and thus contribute to quantitative disease resistance (QDR). Here, we selected 10 relevant new effector genes, and we generated OEC transformants to screen a collection of 130 B. napus genotypes, representative of the available diversity in the species. Five B. napus accessions showed a typical hypersensitive response when challenged with effectors LmSTEE98 or LmSTEE6826 at the cotyledon stage, and all belong to the semi-winter type of the diversity panel. In addition, five winter-type genotypes displayed an intermediate response to another late effector, LmSTEE7919. These new interactions now have to be genetically validated to check that they also correspond to gene-for-gene interactions. In all cases, they potentially provide novel resources, easy to breed for, and accounting for part of the quantitative resistance in a species for which we are currently facing limited resistance sources.
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Affiliation(s)
- Audren Jiquel
- INRAE, AgroParisTech, UR BIOGERUniversité Paris‐SaclayThiverval‐GrignonFrance
- Lidea SemencesMondonvilleFrance
| | - Elise J. Gay
- INRAE, AgroParisTech, UR BIOGERUniversité Paris‐SaclayThiverval‐GrignonFrance
| | | | | | | | | | | | | | - Thierry Rouxel
- INRAE, AgroParisTech, UR BIOGERUniversité Paris‐SaclayThiverval‐GrignonFrance
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Inturrisi F, Bayer PE, Cantila AY, Tirnaz S, Edwards D, Batley J. In silico integration of disease resistance QTL, genes and markers with the Brassica juncea physical map. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:37. [PMID: 37309382 PMCID: PMC10248627 DOI: 10.1007/s11032-022-01309-5] [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: 12/30/2021] [Accepted: 06/09/2022] [Indexed: 06/14/2023]
Abstract
Brassica juncea (AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences for B. juncea has made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be identified by co-localization with genetically mapped disease resistance quantitative trait loci (QTL). Here we identify and characterise disease resistance gene analogs (RGAs), including nucleotide-binding site-leucine-rich repeat (NLR), receptor-like kinase (RLK) and receptor-like protein (RLP) classes, and investigate their association with disease resistance QTL intervals. The molecular genetic marker sequences for four white rust (Albugo candida) disease resistance QTL, six blackleg (Leptosphaeria maculans) disease resistance QTL and BjCHI1, a gene cloned from B. juncea for hypocotyl rot disease, were extracted from previously published studies and used to compare with candidate RGAs. Our results highlight the complications for the identification of functional resistance genes, including the duplicated appearance of genetic markers for several resistance loci, including Ac2(t), AcB1-A4.1, AcB1-A5.1, Rlm6 and PhR2 in both the A and B genomes, due to the presence of homoeologous regions. Furthermore, the white rust loci, Ac2(t) and AcB1-A4.1, mapped to the same position on chromosome A04 and may be different alleles of the same gene. Despite these challenges, a total of nine candidate genomic regions hosting 14 RLPs, 28 NLRs and 115 RLKs were identified. This study facilitates the mapping and cloning of functional resistance genes for applications in crop improvement programs. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01309-5.
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Affiliation(s)
- Fabian Inturrisi
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Aldrin Y. Cantila
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
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Frąc M, Kaczmarek J, Jędryczka M. Metabolic Capacity Differentiates Plenodomus lingam from P. biglobosus Subclade 'brassicae', the Causal Agents of Phoma Leaf Spotting and Stem Canker of Oilseed Rape ( Brassica napus) in Agricultural Ecosystems. Pathogens 2022; 11:pathogens11010050. [PMID: 35055998 PMCID: PMC8778923 DOI: 10.3390/pathogens11010050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
In contrast to the long-lasting taxonomic classification of Plenodomus lingam and P. biglobosus as one species, formerly termed Leptosphaeria maculans, both species form separate monophyletic groups, comprising sub-classes, differing considerably with epidemiology towards Brassicaceae plants. Considering the great differences between P. lingam and P. biglobosus, we hypothesized their metabolic capacities vary to a great extent. The experiment was done using the FF microplates (Biolog Inc., Hayward, CA, USA) containing 95 carbon sources and tetrazolium dye. The fungi P. lingam and P. biglobosus subclade 'brassicae' (3 isolates per group) were cultured on PDA medium for 6 weeks at 20 °C and then fungal spores were used as inoculum of microplates. The test was carried out in triplicate. We have demonstrated that substrate richness, calculated as the number of utilized substrates (measured at λ490 nm), and the number of substrates allowing effective growth of the isolates (λ750 nm), showed significant differences among tested species. The most efficient isolate of P. lingam utilized 36 carbon sources, whereas P. biglobosus utilized 60 substrates. Among them, 25-29 carbon sources for P. lingam and 34-48 substrates for P. biglobosus were efficiently used, allowing their growth. Cluster analysis based on Senath criteria divided P. biglobosus into two groups and P. lingam isolates formed one group (33% similarity). We deduce the similarities between the tested species help them coexist on the same host plant and the differences greatly contribute to their different lifestyles, with P. biglobosus being less specialized and P. lingam coevolving more strictly with the host plant.
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Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland;
| | - Joanna Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | - Małgorzata Jędryczka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
- Correspondence:
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Schnippenkoetter W, Hoque M, Maher R, Van de Wouw A, Hands P, Rolland V, Barrett L, Sprague S. Comparison of non-subjective relative fungal biomass measurements to quantify the Leptosphaeria maculans-Brassica napus interaction. PLANT METHODS 2021; 17:122. [PMID: 34852830 PMCID: PMC8638343 DOI: 10.1186/s13007-021-00822-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/17/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, is a serious threat to canola (Brassica napus) production worldwide. Quantitative resistance to this disease is a highly desirable trait but is difficult to precisely phenotype. Visual scores can be subjective and are prone to assessor bias. Methods to assess variation in quantitative resistance more accurately were developed based on quantifying in planta fungal biomass, including the Wheat Germ Agglutinin Chitin Assay (WAC), qPCR and ddPCR assays. RESULTS Disease assays were conducted by inoculating a range of canola cultivars with L. maculans isolates in glasshouse experiments and assessing fungal biomass in cotyledons, petioles and stem tissue harvested at different timepoints post-inoculation. PCR and WAC assay results were well correlated, repeatable across experiments and host tissues, and able to differentiate fungal biomass in different host-isolate treatments. In addition, the ddPCR assay was shown to differentiate between L. maculans isolates. CONCLUSIONS The ddPCR assay is more sensitive in detecting pathogens and more adaptable to high-throughput methods by using robotic systems than the WAC assay. Overall, these methods proved accurate and non-subjective, providing alternatives to visual assessments to quantify the L. maculans-B. napus interaction in all plant tissues throughout the progression of the disease in seedlings and mature plants and have potential for fine-scale blackleg resistance phenotyping in canola.
