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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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Ge W, Lv M, Feng H, Wang X, Zhang B, Li K, Zhang J, Zou J, Ji R. Analysis of the role of BrRPP1 gene in Chinese cabbage infected by Plasmodiophora brassicae. FRONTIERS IN PLANT SCIENCE 2023; 14:1082395. [PMID: 36760653 PMCID: PMC9905630 DOI: 10.3389/fpls.2023.1082395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The clubroot disease caused by Plasmodiophora brassicae (P. brassicae) poses a serious threat to the economic value of cruciferous crops, which is a serious problem to be solved worldwide. Some resistance genes to clubroot disease in Brassica rapa L. ssp pekinensis cause by P. brassicae have been located on different chromosomes. Among them, Rcr1 and Rcr2 were mapped to the common candidate gene Bra019410, but its resistance mechanism is not clear yet. METHODS In this experiment, the differences of BrRPP1 between the resistant and susceptible material of Chinese cabbage were analyzed by gene cloning and qRT-PCR. The gene function was verified by Arabidopsis homologous mutants. The expression site of BrRPP1 gene in cells was analyzed by subcellular localization. Finally, the candidate interaction protein of BrRPP1 was screened by yeast two-hybrid library. RESULTS The results showed that the cDNA sequence, upstream promoter sequence and expression level of BrRPP1 were quite different between the resistant and susceptible material. The resistance investigation found that the Arabidopsis mutant rpp1 was more susceptible to clubroot disease than the wild type, which suggested that the deletion of rpp1 reduces resistance of plant to clubroot disease. Subcellular location analysis confirmed that BrRPP1 was located in the nucleus. The interaction proteins of BrRPP1 screened from cDNA Yeast Library by yeast two-hybrid are mainly related to photosynthesis, cell wall modification, jasmonic acid signal transduction and programmed cell death. DISCUSSION BrRPP1 gene contains TIR-NBS-LRR domain and belongs to R gene. The cDNA and promoter sequence of BrRPP1 in resistant varieties was different from that in susceptible varieties led to the significant difference of the gene expression of BrRPP1 between the resistant varieties and the susceptible varieties. The high expression of BrRPP1 gene in resistant varieties enhanced the resistance of Chinese cabbage to P. brassicae, and the interaction proteins of BrRPP1 are mainly related to photosynthesis, cell wall modification, jasmonic acid signal transduction and programmed cell death. These results provide important clues for understanding the mechanism of BrRPP1 in the resistance of B. rapa to P. brassicae.
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Guimaraes PM, Quintana AC, Mota APZ, Berbert PS, Ferreira DDS, de Aguiar MN, Pereira BM, de Araújo ACG, Brasileiro ACM. Engineering Resistance against Sclerotinia sclerotiorum Using a Truncated NLR (TNx) and a Defense-Priming Gene. PLANTS (BASEL, SWITZERLAND) 2022; 11:3483. [PMID: 36559595 PMCID: PMC9786959 DOI: 10.3390/plants11243483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The association of both cell-surface PRRs (Pattern Recognition Receptors) and intracellular receptor NLRs (Nucleotide-Binding Leucine-Rich Repeat) in engineered plants have the potential to activate strong defenses against a broad range of pathogens. Here, we describe the identification, characterization, and in planta functional analysis of a novel truncated NLR (TNx) gene from the wild species Arachis stenosperma (AsTIR19), with a protein structure lacking the C-terminal LRR (Leucine Rich Repeat) domain involved in pathogen perception. Overexpression of AsTIR19 in tobacco plants led to a significant reduction in infection caused by Sclerotinia sclerotiorum, with a further reduction in pyramid lines containing an expansin-like B gene (AdEXLB8) potentially involved in defense priming. Transcription analysis of tobacco transgenic lines revealed induction of hormone defense pathways (SA; JA-ET) and PRs (Pathogenesis-Related proteins) production. The strong upregulation of the respiratory burst oxidase homolog D (RbohD) gene in the pyramid lines suggests its central role in mediating immune responses in plants co-expressing the two transgenes, with reactive oxygen species (ROS) production enhanced by AdEXLB8 cues leading to stronger defense response. Here, we demonstrate that the association of potential priming elicitors and truncated NLRs can produce a synergistic effect on fungal resistance, constituting a promising strategy for improved, non-specific resistance to plant pathogens.
