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Leitão ST, Rubiales D, Vaz Patto MC. Identification of novel sources of partial and incomplete hypersensitive resistance to rust and associated genomic regions in common bean. BMC Plant Biol 2023; 23:610. [PMID: 38041043 PMCID: PMC10691055 DOI: 10.1186/s12870-023-04619-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
Common bean (Phaseolus vulgaris) is one of the legume crops most consumed worldwide and bean rust is one of the most severe foliar biotrophic fungal diseases impacting its production. In this work, we searched for new sources of rust resistance (Uromyces appendiculatus) in a representative collection of the Portuguese germplasm, known to have accessions with an admixed genetic background between Mesoamerican and Andean gene pools. We identified six accessions with incomplete hypersensitive resistance and 20 partially resistant accessions of Andean, Mesoamerican, and admixed origin. We detected 11 disease severity-associated single-nucleotide polymorphisms (SNPs) using a genome-wide association approach. Six of the associations were related to partial (incomplete non-hypersensitive) resistance and five to incomplete hypersensitive resistance, and the proportion of variance explained by each association varied from 4.7 to 25.2%. Bean rust severity values ranged from 0.2 to 49.1% and all the infection types were identified, reflecting the diversity of resistance mechanisms deployed by the Portuguese germplasm.The associations with U. appendiculatus partial resistance were located in chromosome Pv08, and with incomplete hypersensitive resistance in chromosomes Pv06, Pv07, and Pv08, suggesting an oligogenic inheritance of both types of resistance. A resolution to the gene level was achieved for eight of the associations. The candidate genes proposed included several resistance-associated enzymes, namely β-amylase 7, acyl-CoA thioesterase, protein kinase, and aspartyl protease. Both SNPs and candidate genes here identified constitute promising genomics targets to develop functional molecular tools to support bean rust resistance precision breeding.
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Affiliation(s)
- Susana Trindade Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, 2780-157, Portugal.
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, 2780-157, Portugal
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Owoloye A, Olufemi M, Idowu ET, Oyebola KM. Prevalence of potential mediators of artemisinin resistance in African isolates of Plasmodium falciparum. Malar J 2021; 20:451. [PMID: 34856982 PMCID: PMC8638531 DOI: 10.1186/s12936-021-03987-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/16/2021] [Indexed: 11/30/2022] Open
Abstract
Background The devastating public health impact of malaria has prompted the need for effective interventions. Malaria control gained traction after the introduction of artemisinin-based combination therapy (ACT). However, the emergence of artemisinin (ART) partial resistance in Southeast Asia and emerging reports of delayed parasite sensitivity to ACT in African parasites signal a gradual trend towards treatment failure. Monitoring the prevalence of mutations associated with artemisinin resistance in African populations is necessary to stop resistance in its tracks. Mutations in Plasmodium falciparum genes pfk13, pfcoronin and pfatpase6 have been linked with ART partial resistance. Methods Findings from published research articles on the prevalence of pfk13, pfcoronin and pfatpase6 polymorphisms in Africa were collated. PubMed, Embase and Google Scholar were searched for relevant articles reporting polymorphisms in these genes across Africa from 2014 to August 2021, for pfk13 and pfcoronin. For pfatpase6, relevant articles between 2003 and August 2021 were retrieved. Results Eighty-seven studies passed the inclusion criteria for this analysis and reported 742 single nucleotide polymorphisms in 37,864 P. falciparum isolates from 29 African countries. Five validated-pfk13 partial resistance markers were identified in Africa: R561H in Rwanda and Tanzania, M476I in Tanzania, F446I in Mali, C580Y in Ghana, and P553L in an Angolan isolate. In Tanzania, three (L263E, E431K, S769N) of the four mutations (L263E, E431K, A623E, S769N) in pfatpase6 gene associated with high in vitro IC50 were reported. pfcoronin polymorphisms were reported in Senegal, Gabon, Ghana, Kenya, and Congo, with P76S being the most prevalent mutation. Conclusions This meta-analysis provides an overview of the prevalence and widespread distribution of pfk13, pfcoronin and pfatpase6 mutations in Africa. Understanding the phenotypic consequences of these mutations can provide information on the efficacy status of artemisinin-based treatment of malaria across the continent. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03987-6.