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Affiliation(s)
| | - Mohammad Hoque
- CSIRO Agriculture and Food, 1 Clunies Ross Street, Canberra, ACT 2601 Australia
| | - Rebecca Maher
- CSIRO Agriculture and Food, 1 Clunies Ross Street, Canberra, ACT 2601 Australia
| | - Angela Van de Wouw
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Phillip Hands
- CSIRO Agriculture and Food, 1 Clunies Ross Street, Canberra, ACT 2601 Australia
| | - Vivien Rolland
- CSIRO Agriculture and Food, 1 Clunies Ross Street, Canberra, ACT 2601 Australia
| | - Luke Barrett
- CSIRO Agriculture and Food, 1 Clunies Ross Street, Canberra, ACT 2601 Australia
| | - Susan Sprague
- CSIRO Agriculture and Food, 1 Clunies Ross Street, Canberra, ACT 2601 Australia
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Vollrath P, Chawla HS, Alnajar D, Gabur I, Lee H, Weber S, Ehrig L, Koopmann B, Snowdon RJ, Obermeier C. Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:749491. [PMID: 34868134 PMCID: PMC8636856 DOI: 10.3389/fpls.2021.749491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/29/2021] [Indexed: 05/15/2023]
Abstract
Blackleg is one of the major fungal diseases in oilseed rape/canola worldwide. Most commercial cultivars carry R gene-mediated qualitative resistances that confer a high level of race-specific protection against Leptosphaeria maculans, the causal fungus of blackleg disease. However, monogenic resistances of this kind can potentially be rapidly overcome by mutations in the pathogen's avirulence genes. To counteract pathogen adaptation in this evolutionary arms race, there is a tremendous demand for quantitative background resistance to enhance durability and efficacy of blackleg resistance in oilseed rape. In this study, we characterized genomic regions contributing to quantitative L. maculans resistance by genome-wide association studies in a multiparental mapping population derived from six parental elite varieties exhibiting quantitative resistance, which were all crossed to one common susceptible parental elite variety. Resistance was screened using a fungal isolate with no corresponding avirulence (AvrLm) to major R genes present in the parents of the mapping population. Genome-wide association studies revealed eight significantly associated quantitative trait loci (QTL) on chromosomes A07 and A09, with small effects explaining 3-6% of the phenotypic variance. Unexpectedly, the qualitative blackleg resistance gene Rlm9 was found to be located within a resistance-associated haploblock on chromosome A07. Furthermore, long-range sequence data spanning this haploblock revealed high levels of single-nucleotide and structural variants within the Rlm9 coding sequence among the parents of the mapping population. The results suggest that novel variants of Rlm9 could play a previously unknown role in expression of quantitative disease resistance in oilseed rape.
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Affiliation(s)
- Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet S. Chawla
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dima Alnajar
- Plant Pathology and Crop Protection Division, Department of Crop Sciences, Georg August University of Göttingen, Göttingen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
- Department of Plant Sciences, Faculty of Agriculture, Iasi University of Life Sciences, Iaşi, Romania
| | - HueyTyng Lee
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Sven Weber
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Lennard Ehrig
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Birger Koopmann
- Plant Pathology and Crop Protection Division, Department of Crop Sciences, Georg August University of Göttingen, Göttingen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
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10
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Amas J, Anderson R, Edwards D, Cowling W, Batley J. Status and advances in mining for blackleg (Leptosphaeria maculans) quantitative resistance (QR) in oilseed rape (Brassica napus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3123-3145. [PMID: 34104999 PMCID: PMC8440254 DOI: 10.1007/s00122-021-03877-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/29/2021] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Quantitative resistance (QR) loci discovered through genetic and genomic analyses are abundant in the Brassica napus genome, providing an opportunity for their utilization in enhancing blackleg resistance. Quantitative resistance (QR) has long been utilized to manage blackleg in Brassica napus (canola, oilseed rape), even before major resistance genes (R-genes) were extensively explored in breeding programmes. In contrast to R-gene-mediated qualitative resistance, QR reduces blackleg symptoms rather than completely eliminating the disease. As a polygenic trait, QR is controlled by numerous genes with modest effects, which exerts less pressure on the pathogen to evolve; hence, its effectiveness is more durable compared to R-gene-mediated resistance. Furthermore, combining QR with major R-genes has been shown to enhance resistance against diseases in important crops, including oilseed rape. For these reasons, there has been a renewed interest among breeders in utilizing QR in crop improvement. However, the mechanisms governing QR are largely unknown, limiting its deployment. Advances in genomics are facilitating the dissection of the genetic and molecular underpinnings of QR, resulting in the discovery of several loci and genes that can be potentially deployed to enhance blackleg resistance. Here, we summarize the efforts undertaken to identify blackleg QR loci in oilseed rape using linkage and association analysis. We update the knowledge on the possible mechanisms governing QR and the advances in searching for the underlying genes. Lastly, we lay out strategies to accelerate the genetic improvement of blackleg QR in oilseed rape using improved phenotyping approaches and genomic prediction tools.