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Affiliation(s)
- Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
| | | | - Ana Paula Zotta Mota
- INRAE, Institut Sophia Agrobiotech, CNRS, Université Côte d’Azur, 06903 Sophia Antipolis, France
| | | | | | | | | | | | - Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
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Cantila AY, Thomas WJW, Bayer PE, Edwards D, Batley J. Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:3010. [PMID: 36432742 PMCID: PMC9693284 DOI: 10.3390/plants11223010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
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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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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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Zhang Q, Dandena H, McCausland M, Liu H, Liu Z, Xu W, Li G. Genetic Analysis of a Horizontal Resistance Locus BLMR2 in Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:663868. [PMID: 34113364 PMCID: PMC8186441 DOI: 10.3389/fpls.2021.663868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/12/2021] [Indexed: 05/25/2023]
Abstract
Leptosphaeria maculans causes blackleg disease in Brassica napus. The blackleg disease is mainly controlled by resistance genes in B. napus. Previous studies have shown that the blackleg resistant BLMR2 locus that conferred horizontal resistance under field conditions, is located on chromosome A10 of B. napus. The purpose of this study is to fine map this locus and hence identify a candidate gene underlying horizontal resistance. The spectrum of resistance to L. maculans isolates of the resistance locus BLMR2 was analyzed using near isogenic lines, resistant, and susceptible cultivars. The results showed that this locus was horizontally resistant to all isolates tested. Sequence characterized amplified regions (SCAR), simple sequence repeats (SSR), and single nucleotide polymorphism (SNP) markers were developed in the chromosome region of BLMR2 and a fine genetic map was constructed. Two molecular markers narrowed BLMR2 in a 53.37 kb region where six genes were annotated. Among the six annotated genes, BnaA10g11280D/BnaA10g11290D encoding a cytochrome P450 protein were predicted as the candidate of BLMR2. Based on the profiling of pathogen induced transcriptome, three expressed genes in the six annotated genes were identified while only cytochrome P450 showed upregulation. The candidate corresponds to the gene involved in the indole glucosinolate biosynthesis pathway and plant basal defense in Arabidopsis thaliana. The molecular markers identified in this study will allow the quick incorporation of the BLMR2 allele in rapeseed cultivars to enhance blackleg resistance.
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Singh KP, Kumari P, Rai PK. Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement in Brassica juncea. FRONTIERS IN PLANT SCIENCE 2021; 12:617405. [PMID: 33747001 PMCID: PMC7965955 DOI: 10.3389/fpls.2021.617405] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/08/2021] [Indexed: 05/15/2023]
Abstract
Brassica juncea is a major oilseed crop in tropical and subtropical countries, especially in south-east Asia like India, China, Bangladesh, and Pakistan. The widespread cultivation of genetically similar varieties tends to attract fungal pathogens which cause heavy yield losses in the absence of resistant sources. The conventional disease management techniques are often expensive, have limited efficacy, and cause additional harm to the environment. A substantial approach is to identify and use of resistance sources within the Brassica hosts and other non-hosts to ensure sustainable oilseed crop production. In the present review, we discuss six major fungal pathogens of B. juncea: Sclerotinia stem rot (Sclerotinia sclerotiorum), Alternaria blight (Alternaria brassicae), White rust (Albugo candida), Downy mildew (Hyaloperonospora parasitica), Powdery mildew (Erysiphe cruciferarum), and Blackleg (Leptoshaeria maculans). From discussing studies on pathogen prevalence in B. juncea, the review then focuses on highlighting the resistance sources and quantitative trait loci/gene identified so far from Brassicaceae and non-filial sources against these fungal pathogens. The problems in the identification of resistance sources for B. juncea concerning genome complexity in host subpopulation and pathotypes were addressed. Emphasis has been laid on more elaborate and coordinated research to identify and deploy R genes, robust techniques, and research materials. Examples of fully characterized genes conferring resistance have been discussed that can be transformed into B. juncea using advanced genomics tools. Lastly, effective strategies for B. juncea improvement through introgression of novel R genes, development of pre-breeding resistant lines, characterization of pathotypes, and defense-related secondary metabolites have been provided suggesting the plan for the development of resistant B. juncea.