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Affiliation(s)
- Afolabi Owoloye
- Genomic Research in Biomedicine Laboratory, Biochemistry and Nutrition Department, Nigerian Institute of Medical Research, Lagos, Nigeria.,Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Michael Olufemi
- Genomic Research in Biomedicine Laboratory, Biochemistry and Nutrition Department, Nigerian Institute of Medical Research, Lagos, Nigeria.,Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Emmanuel T Idowu
- Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Kolapo M Oyebola
- Genomic Research in Biomedicine Laboratory, Biochemistry and Nutrition Department, Nigerian Institute of Medical Research, Lagos, Nigeria. .,Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria. .,Sickle Cell Branch, National Heart Lung and Blood Institute, US National Institutes of Health, Bethesda, MD, USA.
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Moury B, Lebaron C, Szadkowski M, Ben Khalifa M, Girardot G, Bolou Bi BA, Koné D, Nitiema LW, Fakhfakh H, Gallois JL. Knock-out mutation of eukaryotic initiation factor 4E2 (eIF4E2) confers resistance to pepper veinal mottle virus in tomato. Virology 2020; 539:11-7. [PMID: 31622792 DOI: 10.1016/j.virol.2019.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 11/23/2022]
Abstract
Translation initiation factors 4E (eIF4E) are the main source of resistance to potyvirus. We systematically assessed tomato single and double knock-out (KO) mutants of members of the eIF4E-coding gene family for resistance to Pepper veinal mottle virus (PVMV), a major constraint to tomato production. We show that the KO mutant of eIF4E2 has partial resistance to PVMV isolate IC, with plants harboring weak symptoms and low virus loads at the systemic level. The causal effect of eIF4E2 loss-of-function on resistance was confirmed on a progeny segregating for the KO mutation. The eIF4E2 KO mutant was resistant to six of the eight PVMV isolates tested and no resistance to other potyviruses was observed. This is the first evidence that mutation of eIF4E2 is in itself conferring resistance to a potyvirus and 3D protein modelling suggests that the eIF4E2 gene could be converted into a functional resistance allele.
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Omrani M, Roth M, Roch G, Blanc A, Morris CE, Audergon JM. Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker. BMC Plant Biol 2019; 19:31. [PMID: 30665361 PMCID: PMC6341767 DOI: 10.1186/s12870-019-1631-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/04/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Diseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among them, bacterial canker of apricot is exceedingly difficult to control due to a lack of efficient prophylactic measures. Several sources of partial resistance have been identified among genetic resources but the underlying genetic pattern has not been elucidated thus far. In this study, we phenotyped bacterial canker susceptibility in an apricot core-collection of 73 accessions over 4 years by measuring canker and superficial browning lengths issued from artificial inoculations in the orchard. In order to investigate the genetic architecture of partial resistance, we performed a genome-wide association study using best linear unbiased predictors on genetic (G) and genetic x year (G × Y) interaction effects extracted from linear mixed models. Using a set of 63,236 single-nucleotide polymorphism markers genotyped in the germplasm over the whole genome, multi-locus and multi-variate mixed models aimed at mapping the resistance while controlling for relatedness between individuals. RESULTS We detected 11 significant associations over 7 candidate loci linked to disease resistance under the two most severe years. Colocalizations between G and G × Y terms indicated a modulation on allelic effect depending on environmental conditions. Among the candidate loci, two loci on chromosomes 5 and 6 had a high impact on both canker length and superficial browning, explaining 41 and 26% of the total phenotypic variance, respectively. We found unexpected long-range linkage disequilibrium (LD) between these two markers revealing an inter-chromosomal LD block linking the two underlying genes. This result supports the hypothesis of a co-adaptation effect due to selection through population demography. Candidate genes annotations suggest a functional pathway involving abscisic acid, a hormone mainly known for mediating abiotic stress responses but also reported as a potential factor in plant-pathogen interactions. CONCLUSIONS Our study contributed to the first detailed characterization of the genetic determinants of partial resistance to bacterial canker in a Rosaceae species. It provided tools for fruit tree breeding by identifying progenitors with favorable haplotypes and by providing major-effect markers for a marker-assisted selection strategy.