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Affiliation(s)
- Junrey Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - Robyn Anderson
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - Wallace Cowling
- School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
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11
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Jiquel A, Gervais J, Geistodt‐Kiener A, Delourme R, Gay EJ, Ollivier B, Fudal I, Faure S, Balesdent M, Rouxel T. A gene-for-gene interaction involving a 'late' effector contributes to quantitative resistance to the stem canker disease in Brassica napus. THE NEW PHYTOLOGIST 2021; 231:1510-1524. [PMID: 33621369 PMCID: PMC8360019 DOI: 10.1111/nph.17292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/15/2021] [Indexed: 05/19/2023]
Abstract
The control of stem canker disease of Brassica napus (rapeseed), caused by the fungus Leptosphaeria maculans is based largely on plant genetic resistance: single-gene specific resistance (Rlm genes) or quantitative, polygenic, adult-stage resistance. Our working hypothesis was that quantitative resistance partly obeys the gene-for-gene model, with resistance genes 'recognizing' fungal effectors expressed during late systemic colonization. Five LmSTEE (stem-expressed effector) genes were selected and placed under the control of the AvrLm4-7 promoter, an effector gene highly expressed at the cotyledon stage of infection, for miniaturized cotyledon inoculation test screening of a gene pool of 204 rapeseed genotypes. We identified a rapeseed genotype, 'Yudal', expressing hypersensitive response to LmSTEE98. The LmSTEE98-RlmSTEE98 interaction was further validated by inactivation of the LmSTEE98 gene with a CRISPR-Cas9 approach. Isolates with mutated versions of LmSTEE98 induced more severe stem symptoms than the wild-type isolate in 'Yudal'. This single-gene resistance was mapped in a 0.6 cM interval of the 'Darmor_bzh' × 'Yudal' genetic map. One typical gene-for-gene interaction contributes partly to quantitative resistance when L. maculans colonizes the stems of rapeseed. With numerous other effectors specific to stem colonization, our study provides a new route for resistance gene discovery, elucidation of quantitative resistance mechanisms and selection for durable resistance.
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Affiliation(s)
- Audren Jiquel
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
- Euralis Semences6 Chemin des PanedautesMondonville31700France
| | - Julie Gervais
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Aude Geistodt‐Kiener
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
- Université Paris‐SaclayRoute de l'Orme aux MerisiersSaint‐Aubin91190France
| | | | - Elise J. Gay
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
- Université Paris‐SaclayRoute de l'Orme aux MerisiersSaint‐Aubin91190France
| | - Bénédicte Ollivier
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Isabelle Fudal
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | | | - Marie‐Hélène Balesdent
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Thierry Rouxel
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
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12
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Yang H, Mohd Saad NS, Ibrahim MI, Bayer PE, Neik TX, Severn-Ellis AA, Pradhan A, Tirnaz S, Edwards D, Batley J. Candidate Rlm6 resistance genes against Leptosphaeria. maculans identified through a genome-wide association study in Brassica juncea (L.) Czern. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2035-2050. [PMID: 33768283 DOI: 10.1007/s00122-021-03803-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
One hundred and sixty-seven B. juncea varieties were genotyped on the 90K Brassica assay (42,914 SNPs), which led to the identification of sixteen candidate genes for Rlm6. Brassica species are at high risk of severe crop loss due to pathogens, especially Leptosphaeria maculans (the causal agent of blackleg). Brassica juncea (L.) Czern is an important germplasm resource for canola improvement, due to its good agronomic traits, such as heat and drought tolerance and high blackleg resistance. The present study is the first using genome-wide association studies to identify candidate genes for blackleg resistance in B. juncea based on genome-wide SNPs obtained from the Illumina Infinium 90 K Brassica SNP array. The verification of Rlm6 in B. juncea was performed through a cotyledon infection test. Genotyping 42,914 single nucleotide polymorphisms (SNPs) in a panel of 167 B. juncea lines revealed a total of seven SNPs significantly associated with Rlm6 on chromosomes A07 and B04 in B. juncea. Furthermore, 16 candidate Rlm6 genes were found in these regions, defined as nucleotide binding site leucine-rich-repeat (NLR), leucine-rich repeat RLK (LRR-RLK) and LRR-RLP genes. This study will give insights into the blackleg resistance in B. juncea and facilitate identification of functional blackleg resistance genes which can be used in Brassica breeding.
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Affiliation(s)
- Hua Yang
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | | | | | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Anita A Severn-Ellis
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Aneeta Pradhan
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia.
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13
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Quezada-Martinez D, Addo Nyarko CP, Schiessl SV, Mason AS. Using wild relatives and related species to build climate resilience in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1711-1728. [PMID: 33730183 PMCID: PMC8205867 DOI: 10.1007/s00122-021-03793-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/12/2021] [Indexed: 05/18/2023]
Abstract
Climate change will have major impacts on crop production: not just increasing drought and heat stress, but also increasing insect and disease loads and the chance of extreme weather events and further adverse conditions. Often, wild relatives show increased tolerances to biotic and abiotic stresses, due to reduced stringency of selection for yield and yield-related traits under optimum conditions. One possible strategy to improve resilience in our modern-day crop cultivars is to utilize wild relative germplasm in breeding, and attempt to introgress genetic factors contributing to greater environmental tolerances from these wild relatives into elite crop types. However, this approach can be difficult, as it relies on factors such as ease of hybridization and genetic distance between the source and target, crossover frequencies and distributions in the hybrid, and ability to select for desirable introgressions while minimizing linkage drag. In this review, we outline the possible effects that climate change may have on crop production, introduce the Brassica crop species and their wild relatives, and provide an index of useful traits that are known to be present in each of these species that may be exploitable through interspecific hybridization-based approaches. Subsequently, we outline how introgression breeding works, what factors affect the success of this approach, and how this approach can be optimized so as to increase the chance of recovering the desired introgression lines. Our review provides a working guide to the use of wild relatives and related crop germplasm to improve biotic and abiotic resistances in Brassica crop species.
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Affiliation(s)
- Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Charles P Addo Nyarko
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Sarah V Schiessl
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany.
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
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14
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Quezada-Martinez D, Addo Nyarko CP, Schiessl SV, Mason AS. Using wild relatives and related species to build climate resilience in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1711-1728. [PMID: 33730183 DOI: 10.1007/s00122-021-03793-3.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/12/2021] [Indexed: 05/24/2023]
Abstract
Climate change will have major impacts on crop production: not just increasing drought and heat stress, but also increasing insect and disease loads and the chance of extreme weather events and further adverse conditions. Often, wild relatives show increased tolerances to biotic and abiotic stresses, due to reduced stringency of selection for yield and yield-related traits under optimum conditions. One possible strategy to improve resilience in our modern-day crop cultivars is to utilize wild relative germplasm in breeding, and attempt to introgress genetic factors contributing to greater environmental tolerances from these wild relatives into elite crop types. However, this approach can be difficult, as it relies on factors such as ease of hybridization and genetic distance between the source and target, crossover frequencies and distributions in the hybrid, and ability to select for desirable introgressions while minimizing linkage drag. In this review, we outline the possible effects that climate change may have on crop production, introduce the Brassica crop species and their wild relatives, and provide an index of useful traits that are known to be present in each of these species that may be exploitable through interspecific hybridization-based approaches. Subsequently, we outline how introgression breeding works, what factors affect the success of this approach, and how this approach can be optimized so as to increase the chance of recovering the desired introgression lines. Our review provides a working guide to the use of wild relatives and related crop germplasm to improve biotic and abiotic resistances in Brassica crop species.