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Affiliation(s)
- Kaushal Pratap Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, India
- *Correspondence: Kaushal Pratap Singh,
| | - Preetesh Kumari
- Genetics Division, ICAR-Indian Agricultural Research Institute, New Delhi, India
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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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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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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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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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Albert I, Hua C, Nürnberger T, Pruitt RN, Zhang L. Surface Sensor Systems in Plant Immunity. PLANT PHYSIOLOGY 2020; 182:1582-1596. [PMID: 31822506 PMCID: PMC7140916 DOI: 10.1104/pp.19.01299] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/21/2019] [Indexed: 05/04/2023]
Abstract
Protein complexes at the cell surface facilitate the detection of danger signals from diverse pathogens and initiate a series of complex intracellular signaling events that result in various immune responses.
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Affiliation(s)
- Isabell Albert
- Department of Plant Biochemistry, Centre for Plant Molecular Biology, Eberhard Karls University, D-72076 Tübingen, Germany
| | - Chenlei Hua
- Department of Plant Biochemistry, Centre for Plant Molecular Biology, Eberhard Karls University, D-72076 Tübingen, Germany
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre for Plant Molecular Biology, Eberhard Karls University, D-72076 Tübingen, Germany
- Department of Biochemistry, University of Johannesburg, Johannesburg 2001, South Africa
| | - Rory N Pruitt
- Department of Plant Biochemistry, Centre for Plant Molecular Biology, Eberhard Karls University, D-72076 Tübingen, Germany
| | - Lisha Zhang
- Department of Plant Biochemistry, Centre for Plant Molecular Biology, Eberhard Karls University, D-72076 Tübingen, Germany
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14
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Lv H, Fang Z, Yang L, Zhang Y, Wang Y. An update on the arsenal: mining resistance genes for disease management of Brassica crops in the genomic era. HORTICULTURE RESEARCH 2020; 7:34. [PMID: 32194970 PMCID: PMC7072071 DOI: 10.1038/s41438-020-0257-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 05/18/2023]
Abstract
Brassica species include many economically important crops that provide nutrition and health-promoting substances to humans worldwide. However, as with all crops, their production is constantly threatened by emerging viral, bacterial, and fungal diseases, whose incidence has increased in recent years. Traditional methods of control are often costly, present limited effectiveness, and cause environmental damage; instead, the ideal approach is to mine and utilize the resistance genes of the Brassica crop hosts themselves. Fortunately, the development of genomics, molecular genetics, and biological techniques enables us to rapidly discover and apply resistance (R) genes. Herein, the R genes identified in Brassica crops are summarized, including their mapping and cloning, possible molecular mechanisms, and application in resistance breeding. Future perspectives concerning how to accurately discover additional R gene resources and efficiently utilize these genes in the genomic era are also discussed.
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Affiliation(s)
- Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
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15
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Zhou T, Xu W, Hirani AH, Liu Z, Tuan PA, Ayele BT, Daayf F, McVetty PBE, Duncan RW, Li G. Transcriptional Insight Into Brassica napus Resistance Genes LepR3 and Rlm2-Mediated Defense Response Against the Leptosphaeria maculans Infection. FRONTIERS IN PLANT SCIENCE 2019; 10:823. [PMID: 31333690 PMCID: PMC6615431 DOI: 10.3389/fpls.2019.00823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
The phytopathogenic fungus Leptosphaeria maculans causes the blackleg disease on Brassica napus, resulting in severe loss of rapeseed production. Breeding of resistant cultivars containing race-specific resistance genes is provably effective to combat this disease. While two allelic resistance genes LepR3 and Rlm2 recognizing L. maculans avirulence genes AvrLm1 and AvrLm2 at plant apoplastic space have been cloned in B. napus, the downstream gene expression network underlying the resistance remains elusive. In this study, transgenic lines expressing LepR3 and Rlm2 were created in the susceptible "Westar" cultivar and inoculated with L. maculans isolates containing different sets of AvrLm1 and AvrLm2 for comparative transcriptomic analysis. Through grouping the RNA-seq data based on different levels of defense response, we find LepR3 and Rlm2 orchestrate a hierarchically regulated gene expression network, consisting of induced ABA acting independently of the disease reaction, activation of signal transduction pathways with gradually increasing intensity from compatible to incompatible interaction, and specifically induced enzymatic and chemical actions contributing to hypersensitive response with recognition of AvrLm1 and AvrLm2. This study provides an unconventional investigation into LepR3 and Rlm2-mediated plant defense machinery and adds novel insight into the interaction between surface-localized receptor-like proteins (RLPs) and apoplastic fungal pathogens.