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Affiliation(s)
- Mariem Omrani
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
- INRA, UR407 Pathologie Végétale, Centre de Recherche PACA, Montfavet, France
- ENGREF, AgroParisTech, Paris, France
| | - Morgane Roth
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
- Present Address: Agroscope, Research Division Plant Breeding, Wädenswil, Switzerland
| | - Guillaume Roch
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
- CEP Innovation, Lyon, France
| | - Alain Blanc
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
| | - Cindy E. Morris
- INRA, UR407 Pathologie Végétale, Centre de Recherche PACA, Montfavet, France
| | - Jean-Marc Audergon
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
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Loarce Y, Dongil P, Fominaya A, González JM, Ferrer E. PK-profiling method for identifying the expression of resistance-associated genes in partially resistant oats to crown rust. BMC Plant Biol 2018; 18:376. [PMID: 30594125 PMCID: PMC6311036 DOI: 10.1186/s12870-018-1604-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Protein kinases play a key role in plant cell homeostasis and the activation of defense mechanisms. Partial resistance to fungi in plants is interesting because of its durability. However, the variable number of minor loci associated with this type of resistance hampers the reliable identification of the full range of genes involved. The present work reports the technique of protein kinase (PK)-profiling for the identification of the PK genes induced in the partially resistant oats line MN841801-1 following exposure to the fungus Puccinia coronata. This is the first time this technique has been used with cDNA (complementary DNA) from a suppression subtractive hybridization library obtained after the hybridization of cDNAs from inoculated and mock-inoculated plants. RESULTS Six degenerate primers based on the conserved domains of protein kinases were used in a PK-profiling assay including cDNA from mock-inoculated leaves and subtracted cDNA. Of the 75.7% of sequences cloned and sequenced that showed significant similarity to resistance genes, 76% were found to code for PKs. Translation and ClustalW2 alignment of each sequence cloned with the complete sequences of the most similar B. distachyon PKs allowed those of the partially resistant oat line to be deduced and characterized. Further, a phylogenetic study carried out after alignment of these B. distachyon PK sequences with the most similar protein sequences of related species also allowed to deduce different functions for the PK cloned. RT-qPCR (Reverse Transcription-quantitative PCR) was analyzed on nine representative sequences to validate the reliability of the employed PK-profiling method as a tool for identifying the expression of resistance-associated genes. CONCLUSIONS PK-profiling would appear to be a useful tool for the identification of the PKs expressed in oats after challenge by P. coronata, and perhaps other pathogens. Most of the PKs studied are related to receptor-like protein kinases expressed shortly after infection. This is in agreement with previous studies indicating a close relationship between partial resistance and the first layer of defense against pathogen used by plants.
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Affiliation(s)
- Yolanda Loarce
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Pilar Dongil
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Araceli Fominaya
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Juan M. González
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Esther Ferrer
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
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Ziems LA, Franckowiak JD, Platz GJ, Mace ES, Park RF, Singh D, Jordan DR, Hickey LT. Investigating successive Australian barley breeding populations for stable resistance to leaf rust. Theor Appl Genet 2017; 130:2463-2477. [PMID: 28836114 DOI: 10.1007/s00122-017-2970-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene Rph20 to provide stable leaf rust resistance across environments. Stable resistance to barley leaf rust (BLR, caused by Puccinia hordei) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with Rph20 to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene Rph20 was the only active resistance region consistently detected across BPs. Of the QTL identified, RphQ27 on chromosome 6HL was considered the best candidate for pairing with Rph20. RphQ27 did not align or share proximity with known genes and was detected in three of the four BPs. The combination of RphQ27 and Rph20 was of low frequency in the breeding material; however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across diverse environments.
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Affiliation(s)
- L A Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - J D Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - G J Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - E S Mace
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - R F Park
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D Singh
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D R Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - L T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
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Schneider R, Rolling W, Song Q, Cregan P, Dorrance AE, McHale LK. Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea. BMC Genomics 2016; 17:607. [PMID: 27515508 PMCID: PMC4982113 DOI: 10.1186/s12864-016-2918-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 07/07/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae. RESULTS Resistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes. CONCLUSIONS QTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial resistance to P. sojae.