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Affiliation(s)
- Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Charles P Addo Nyarko
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Sarah V Schiessl
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany.
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
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15
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Raman H, Raman R, Qiu Y, Zhang Y, Batley J, Liu S. The Rlm13 Gene, a New Player of Brassica napus- Leptosphaeria maculans Interaction Maps on Chromosome C03 in Canola. FRONTIERS IN PLANT SCIENCE 2021; 12:654604. [PMID: 34054900 PMCID: PMC8150007 DOI: 10.3389/fpls.2021.654604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/25/2021] [Indexed: 05/24/2023]
Abstract
Canola exhibits an extensive genetic variation for resistance to blackleg disease, caused by the fungal pathogen Leptosphaeria maculans. Despite the identification of several Avr effectors and R (race-specific) genes, specific interactions between Avr-R genes are not yet fully understood in the Brassica napus-L. maculans pathosystem. In this study, we investigated the genetic basis of resistance in an F2 : 3 population derived from Australian canola varieties CB-Telfer (Rlm4)/ATR-Cobbler (Rlm4) using a single-spore isolate of L. maculans, PHW1223. A genetic linkage map of the CB-Telfer/ATR-Cobbler population was constructed using 7,932 genotyping-by-sequencing-based DArTseq markers and subsequently utilized for linkage and haplotype analyses. Genetic linkage between DArTseq markers and resistance to PHW1223 isolate was also validated using the B. napus 60K Illumina Infinium array. Our results revealed that a major locus for resistance, designated as Rlm13, maps on chromosome C03. To date, no R gene for resistance to blackleg has been reported on the C subgenome in B. napus. Twenty-four candidate R genes were predicted to reside within the quantitative trait locus (QTL) region. We further resequenced both the parental lines of the mapping population (CB-Telfer and ATR-Cobbler, > 80 × coverage) and identified several structural sequence variants in the form of single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and presence/absence variations (PAVs) near Rlm13. Comparative mapping revealed that Rlm13 is located within the homoeologous A03/C03 region in ancestral karyotype block "R" of Brassicaceae. Our results provide a "target" for further understanding the Avr-Rlm13 gene interaction as well as a valuable tool for increasing resistance to blackleg in canola germplasm.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yuanyuan Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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16
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Cantila AY, Saad NSM, Amas JC, Edwards D, Batley J. Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives. Int J Mol Sci 2020; 22:E313. [PMID: 33396785 PMCID: PMC7795555 DOI: 10.3390/ijms22010313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/20/2022] Open
Abstract
Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia; (A.Y.C.); (N.S.M.S.); (J.C.A.); (D.E.)
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17
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Neik TX, Amas J, Barbetti M, Edwards D, Batley J. Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1336. [PMID: 33050509 PMCID: PMC7599536 DOI: 10.3390/plants9101336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.
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Affiliation(s)
- Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway 47500, Selangor, Malaysia;
| | - Junrey Amas
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Martin Barbetti
- School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
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18
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Fikere M, Barbulescu DM, Malmberg MM, Spangenberg GC, Cogan NOI, Daetwyler HD. Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence. Sci Rep 2020; 10:14300. [PMID: 32868838 PMCID: PMC7459325 DOI: 10.1038/s41598-020-71274-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022] Open
Abstract
Blackleg disease causes yield losses in canola (Brassica napus L.). To identify resistance genes and genomic regions, genome-wide association studies (GWAS) of 585 diverse winter and spring canola accessions were performed using imputed whole-genome sequence (WGS) and transcriptome genotype-by-sequencing (GBSt). Blackleg disease phenotypes were collected across three years in six trials. GWAS were performed in several ways and their respective power was judged by the number of significant single nucleotide polymorphisms (SNP), the false discovery rate (FDR), and the percentage of SNP that validated in additional field trials in two subsequent years. WGS GWAS with 1,234,708 million SNP detected a larger number of significant SNP, achieved a lower FDR and a higher validation rate than GBSt with 64,072 SNP. A meta-analysis combining survival and average internal infection resulted in lower FDR but also lower validation rates. The meta-analysis GWAS identified 79 genomic regions (674 SNP) conferring potential resistance to L. maculans. While several GWAS signals localised in regions of known Rlm genes, fifty-three new potential resistance regions were detected. Seventeen regions had underlying genes with putative functions related to disease defence or stress response in Arabidopsis thaliana. This study provides insight into the genetic architecture and potential molecular mechanisms underlying canola L. maculans resistance.
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Affiliation(s)
- M Fikere
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.,Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - D M Barbulescu
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3401, Australia
| | - M M Malmberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - G C Spangenberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - N O I Cogan
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - H D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia. .,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.