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Affiliation(s)
- Tengsheng Zhou
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Wen Xu
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Arvind H. Hirani
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Zheng Liu
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Pham Anh Tuan
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Belay T. Ayele
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Fouad Daayf
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | | | - Robert W. Duncan
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Genyi Li
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
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16
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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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17
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Ghanbarnia K, Ma L, Larkan NJ, Haddadi P, Fernando WGD, Borhan MH. Leptosphaeria maculans AvrLm9: a new player in the game of hide and seek with AvrLm4-7. MOLECULAR PLANT PATHOLOGY 2018; 19:1754-1764. [PMID: 29330918 PMCID: PMC6638032 DOI: 10.1111/mpp.12658] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 05/14/2023]
Abstract
Blackleg disease of Brassica napus caused by Leptosphaeria maculans (Lm) is largely controlled by the deployment of race-specific resistance (R) genes. However, selection pressure exerted by R genes causes Lm to adapt and give rise to new virulent strains through mutation and deletion of effector genes. Therefore, a knowledge of effector gene function is necessary for the effective management of the disease. Here, we report the cloning of Lm effector AvrLm9 which is recognized by the resistance gene Rlm9 in B. napus cultivar Goéland. AvrLm9 was mapped to scaffold 7 of the Lm genome, co-segregating with the previously reported AvrLm5 (previously known as AvrLmJ1). Comparison of AvrLm5 alleles amongst the 37 re-sequenced Lm isolates and transgenic complementation identified a single point mutation correlating with the AvrLm9 phenotype. Therefore, we renamed this gene as AvrLm5-9 to reflect the dual specificity of this locus. Avrlm5-9 transgenic isolates were avirulent when inoculated on the B. napus cultivar Goéland. The expression of AvrLm5-9 during infection was monitored by RNA sequencing. The recognition of AvrLm5-9 by Rlm9 is masked in the presence of AvrLm4-7, another Lm effector. AvrLm5-9 and AvrLm4-7 do not interact, and AvrLm5-9 is expressed in the presence of AvrLm4-7. AvrLm5-9 is the second Lm effector for which host recognition is masked by AvrLm4-7. An understanding of this complex interaction will provide new opportunities for the engineering of broad-spectrum recognition.
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Affiliation(s)
- Kaveh Ghanbarnia
- Saskatoon Research and Development Centre, Agriculture and Agri‐Food CanadaSaskatoonSKCanada S7N 0X2
- Department of Plant ScienceUniversity of ManitobaWinnipegMBCanada R3T 2N2
| | - Lisong Ma
- Saskatoon Research and Development Centre, Agriculture and Agri‐Food CanadaSaskatoonSKCanada S7N 0X2
| | - Nicholas J. Larkan
- Saskatoon Research and Development Centre, Agriculture and Agri‐Food CanadaSaskatoonSKCanada S7N 0X2
- Armatus Genetics Inc.SaskatoonSKCanada S7J 4M2
| | - Parham Haddadi
- Saskatoon Research and Development Centre, Agriculture and Agri‐Food CanadaSaskatoonSKCanada S7N 0X2
| | | | - Mohammad Hossein Borhan
- Saskatoon Research and Development Centre, Agriculture and Agri‐Food CanadaSaskatoonSKCanada S7N 0X2
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18
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Hurgobin B, Golicz AA, Bayer PE, Chan CK, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin IAP, Pires JC, Chalhoub B, King GJ, Snowdon R, Batley J, Edwards D. Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1265-1274. [PMID: 29205771 PMCID: PMC5999312 DOI: 10.1111/pbi.12867] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 05/08/2023]
Abstract
Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.