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Affiliation(s)
- Rhiannon Schneider
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Present Address: Pioneer Hi-Bred International Inc., Napoleon, OH, 43545, USA
| | - William Rolling
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Qijian Song
- US Department of Agriculture, Soybean Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Perry Cregan
- US Department of Agriculture, Soybean Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Anne E Dorrance
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Leah K McHale
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA.
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Lavaud C, Baviere M, Le Roy G, Hervé MR, Moussart A, Delourme R, Pilet-Nayel ML. Single and multiple resistance QTL delay symptom appearance and slow down root colonization by Aphanomyces euteiches in pea near isogenic lines. BMC Plant Biol 2016; 16:166. [PMID: 27465043 PMCID: PMC4964060 DOI: 10.1186/s12870-016-0822-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/26/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Understanding the effects of resistance QTL on pathogen development cycle is an important issue for the creation of QTL combination strategies to durably increase disease resistance in plants. The oomycete pathogen Aphanomyces euteiches, causing root rot disease, is one of the major factors limiting the pea crop in the main producing countries. No commercial resistant varieties are currently available in Europe. Resistance alleles at seven main QTL were recently identified and introgressed into pea agronomic lines, resulting in the creation of Near Isogenic Lines (NILs) at the QTL. This study aimed to determine the effect of main A. euteiches resistance QTL in NILs on different steps of the pathogen life cycle. RESULTS NILs carrying resistance alleles at main QTL in susceptible genetic backgrounds were evaluated in a destructive test under controlled conditions. The development of root rot disease severity and pathogen DNA levels in the roots was measured during ten days after inoculation. Significant effects of several resistance alleles at the two major QTL Ae-Ps7.6 and Ae-Ps4.5 were observed on symptom appearance and root colonization by A. euteiches. Some resistance alleles at three other minor-effect QTL (Ae-Ps2.2, Ae-Ps3.1 and Ae-Ps5.1) significantly decreased root colonization. The combination of resistance alleles at two or three QTL including the major QTL Ae-Ps7.6 (Ae-Ps5.1/Ae-Ps7.6 or Ae-Ps2.2/Ae-Ps3.1/Ae-Ps7.6) had an increased effect on delaying symptom appearance and/or slowing down root colonization by A. euteiches and on plant resistance levels, compared to the effects of individual or no resistance alleles. CONCLUSIONS This study demonstrated the effects of single or multiple resistance QTL on delaying symptom appearance and/or slowing down colonization by A. euteiches in pea roots, using original plant material and a precise pathogen quantification method. Our findings suggest that single resistance QTL can act on multiple or specific steps of the disease development cycle and that their actions could be pyramided to increase partial resistance in future pea varieties. Further studies are needed to investigate QTL effects on different steps of the pathogen life cycle, as well as the efficiency and durability of pyramiding strategies using QTL which appear to act on the same stage of the pathogen cycle.
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Affiliation(s)
- C Lavaud
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
| | - M Baviere
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
| | - G Le Roy
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
| | - M R Hervé
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
| | - A Moussart
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
- Terres Inovia, 11 rue de Monceau, CS 60003, 75378, Paris cedex 08, France
| | - R Delourme
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France
| | - M-L Pilet-Nayel
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu cedex, France.
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French E, Kim BS, Iyer-Pascuzzi AS. Mechanisms of quantitative disease resistance in plants. Semin Cell Dev Biol 2016; 56:201-208. [PMID: 27212254 DOI: 10.1016/j.semcdb.2016.05.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/18/2016] [Indexed: 11/29/2022]
Abstract
Quantitative disease resistance (QDR) causes the reduction, but not absence, of disease, and is a major type of disease resistance for many crop species. QDR results in a continuous distribution of disease scores across a segregating population, and is typically due to many genes with small effects. It may also be a source of durable resistance. The past decade has seen significant progress in cloning genes underlying QDR. In this review, we focus on these recently cloned genes and identify new themes of QDR emerging from these studies.