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19
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Raman H, Raman R, McVittie B, Borg L, Diffey S, Singh Yadav A, Balasubramanian S, Farquhar G. Genetic and physiological bases for variation in water use efficiency in canola. Food Energy Secur 2020. [DOI: 10.1002/fes3.237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries Wagga Wagga Agricultural Institute Wagga Wagga NSW Australia
| | - Rosy Raman
- NSW Department of Primary Industries Wagga Wagga Agricultural Institute Wagga Wagga NSW Australia
| | - Brett McVittie
- NSW Department of Primary Industries Wagga Wagga Agricultural Institute Wagga Wagga NSW Australia
| | - Lauren Borg
- University of Wollongong Wollongong NSW Australia
| | | | | | | | - Graham Farquhar
- Research School of Biology Australian National University Canberra ACT Australia
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20
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Raman H, McVittie B, Pirathiban R, Raman R, Zhang Y, Barbulescu DM, Qiu Y, Liu S, Cullis B. Genome-Wide Association Mapping Identifies Novel Loci for Quantitative Resistance to Blackleg Disease in Canola. FRONTIERS IN PLANT SCIENCE 2020; 11:1184. [PMID: 32849733 PMCID: PMC7432127 DOI: 10.3389/fpls.2020.01184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/21/2020] [Indexed: 05/03/2023]
Abstract
Blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, continues to be a major concern for sustainable production of canola (Brassica napus L.) in many parts of the world. The deployment of effective quantitative resistance (QR) is recognized as a durable strategy in providing natural defense to pathogens. Herein, we uncover loci for resistance to blackleg in a genetically diverse panel of canola accessions by exploiting historic recombination events which occurred during domestication and selective breeding by genome-wide association analysis (GWAS). We found extensive variation in resistance to blackleg at the adult plant stage, including for upper canopy infection. Using the linkage disequilibrium and genetic relationship estimates from 12,414 high quality SNPs, GWAS identified 59 statistically significant and "suggestive" SNPs on 17 chromosomes of B. napus genome that underlie variation in resistance to blackleg, evaluated under field and shade-house conditions. Each of the SNP association accounted for up to 25.1% of additive genetic variance in resistance among diverse panel of accessions. To understand the homology of QR genomic regions with Arabidopsis thaliana genome, we searched the synteny between QR regions with 22 ancestral blocks of Brassicaceae. Comparative analyses revealed that 25 SNP associations for QR were localized in nine ancestral blocks, as a result of genomic rearrangements. We further showed that phenological traits such as flowering time, plant height, and maturity confound the genetic variation in resistance. Altogether, these findings provided new insights on the complex genetic control of the blackleg resistance and further expanded our understanding of its genetic architecture.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Brett McVittie
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Ramethaa Pirathiban
- Centre for Bioinformatics and Biometrics, National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW, Australia
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yuanyuan Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Denise M. Barbulescu
- Department of Jobs, Precincts and Regions, Agriculture Victoria, Horsham, VIC, Australia
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Brian Cullis
- Centre for Bioinformatics and Biometrics, National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW, Australia
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21
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Fu F, Zhang X, Liu F, Peng G, Yu F, Fernando D. Identification of resistance loci in Chinese and Canadian canola/rapeseed varieties against Leptosphaeria maculans based on genome-wide association studies. BMC Genomics 2020; 21:501. [PMID: 32693834 PMCID: PMC7372758 DOI: 10.1186/s12864-020-06893-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/07/2020] [Indexed: 01/08/2023] Open
Abstract
Background The fungal pathogen Leptosphaeria maculans (Lm). causes blackleg disease on canola/rapeseed in many parts of the world. It is important to use resistant cultivars to manage the disease and minimize yield losses. In this study, twenty-two Lm isolates were used to identify resistance genes in a collection of 243 canola/rapeseed (Brassica napus L.) accessions from Canada and China. These Lm isolates carry different compliments of avirulence genes, and the investigation was based on a genome-wide association study (GWAS) and genotype-by-sequencing (GBS). Results Using the CROP-SNP pipeline, a total of 81,471 variants, including 78,632 SNPs and 2839 InDels, were identified. The GWAS was performed using TASSEL 5.0 with GLM + Q model. Thirty-two and 13 SNPs were identified from the Canadian and Chinese accessions, respectively, tightly associated with blackleg resistance with P values < 1 × 10− 4. These SNP loci were distributed on chromosomes A03, A05, A08, A09, C01, C04, C05, and C07, with the majority of them on A08 followed by A09 and A03. The significant SNPs identified on A08 were all located in a 2010-kb region and associated with resistance to 12 of the 22 Lm isolates. Furthermore, 25 resistance gene analogues (RGAs) were identified in these regions, including two nucleotide binding site (NBS) domain proteins, fourteen RLKs, three RLPs and six TM-CCs. These RGAs can be the potential candidate genes for blackleg resistance. Conclusion This study provides insights into potentially new genomic regions for discovery of additional blackleg resistance genes. The identified regions associated with blackleg resistance in the germplasm collection may also contribute directly to the development of canola varieties with novel resistance genes against blackleg of canola.
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Affiliation(s)
- Fuyou Fu
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Xuehua Zhang
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Fei Liu
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Gary Peng
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada.
| | - Dilantha Fernando
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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Hubbard M, Zhai C, Peng G. Exploring Mechanisms of Quantitative Resistance to Leptosphaeria maculans (Blackleg) in the Cotyledons of Canola ( Brassica napus) Based on Transcriptomic and Microscopic Analyses. PLANTS 2020; 9:plants9070864. [PMID: 32650490 PMCID: PMC7411684 DOI: 10.3390/plants9070864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 01/08/2023]
Abstract
Using resistant cultivars is a common approach to managing blackleg of canola/rapeseed caused by Leptosphaeria maculans (Lm). Quantitative resistance (QR), as opposed to major-gene resistance, is of interest because it is generally more durable, due to its multi-genetic basis. However, the mechanisms and genes underlying QR are mostly unknown. In this study, potential QR modes of action in “74-44 BL” was explored. This Canadian canola cultivar showed moderate but consistent race-nonspecific resistance at the cotyledon and adult-plant stages. A susceptible cultivar, “Westar”, was used as a control. After inoculation, the lesions developed more slowly on the cotyledons of 74-44 BL than those of Westar. We used RNA sequencing (-RNA-seq) to identify genes and their functions, putatively related to this resistance, and found that genes involved in programmed cell death (PCD), reactive oxygen species (ROS), signal transduction or intracellular endomembrane transport were most differentially expressed. ROS production was assessed in relation to Lm hyphal growth and lesion size; it occurred beyond the tissue colonized by Lm in 74-44 BL and appeared to trigger rapid cell death, limiting cotyledon colonization by Lm. In contrast, Lm grew more rapidly in Westar, often catching up with the ring of ROS and surpassing lesion boundaries. It appears that QR in 74-44 BL cotyledons is associated with limited colonization by Lm possibly mediated via ROS. The RNA-seq data also showed a link between ROS, signal transduction, and endomembrane vesicle trafficking, as well as PCD in the resistance. These results provide a starting point for a better understanding of the mechanisms behind QR against Lm in canola.