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Affiliation(s)
- Bhavna Hurgobin
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
- School of Agriculture and Food SciencesUniversity of QueenslandSt. LuciaQLDAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVICAustralia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Chon‐Kit Kenneth Chan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Aria Dolatabadian
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Sarah V. Schiessl
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Birgit Samans
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Juan D. Montenegro
- School of Agriculture and Food SciencesUniversity of QueenslandSt. LuciaQLDAustralia
| | | | - J. Chris Pires
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Boulos Chalhoub
- Institute of System and Synthetic Biology, Organization and Evolution of Complex GenomesInstitut National de la Recherche agronomique, GenopoleCentre National de la Recherche ScientifiqueUniversité d'Evry Val d'EssonneUniversité Paris‐SaclayEvryFrance
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Rod Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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19
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Malmberg MM, Pembleton LW, Baillie RC, Drayton MC, Sudheesh S, Kaur S, Shinozuka H, Verma P, Spangenberg GC, Daetwyler HD, Forster JW, Cogan NO. Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:877-889. [PMID: 28913899 PMCID: PMC5866951 DOI: 10.1111/pbi.12835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/03/2017] [Accepted: 09/08/2017] [Indexed: 05/09/2023]
Abstract
The application of genomics in crops has the ability to significantly improve genetic gain for agriculture. Many marker-dense tools have been developed, but few have seen broad adoption in plant genomics due to issues of significant variations of genome size, levels of ploidy, single nucleotide polymorphism (SNP) frequency and reproductive habit. When combined with limited breeding activities, small research communities and scant sequence resources, the suitability of popular systems is often suboptimal and routinely fails to effectively balance cost-effectiveness and sample throughput. Genotyping-by-sequencing (GBS) encompasses a range of protocols including resequencing of the transcriptome. This study describes a skim GBS-transcriptomics (GBS-t) approach developed to be broadly applicable, cost-effective and high-throughput while still assaying a significant number of SNP loci. A range of crop species with differing levels of ploidy and degree of inbreeding/outbreeding were chosen, including perennial ryegrass, a diploid outbreeding forage grass; phalaris, a putative segmental allotetraploid outbreeding forage grass; lentil, a diploid inbreeding grain legume; and canola, an allotetraploid partially outbreeding oilseed. GBS-t was validated as a simple and largely automated, cost-effective method which generates sufficient SNPs (from 89 738 to 231 977) with acceptable levels of missing data and even genome coverage from c. 3 million sequence reads per sample. GBS-t is therefore a broadly applicable system suitable for many crops, offering advantages over other systems. The correct choice of subsequent sequence analysis software is important, and the bioinformatics process should be iterative and tailored to the specific challenges posed by ploidy variation and extent of heterozygosity.
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Affiliation(s)
- M. Michelle Malmberg
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
- School of Applied Systems BiologyLa Trobe UniversityBundooraVictoria 3086Australia
| | - Luke W. Pembleton
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
| | - Rebecca C. Baillie
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
| | - Michelle C. Drayton
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
| | - Shimna Sudheesh
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
| | - Sukhjiwan Kaur
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
| | - Hiroshi Shinozuka
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
| | - Preeti Verma
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
| | - German C. Spangenberg
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
- School of Applied Systems BiologyLa Trobe UniversityBundooraVictoria 3086Australia
| | - Hans D. Daetwyler
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
- School of Applied Systems BiologyLa Trobe UniversityBundooraVictoria 3086Australia
| | - John W. Forster
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
- School of Applied Systems BiologyLa Trobe UniversityBundooraVictoria 3086Australia
| | - Noel O.I. Cogan
- Agriculture VictoriaAgriBioCentre for AgriBioscience5 Ring RoadBundooraVictoria 3083Australia
- School of Applied Systems BiologyLa Trobe UniversityBundooraVictoria 3086Australia
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20
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Luo Z, Wang M, Long Y, Huang Y, Shi L, Zhang C, Liu X, Fitt BDL, Xiang J, Mason AS, Snowdon RJ, Liu P, Meng J, Zou J. Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1569-1585. [PMID: 28455767 PMCID: PMC5719798 DOI: 10.1007/s00122-017-2911-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/19/2017] [Indexed: 05/10/2023]
Abstract
A comprehensive linkage atlas for seed yield in rapeseed. Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.