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Affiliation(s)
- Elizabeth French
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, United States
| | - Bong-Suk Kim
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, United States
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, United States.
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Lemarié S, Robert-Seilaniantz A, Lariagon C, Lemoine J, Marnet N, Jubault M, Manzanares-Dauleux MJ, Gravot A. Both the Jasmonic Acid and the Salicylic Acid Pathways Contribute to Resistance to the Biotrophic Clubroot Agent Plasmodiophora brassicae in Arabidopsis. Plant Cell Physiol 2015; 56:2158-68. [PMID: 26363358 DOI: 10.1093/pcp/pcv127] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/02/2015] [Indexed: 05/18/2023]
Abstract
The role of salicylic acid (SA) and jasmonic acid (JA) signaling in resistance to root pathogens has been poorly documented. We assessed the contribution of SA and JA to basal and partial resistance of Arabidopsis to the biotrophic clubroot agent Plasmodiophora brassicae. SA and JA levels as well as the expression of the SA-responsive genes PR2 and PR5 and the JA-responsive genes ARGAH2 and THI2.1 were monitored in infected roots of the accessions Col-0 (susceptible) and Bur-0 (partially resistant). SA signaling was activated in Bur-0 but not in Col-0. The JA pathway was weakly activated in Bur-0 but was strongly induced in Col-0. The contribution of both pathways to clubroot resistance was then assessed using exogenous phytohormone application and mutants affected in SA or JA signaling. Exogenous SA treatment decreased clubroot symptoms in the two Arabidopsis accessions, whereas JA treatment reduced clubroot symptoms only in Col-0. The cpr5-2 mutant, in which SA responses are constitutively induced, was more resistant to clubroot than the corresponding wild type, and the JA signaling-deficient mutant jar1 was more susceptible. Finally, we showed that the JA-mediated induction of NATA1 drove N(δ)-acetylornithine biosynthesis in infected Col-0 roots. The 35S::NATA1 and nata1 lines displayed reduced or enhanced clubroot symptoms, respectively, thus suggesting that in Col-0 this pathway was involved in the JA-mediated basal clubroot resistance. Overall, our data support the idea that, depending on the Arabidopsis accession, both SA and JA signaling can play a role in partial inhibition of clubroot development in compatible interactions with P. brassicae.
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Affiliation(s)
| | | | | | | | - Nathalie Marnet
- Plateau de Profilage Métabolique et Métabolomique (P2M2) Centre de Recherche Angers Nantes BIA, INRA de Rennes, F-35653 Le Rheu, France
| | | | | | - Antoine Gravot
- Université Rennes 1, UMR1349 IGEPP, F-35000 Rennes, France
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Caffier V, Lasserre-Zuber P, Giraud M, Lascostes M, Stievenard R, Lemarquand A, van de Weg E, Expert P, Denancé C, Didelot F, Le Cam B, Durel CE. Erosion of quantitative host resistance in the apple×Venturia inaequalis pathosystem. Infect Genet Evol 2014; 27:481-9. [PMID: 24530903 DOI: 10.1016/j.meegid.2014.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 01/31/2014] [Accepted: 02/07/2014] [Indexed: 12/20/2022]
Abstract
Theoretical approaches predict that host quantitative resistance selects for pathogens with a high level of pathogenicity, leading to erosion of the resistance. This process of erosion has, however, rarely been experimentally demonstrated. To investigate the erosion of apple quantitative resistance to scab disease, we surveyed scab incidence over time in a network of three orchards planted with susceptible and quantitatively resistant apple genotypes. We sampled Venturiainaequalis isolates from two of these orchards at the beginning of the experiment and we tested their quantitative components of pathogenicity (i.e., global disease severity, lesion density, lesion size, latent period) under controlled conditions. The disease severity produced by the isolates on the quantitatively resistant apple genotypes differed between the sites. Our study showed that quantitative resistance may be subject to erosion and even complete breakdown, depending on the site. We observed this evolution over time for apple genotypes that combine two broad-spectrum scab resistance QTLs, F11 and F17, showing a significant synergic effect of this combination in favour of resistance (i.e., favourable epistatic effect). We showed that isolates sampled in the orchard where the resistance was inefficient presented a similar level of pathogenicity on both apple genotypes with quantitative resistance and susceptible genotypes. As a consequence, our results revealed a case where the use of quantitative resistance may result in the emergence of a generalist pathogen population that has extended its pathogenicity range by performing similarly on susceptible and resistant genotypes. This emphasizes the need to develop quantitative resistances conducive to trade-offs within the pathogen populations concerned.