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Affiliation(s)
- Michelle Hubbard
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK S7N 0X2, Canada;
| | - Chun Zhai
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2, Canada;
| | - Gary Peng
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2, Canada;
- Correspondence: ; Tel.: +1-306-385-9410
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Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.). Sci Rep 2020; 10:4416. [PMID: 32157120 PMCID: PMC7064481 DOI: 10.1038/s41598-020-61211-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 02/19/2020] [Indexed: 01/10/2023] Open
Abstract
Sustainable canola production is essential to meet growing human demands for vegetable oil, biodiesel, and meal for stock feed markets. Blackleg, caused by the fungal pathogen, Leptosphaeria maculans is a devastating disease that can lead to significant yield loss in many canola production regions worldwide. Breakdown of race-specific resistance to L. maculans in commercial cultivars poses a constant threat to the canola industry. To identify new alleles, especially for quantitative resistance (QR), we analyzed 177 doubled haploid (DH) lines derived from an RP04/Ag-Outback cross. DH lines were evaluated for QR under field conditions in three experiments conducted at Wagga Wagga (2013, 2014) and Lake Green (2015), and under shade house conditions using the 'ascospore shower' test. DH lines were also characterized for qualitative R gene-mediated resistance via cotyledon tests with two differential single spore isolates, IBCN17 and IBCN76, under glasshouse conditions. Based on 18,851 DArTseq markers, a linkage map representing 2,019 unique marker bins was constructed and then utilized for QTL detection. Marker regression analysis identified 22 significant marker associations for resistance, allowing identification of two race-specific resistance R genes, Rlm3 and Rlm4, and 21 marker associations for QR loci. At least three SNP associations for QR were repeatedly detected on chromosomes A03, A07 and C04 across phenotyping environments. Physical mapping of markers linked with these consistent QR loci on the B. napus genome assembly revealed their localization in close proximity of the candidate genes of B. napus BnaA03g26760D (A03), BnaA07g20240D (A07) and BnaC04g02040D (C04). Annotation of these candidate genes revealed their association with protein kinase and jumonji proteins implicated in defense resistance. Both Rlm3 and Rlm4 genes identified in this DH population did not show any association with resistance loci detected under either field and/or shade house conditions (ascospore shower) suggesting that both genes are ineffective in conferring resistance to L. maculans in Australian field conditions. Taken together, our study identified sequence-based molecular markers for dissecting R and QR loci to L. maculans in a canola DH population from the RP04/Ag-Outback cross.
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Raman H, Raman R, Qiu Y, Yadav AS, Sureshkumar S, Borg L, Rohan M, Wheeler D, Owen O, Menz I, Balasubramanian S. GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola. BMC Genomics 2019; 20:636. [PMID: 31387521 PMCID: PMC6685183 DOI: 10.1186/s12864-019-5964-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. However, our understanding of underlying genes and their role in canola productivity is limited. Results We report our analyses of a diverse GWAS panel (300–368 accessions) of canola and identify SNPs that are significantly associated with variation in flowering time and response to photoperiod across multiple locations. We show that several of these associations map in the vicinity of FLOWERING LOCUS T (FT) paralogs and its known transcriptional regulators. Complementary QTL and eQTL mapping studies, conducted in an Australian doubled haploid population, also detected consistent genomic regions close to the FT paralogs associated with flowering time and yield-related traits. FT sequences vary between accessions. Expression levels of FT in plants grown in field (or under controlled environment cabinets) correlated with flowering time. We show that markers linked to the FT paralogs display association with variation in multiple traits including flowering time, plant emergence, shoot biomass and grain yield. Conclusions Our findings suggest that FT paralogs not only control flowering time but also modulate yield-related productivity traits in canola. Electronic supplementary material The online version of this article (10.1186/s12864-019-5964-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Lauren Borg
- Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Maheswaran Rohan
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Oliver Owen
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Ian Menz
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
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Gabur I, Chawla HS, Liu X, Kumar V, Faure S, von Tiedemann A, Jestin C, Dryzska E, Volkmann S, Breuer F, Delourme R, Snowdon R, Obermeier C. Finding invisible quantitative trait loci with missing data. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2102-2112. [PMID: 29729219 PMCID: PMC6230954 DOI: 10.1111/pbi.12942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 05/21/2023]
Abstract
Evolutionary processes during plant polyploidization and speciation have led to extensive presence-absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high-resolution genetic analysis in major crops frequently implements simple, cost-effective, high-throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays; however, these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts. Here, we describe a strategy to recover valuable information from single nucleotide absence polymorphisms (SNaPs) by population-based quality filtering of SNP hybridization data to distinguish patterns associated with genuine deletions from those caused by technical failures. We reveal that including SNaPs in genetic analyses elucidate segregation of small to large-scale structural variants in nested association mapping populations of oilseed rape (Brassica napus), a recent polyploid crop with widespread structural variation. Including SNaP markers in genomewide association studies identified numerous quantitative trait loci, invisible using SNP markers alone, for resistance to two major fungal diseases of oilseed rape, Sclerotinia stem rot and blackleg disease. Our results indicate that PAV has a strong influence on quantitative disease resistance in B. napus and that SNaP analysis using cost-effective SNP array data can provide extensive added value from 'missing data'. This strategy might also be applicable for improving the precision of genetic mapping in many important crop species.