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Affiliation(s)
- Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongju Huang
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bruce D. L. Fitt
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Jinxia Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
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21
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Koh JCO, Barbulescu DM, Norton S, Redden B, Salisbury PA, Kaur S, Cogan N, Slater AT. A multiplex PCR for rapid identification of Brassica species in the triangle of U. PLANT METHODS 2017; 13:49. [PMID: 28638437 PMCID: PMC5472915 DOI: 10.1186/s13007-017-0200-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/08/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Within the Brassicaceae, six species from the genus Brassica are widely cultivated throughout the world as oilseed, condiment, fodder or vegetable crops. The genetic relationships among the six Brassica species are described by U's triangle model. Extensive shared traits and diverse morphotypes among Brassica species make identification and classification based on phenotypic data alone challenging and unreliable, especially when dealing with large germplasm collections. Consequently, a major issue for genebank collections is ensuring the correct identification of species. Molecular genotyping based on simple sequence repeat (SSR) marker sequencing or the Illumina Infinium Brassica napus 60K single nucleotide polymorphism (SNP) array has been used to identify species and assess genetic diversity of Brassica collections. However, these methods are technically challenging, expensive and time-consuming, making them unsuitable for routine or rapid screening of Brassica accessions for germplasm management. A cheaper, faster and simpler method for Brassica species identification is described here. RESULTS A multiplex polymerase chain reaction (MPCR) consisting of new and existing primers specific to the Brassica A, B and C genomes was able to reliably distinguish all six Brassica species in the triangle of U with 16 control samples of known species identity. Further validation against 120 Brassica accessions previously genotyped showed that the MPCR is highly accurate and comparable to more advanced techniques such as SSR marker sequencing or the Illumina Infinium B. napus 60K SNP array. In addition, the MPCR was sensitive enough to detect seed contaminations in pooled seed samples of Brassica accessions. CONCLUSION A cheap and fast multiplex PCR assay for identification of Brassica species in the triangle of U was developed and validated in this study. The MPCR assay can be readily implemented in any basic molecular laboratory and should prove useful for the management of Brassica germplasm collections in genebanks.
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Affiliation(s)
- Joshua C. O. Koh
- Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, 110 Natimuk Rd, Horsham, VIC 3401 Australia
| | - Denise M. Barbulescu
- Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, 110 Natimuk Rd, Horsham, VIC 3401 Australia
| | - Sally Norton
- Department of Economic Development, Jobs, Transport and Resources, Australian Grains Genebank, Private Bag 260, Horsham, VIC 3401 Australia
| | - Bob Redden
- Department of Economic Development, Jobs, Transport and Resources, Australian Grains Genebank, Private Bag 260, Horsham, VIC 3401 Australia
| | - Phil A. Salisbury
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010 Australia
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Sukhjiwan Kaur
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Noel Cogan
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Anthony T. Slater
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia
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22
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Plissonneau C, Blaise F, Ollivier B, Leflon M, Carpezat J, Rouxel T, Balesdent MH. Unusual evolutionary mechanisms to escape effector-triggered immunity in the fungal phytopathogen Leptosphaeria maculans. Mol Ecol 2017; 26:2183-2198. [PMID: 28160497 DOI: 10.1111/mec.14046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/16/2016] [Accepted: 01/17/2017] [Indexed: 12/18/2022]
Abstract
Leptosphaeria maculans is the fungus responsible for the stem canker disease of oilseed rape (Brassica napus). AvrLm3 and AvrLm4-7, two avirulence effector genes of L. maculans, are involved in an unusual relationship: AvrLm4-7 suppresses the Rlm3-mediated resistance. Here, we assessed AvrLm3 polymorphism in a collection of 235 L. maculans isolates. No field isolates exhibited deletion or inactivating mutations in AvrLm3, as observed for other L. maculans avirulence genes. Eleven isoforms of the AvrLm3 protein were found. In isolates virulent towards both Rlm3 and Rlm7 (a3a7), the loss of the Rlm3-mediated resistance response was due to two distinct mechanisms. First, when AvrLm4-7 was inactivated (deletion or inactivating mutations), amino acid substitutions in AvrLm3 generated virulent isoforms of the protein. Second, when only point mutations were observed in AvrLm4-7, a3a7 isolates still contained an avirulent allele of AvrLm3. Directed mutagenesis confirmed that some point mutations in AvrLm4-7 were sufficient for the fungus to escape Rlm7-mediated resistance while maintaining the suppression of the AvrLm3 phenotype. Signatures of positive selection were also identified in AvrLm3. The complex evolutionary mechanisms enabling L. maculans to escape Rlm3-mediated resistance while preserving AvrLm3 integrity, along with observed reduced aggressiveness of isolates silenced for AvrLm3, serves to emphasize the importance of this effector in pathogenicity towards B. napus. While the common response to resistance gene pressure is local selection of isolates depleted in the cognate avirulence gene, this example contributes to complexify the gene-for-gene concept of plant-pathogen evolution with a 'camouflaged' model allowing retention of nondispensable avirulence effectors.
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Affiliation(s)
- C Plissonneau
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France.,Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 16, 8092, Zürich, Switzerland
| | - F Blaise
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - B Ollivier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - M Leflon
- Terres Inovia, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - J Carpezat
- Terres Inovia, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - T Rouxel
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - M-H Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
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Larkan NJ, Yu F, Lydiate DJ, Rimmer SR, Borhan MH. Single R Gene Introgression Lines for Accurate Dissection of the Brassica - Leptosphaeria Pathosystem. FRONTIERS IN PLANT SCIENCE 2016; 7:1771. [PMID: 27965684 PMCID: PMC5124708 DOI: 10.3389/fpls.2016.01771] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/10/2016] [Indexed: 05/18/2023]
Abstract
Seven blackleg resistance (R) genes (Rlm1, Rlm2, Rlm3, Rlm4, LepR1, LepR2 & LepR3) were each introgressed into a common susceptible B. napus doubled-haploid (DH) line through reciprocal back-crossing, producing single-R gene introgression lines (ILs) for use in the pathological and molecular study of Brassica-Leptosphaeria interactions. The genomic positions of the R genes were defined through molecular mapping and analysis with transgenic L. maculans isolates was used to confirm the identity of the introgressed genes where possible. Using L. maculans isolates of contrasting avirulence gene (Avr) profiles, we preformed extensive differential pathology for phenotypic comparison of the ILs to other B. napus varieties, demonstrating the ILs can provide for the accurate assessment of Avr-R gene interactions by avoiding non-Avr dependant alterations to resistance responses which can occur in some commonly used B. napus varieties. Whole-genome SNP-based assessment allowed us to define the donor parent introgressions in each IL and provide a strong basis for comparative molecular dissection of the pathosystem.
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Affiliation(s)
- Nicholas J. Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food CanadaSaskatoon, SK, Canada
- Armatus Genetics Inc.Saskatoon, SK, Canada
| | - Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food CanadaSaskatoon, SK, Canada
| | - Derek J. Lydiate
- Saskatoon Research Centre, Agriculture and Agri-Food CanadaSaskatoon, SK, Canada
| | - S. Roger Rimmer
- Saskatoon Research Centre, Agriculture and Agri-Food CanadaSaskatoon, SK, Canada
| | - M. Hossein Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food CanadaSaskatoon, SK, Canada
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24
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Haddadi P, Ma L, Wang H, Borhan MH. Genome-wide transcriptomic analyses provide insights into the lifestyle transition and effector repertoire of Leptosphaeria maculans during the colonization of Brassica napus seedlings. MOLECULAR PLANT PATHOLOGY 2016; 17:1196-210. [PMID: 26679637 PMCID: PMC6638455 DOI: 10.1111/mpp.12356] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/18/2015] [Accepted: 12/11/2015] [Indexed: 05/08/2023]
Abstract
Molecular interaction between the causal agent of blackleg disease, Leptosphaeria maculans (Lm), and its host, Brassica napus, is largely unknown. We applied a deep RNA-sequencing approach to gain insight into the pathogenicity mechanisms of Lm and the defence response of B. napus. RNA from the infected susceptible B. napus cultivar Topas DH16516, sampled at 2-day intervals (0-8 days), was sequenced and used for gene expression profiling. Patterns of gene expression regulation in B. napus showed multifaceted defence responses evident by the differential expression of genes encoding the pattern recognition receptor CERK1 (chitin elicitor receptor kinase 1), receptor like proteins and WRKY transcription factors. The up-regulation of genes related to salicylic acid and jasmonic acid at the initial and late stages of infection, respectively, provided evidence for the biotrophic and necrotrophic life stages of Lm during the infection of B. napus cotyledons. Lm transition from biotrophy to necrotropy was also supported by the expression function of Lm necrosis and ethylene-inducing (Nep-1)-like peptide. Genes encoding polyketide synthases and non-ribosomal peptide synthetases, with potential roles in pathogenicity, were up-regulated at 6-8 days after inoculation. Among other plant defence-related genes differentially regulated in response to Lm infection were genes involved in the reinforcement of the cell wall and the production of glucosinolates. Dual RNA-sequencing allowed us to define the Lm candidate effectors expressed during the infection of B. napus. Several candidate effectors suppressed Bax-induced cell death when transiently expressed in Nicotiana benthamaina leaves.