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Affiliation(s)
- Iulian Gabur
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
| | | | - Xiwei Liu
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
| | - Vinod Kumar
- IGEPP, INRA, AGROCAMPUS OUESTUniv RennesLe RheuFrance
| | | | - Andreas von Tiedemann
- Section of General Plant Pathology and Crop ProtectionGeorg August UniversityGöttingenGermany
| | | | | | | | | | | | - Rod Snowdon
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
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26
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Raman H, Raman R, Diffey S, Qiu Y, McVittie B, Barbulescu DM, Salisbury PA, Marcroft S, Delourme R. Stable Quantitative Resistance Loci to Blackleg Disease in Canola ( Brassica napus L.) Over Continents. FRONTIERS IN PLANT SCIENCE 2018; 9:1622. [PMID: 30532758 PMCID: PMC6265502 DOI: 10.3389/fpls.2018.01622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/18/2018] [Indexed: 05/02/2023]
Abstract
The hemibiotrophic fungus, Leptosphaeria maculans is the most devastating pathogen, causing blackleg disease in canola (Brassica napus L). To study the genomic regions involved in quantitative resistance (QR), 259-276 DH lines from Darmor-bzh/Yudal (DYDH) population were assessed for resistance to blackleg under shade house and field conditions across 3 years. In different experiments, the broad sense heritability varied from 43 to 95%. A total of 27 significant quantitative trait loci (QTL) for QR were detected on 12 chromosomes and explained between 2.14 and 10.13% of the genotypic variance. Of the significant QTL, at least seven were repeatedly detected across different experiments on chromosomes A02, A07, A09, A10, C01, and C09. Resistance alleles were mainly contributed by 'Darmor-bzh' but 'Yudal' also contributed few of them. Our results suggest that plant maturity and plant height may have a pleiotropic effect on QR in our conditions. We confirmed that Rlm9 which is present in 'Darmor-bzh' is not effective to confer resistance in our Australian field conditions. Comparative mapping showed that several R genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors map in close proximity (within 200 Kb) of the significant trait-marker associations on the reference 'Darmor-bzh' genome assembly. More importantly, eight significant QTL regions were detected across diverse growing environments: Australia, France, and United Kingdom. These stable QTL identified herein can be utilized for enhancing QR in elite canola germplasm via marker- assisted or genomic selection strategies.
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Affiliation(s)
- Harsh Raman
- Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Rosy Raman
- Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Simon Diffey
- Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, NSW, Australia
| | - Yu Qiu
- Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Brett McVittie
- Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | | | - Phil Anthony Salisbury
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | | | - Regine Delourme
- IGEPP, INRA, Agrocampus Ouest, Université Rennes, Le Rheu, France
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CRISPR/Cas9-Mediated Multiplex Genome Editing of the BnWRKY11 and BnWRKY70 Genes in Brassica napus L. Int J Mol Sci 2018; 19:ijms19092716. [PMID: 30208656 PMCID: PMC6163266 DOI: 10.3390/ijms19092716] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/26/2018] [Accepted: 09/07/2018] [Indexed: 02/04/2023] Open
Abstract
Targeted genome editing is a desirable means of basic science and crop improvement. The clustered, regularly interspaced, palindromic repeat (CRISPR)/Cas9 (CRISPR-associated 9) system is currently the simplest and most commonly used system in targeted genomic editing in plants. Single and multiplex genome editing in plants can be achieved under this system. In Arabidopsis, AtWRKY11 and AtWRKY70 genes were involved in JA- and SA-induced resistance to pathogens, in rapeseed (Brassica napus L.), BnWRKY11 and BnWRKY70 genes were found to be differently expressed after inoculated with the pathogenic fungus, Sclerotinia sclerotiorum (Lib.) de Bary. In this study, two Cas9/sgRNA constructs targeting two copies of BnWRKY11 and four copies of BnWRKY70 were designed to generate BnWRKY11 and BnWRKY70 mutants respectively. As a result, twenty-two BnWRKY11 and eight BnWRKY70 independent transformants (T0) were obtained, with the mutation ratios of 54.5% (12/22) and 50% (4/8) in BnWRKY11 and BnWRKY70 transformants respectively. Eight and two plants with two copies of mutated BnWRKY11 and BnWRKY70 were obtained respectively. In T1 generation of each plant examined, new mutations on target genes were detected with high efficiency. The vast majority of BnWRKY70 mutants showed editing in three copies of BnWRKY70 in examined T1 plants. BnWRKY70 mutants exhibited enhanced resistance to Sclerotinia, while BnWRKY11 mutants showed no significant difference in Sclerotinia resistance when compared to non-transgenic plants. In addition, plants that overexpressed BnWRKY70 showed increased sensitivity when compared to non-transgenic plants. Altogether, our results demonstrated that BnWRKY70 may function as a regulating factor to negatively control the Sclerotinia resistance and CRISPR/Cas9 system could be used to generate germplasm in B. napus with high resistance against Sclerotinia.
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28
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Fikere M, Barbulescu DM, Malmberg MM, Shi F, Koh JCO, Slater AT, MacLeod IM, Bowman PJ, Salisbury PA, Spangenberg GC, Cogan NOI, Daetwyler HD. Genomic Prediction Using Prior Quantitative Trait Loci Information Reveals a Large Reservoir of Underutilised Blackleg Resistance in Diverse Canola ( Brassica napus L.) Lines. THE PLANT GENOME 2018; 11. [PMID: 30025024 DOI: 10.3835/plantgenome2017.11.0100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Genomic prediction is becoming a popular plant breeding method to predict the genetic merit of lines. While some genomic prediction results have been reported in canola, none have been evaluated for blackleg disease. Here, we report genomic prediction for seedling emergence, survival rate, and internal infection), using 532 Spring and Winter canola lines. These lines were phenotyped in two replicated blackleg disease nurseries grown at Wickliffe and Green Lake, Victoria, Australia. A transcriptome genotyping-by-sequencing approach revealed 98,054 single nucleotide polymorphisms (SNPs) after quality control. We assessed various genomic prediction scenarios based on Genomic Best Linear Unbiased Prediction (GBLUP), BayesR and BayesRC, which can make use of prior quantitative trait loci information, via cross-validation. Clustering based on genomic relationships showed that Winter and Spring lines were genetically distinct, indicating limited gene flow between sets. Genetic correlations within traits between Spring and Winter lines ranged from 0.68 and 0.90 (mean = 0.76). Based on GBLUP in the whole population, moderate to high genomic prediction accuracies were achieved within environments (0.35-0.74) and were reduced across environments (0.28-0.58). Prediction accuracy within the Spring set ranged from 0.30-0.69, and from 0.19-0.71 within the Winter set. The BayesR model resulted in slightly lower accuracy to GBLUP. The proportion of genetic variance explained by known blackleg quantitative trait loci (QTL) was < 30%, indicating that there is a large reservoir of genetic variation in blackleg traits that remains to be discovered, but can be captured with genomic prediction. However, providing prior information of known QTL in the BayesRC method resulted in an increased prediction accuracy for survival and internal infection, particularly with Spring lines. Overall, these promising results indicate that genomic prediction will be a valuable tool to make use of all genetic variation to improve blackleg resistance in canola.