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Affiliation(s)
- Parham Haddadi
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Lisong Ma
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Haiyan Wang
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Agricultural University of Hebei, Baoding, China, 071001
| | - M Hossein Borhan
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
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Larkan NJ, Raman H, Lydiate DJ, Robinson SJ, Yu F, Barbulescu DM, Raman R, Luckett DJ, Burton W, Wratten N, Salisbury PA, Rimmer SR, Borhan MH. Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus. BMC PLANT BIOLOGY 2016; 16:183. [PMID: 27553246 PMCID: PMC4995785 DOI: 10.1186/s12870-016-0877-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/17/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Resistance to the blackleg disease of Brassica napus (canola/oilseed rape), caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, is determined by both race-specific resistance (R) genes and quantitative resistance loci (QTL), or adult-plant resistance (APR). While the introgression of R genes into breeding material is relatively simple, QTL are often detected sporadically, making them harder to capture in breeding programs. For the effective deployment of APR in crop varieties, resistance QTL need to have a reliable influence on phenotype in multiple environments and be well defined genetically to enable marker-assisted selection (MAS). RESULTS Doubled-haploid populations produced from the susceptible B. napus variety Topas and APR varieties AG-Castle and AV-Sapphire were analysed for resistance to blackleg in two locations over 3 and 4 years, respectively. Three stable QTL were detected in each population, with two loci appearing to be common to both APR varieties. Physical delineation of three QTL regions was sufficient to identify candidate defense-related genes, including a cluster of cysteine-rich receptor-like kinases contained within a 49 gene QTL interval on chromosome A01. Individual L. maculans isolates were used to define the physical intervals for the race-specific R genes Rlm3 and Rlm4 and to identify QTL common to both field studies and the cotyledon resistance response. CONCLUSION Through multi-environment QTL analysis we have identified and delineated four significant and stable QTL suitable for MAS of quantitative blackleg resistance in B. napus, and identified candidate genes which potentially play a role in quantitative defense responses to L. maculans.
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Affiliation(s)
- Nicholas J. Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
- Armatus Genetics Inc, Saskatoon, SK S7W 0C9 Canada
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - Derek J. Lydiate
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - Stephen J. Robinson
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - Denise M. Barbulescu
- Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, Horsham, VIC 3400 Australia
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - David J. Luckett
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - Wayne Burton
- Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, Horsham, VIC 3400 Australia
- Seednet Australia, Golf Course Road, Horsham, VIC 3402 Australia
| | - Neil Wratten
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - Philip A. Salisbury
- Department of Economic Development, Jobs, Transport and Resources, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3083 Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010 Australia
| | - S. Roger Rimmer
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - M. Hossein Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
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Larkan NJ, Ma L, Borhan MH. The Brassica napus receptor-like protein RLM2 is encoded by a second allele of the LepR3/Rlm2 blackleg resistance locus. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:983-92. [PMID: 25644479 DOI: 10.1111/pbi.12341] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 05/02/2023]
Abstract
Leucine-rich repeat receptor-like proteins (LRR-RLPs) are highly adaptable parts of the signalling apparatus for extracellular detection of plant pathogens. Resistance to blackleg disease of Brassica spp. caused by Leptosphaeria maculans is largely governed by host race-specific R-genes, including the LRR-RLP gene LepR3. The blackleg resistance gene Rlm2 was previously mapped to the same genetic interval as LepR3. In this study, the LepR3 locus of the Rlm2 Brassica napus line 'Glacier DH24287' was cloned, and B. napus transformants were analysed for recovery of the Rlm2 phenotype. Multiple B. napus, B. rapa and B. juncea lines were assessed for sequence variation at the locus. Rlm2 was found to be an allelic variant of the LepR3 LRR-RLP locus, conveying race-specific resistance to L. maculans isolates harbouring AvrLm2. Several defence-related LRR-RLPs have previously been shown to associate with the RLK SOBIR1 to facilitate defence signalling. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation of RLM2-SOBIR1 studies revealed that RLM2 interacts with SOBIR1 of Arabidopsis thaliana when co-expressed in Nicotiana benthamiana. The interaction of RLM2 with AtSOBIR1 is suggestive of a conserved defence signalling pathway between B. napus and its close relative A. thaliana.
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Affiliation(s)
- Nicholas J Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Lisong Ma
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
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