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29
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Stotz HU, Harvey PJ, Haddadi P, Mashanova A, Kukol A, Larkan NJ, Borhan MH, Fitt BDL. Genomic evidence for genes encoding leucine-rich repeat receptors linked to resistance against the eukaryotic extra- and intracellular Brassica napus pathogens Leptosphaeria maculans and Plasmodiophora brassicae. PLoS One 2018; 13:e0198201. [PMID: 29856883 PMCID: PMC5983482 DOI: 10.1371/journal.pone.0198201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/15/2018] [Indexed: 01/17/2023] Open
Abstract
Genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) control resistance against intracellular (cell-penetrating) pathogens. However, evidence for a role of genes coding for proteins with LRR domains in resistance against extracellular (apoplastic) fungal pathogens is limited. Here, the distribution of genes coding for proteins with eLRR domains but lacking kinase domains was determined for the Brassica napus genome. Predictions of signal peptide and transmembrane regions divided these genes into 184 coding for receptor-like proteins (RLPs) and 121 coding for secreted proteins (SPs). Together with previously annotated NLRs, a total of 720 LRR genes were found. Leptosphaeria maculans-induced expression during a compatible interaction with cultivar Topas differed between RLP, SP and NLR gene families; NLR genes were induced relatively late, during the necrotrophic phase of pathogen colonization. Seven RLP, one SP and two NLR genes were found in Rlm1 and Rlm3/Rlm4/Rlm7/Rlm9 loci for resistance against L. maculans on chromosome A07 of B. napus. One NLR gene at the Rlm9 locus was positively selected, as was the RLP gene on chromosome A10 with LepR3 and Rlm2 alleles conferring resistance against L. maculans races with corresponding effectors AvrLm1 and AvrLm2, respectively. Known loci for resistance against L. maculans (extracellular hemi-biotrophic fungus), Sclerotinia sclerotiorum (necrotrophic fungus) and Plasmodiophora brassicae (intracellular, obligate biotrophic protist) were examined for presence of RLPs, SPs and NLRs in these regions. Whereas loci for resistance against P. brassicae were enriched for NLRs, no such signature was observed for the other pathogens. These findings demonstrate involvement of (i) NLR genes in resistance against the intracellular pathogen P. brassicae and a putative NLR gene in Rlm9-mediated resistance against the extracellular pathogen L. maculans.
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Affiliation(s)
- Henrik U. Stotz
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
- * E-mail:
| | - Pascoe J. Harvey
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Parham Haddadi
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Alla Mashanova
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Andreas Kukol
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | | | - M. Hossein Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Bruce D. L. Fitt
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
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Chen L, Wan H, Qian J, Guo J, Sun C, Wen J, Yi B, Ma C, Tu J, Song L, Fu T, Shen J. Genome-Wide Association Study of Cadmium Accumulation at the Seedling Stage in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2018; 9:375. [PMID: 29725340 PMCID: PMC5917214 DOI: 10.3389/fpls.2018.00375] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/06/2018] [Indexed: 05/26/2023]
Abstract
Cadmium is a potentially toxic heavy metal to human health. Rapeseed (Brassica napus L.), a vegetable and oilseed crop, might also be a Cd hyperaccumulator, but there is little information on this trait in rapeseed. We evaluated Cd accumulation in different oilseed accessions and employed a genome-wide association study to identify quantitative trait loci (QTLs) related to Cd accumulation. A total of 419 B. napus accessions and inbred lines were genotyped with a 60K Illumina Infinium SNP array of Brassica. Wide genotypic variations in Cd concentration and translocation were found. Twenty-five QTLs integrated with 98 single-nucleotide polymorphisms (SNPs) located at 15 chromosomes were associated with Cd accumulation traits. These QTLs explained 3.49-7.57% of the phenotypic variation observed. Thirty-two candidate genes were identified in these genomic regions, and they were 0.33-497.97 kb away from the SNPs. We found orthologs of Arabidopsis thaliana located near the significant SNPs on the B. napus genome, including NRAMP6 (natural resistance-associated macrophage protein 6), IRT1 (iron-regulated transporter 1), CAD1 (cadmium-sensitive 1), and PCS2 (phytochelatin synthase 2). Of them, four candidate genes were verified by qRT-PCR, the expression levels of which were significantly higher after exposure to Cd than in the controls. Our results might facilitate the study of the genetic basis of Cd accumulation and the cloning of candidate Cd accumulation genes, which could be used to help reduce Cd levels in edible plant parts and/or create more efficient hyperaccumulators.
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Affiliation(s)
- Lunlin Chen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Nanchang Branch of National Center of Oilcrops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Heping Wan
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiali Qian
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianbin Guo
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengming Sun
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Laiqiang Song
- Nanchang Branch of National Center of Oilcrops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Neik TX, Barbetti MJ, Batley J. Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:1788. [PMID: 29163558 PMCID: PMC5681527 DOI: 10.3389/fpls.2017.01788] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Martin J. Barbetti
- School of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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Zhang W, Hu D, Raman R, Guo S, Wei Z, Shen X, Meng J, Raman H, Zou J. Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata. FRONTIERS IN PLANT SCIENCE 2017; 8:615. [PMID: 28484482 PMCID: PMC5401912 DOI: 10.3389/fpls.2017.00615] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/04/2017] [Indexed: 05/21/2023]
Abstract
Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the "YW" cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene regions in the C genome of B. napus. These results would not only provide insights for genetic improvement of this species, but will also identify useful genetic variation hidden in the Cc subgenome of B. carinata to improve canola cultivars.
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Affiliation(s)
- Wenshan Zhang
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an Alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Shaomin Guo
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Zili Wei
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Xueqi Shen
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an Alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
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Bartoli C, Roux F. Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach. FRONTIERS IN PLANT SCIENCE 2017; 8:763. [PMID: 28588588 PMCID: PMC5441063 DOI: 10.3389/fpls.2017.00763] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/24/2017] [Indexed: 05/18/2023]
Abstract
The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA) mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes). In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.
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