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Affiliation(s)
- Valérie Caffier
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, SFR 4207 QUASAV, 49071 Beaucouzé Cedex, France; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France.
| | - Pauline Lasserre-Zuber
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, SFR 4207 QUASAV, 49071 Beaucouzé Cedex, France; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France
| | - Michel Giraud
- CTIFL - Centre Technique Interprofessionnel des Fruits et Légumes, Centre de Lanxade, 24130 Prigonrieux, France
| | - Matthieu Lascostes
- CRRG - Centre Régional de Ressources Génétiques, Ferme du Héron, 59650 Villeneuve d'Ascq, France
| | - René Stievenard
- CRRG - Centre Régional de Ressources Génétiques, Ferme du Héron, 59650 Villeneuve d'Ascq, France
| | - Arnaud Lemarquand
- INRA, Unité Expérimentale Horticole N°34 0449, Centre d'Angers-Nantes, 49071 Beaucouzé Cedex, France
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Pascale Expert
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, SFR 4207 QUASAV, 49071 Beaucouzé Cedex, France; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France
| | - Caroline Denancé
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, SFR 4207 QUASAV, 49071 Beaucouzé Cedex, France; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France
| | - Frédérique Didelot
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, SFR 4207 QUASAV, 49071 Beaucouzé Cedex, France; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France
| | - Bruno Le Cam
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, SFR 4207 QUASAV, 49071 Beaucouzé Cedex, France; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France
| | - Charles-Eric Durel
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, SFR 4207 QUASAV, 49071 Beaucouzé Cedex, France; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, 49045 Angers, France
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Lowe I, Cantu D, Dubcovsky J. Durable resistance to the wheat rusts: Integrating systems biology and traditional phenotype-based research methods to guide the deployment of resistance genes. Euphytica 2011. [PMID: 26900170 DOI: 10.1007/s10681‐010‐0311‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genes which confer partial resistance to the rusts in wheat figure prominently in discussions of potential durable resistance strategies. The positional cloning of the first of these genes, Lr34/Yr18 and Yr36, has revealed different protein structures, suggesting that the category of partial resistance genes, as defined by phenotype, likely groups together suites of functionally heterogenous genes. With the number of mapped partial rust resistance genes increasing rapidly as a result of ongoing advances in marker and sequencing technologies, breeding programs needing to select and prioritize genes for deployment confront a fundamental question: which genes or gene combinations are more likely to provide durable protection against these evolving pathogens? We argue that a refined classification of partial rust resistance genes is required to start answering this question, one based not merely on disease phenotype but also on gene cloning, molecular functional characterization, and interactions with other host and pathogen proteins. Combined with accurate and detailed disease phenotyping and standard genetic studies, an integrated wheat-rust interactome promises to provide the basis for a functional classification of partial resistance genes and thus a conceptual framework for their rational deployment.
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Affiliation(s)
- Iago Lowe
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Dario Cantu
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
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Lowe I, Cantu D, Dubcovsky J. Durable resistance to the wheat rusts: Integrating systems biology and traditional phenotype-based research methods to guide the deployment of resistance genes. Euphytica 2011; 179:69-79. [PMID: 26900170 PMCID: PMC4756431 DOI: 10.1007/s10681-010-0311-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 11/11/2010] [Indexed: 05/18/2023]
Abstract
Genes which confer partial resistance to the rusts in wheat figure prominently in discussions of potential durable resistance strategies. The positional cloning of the first of these genes, Lr34/Yr18 and Yr36, has revealed different protein structures, suggesting that the category of partial resistance genes, as defined by phenotype, likely groups together suites of functionally heterogenous genes. With the number of mapped partial rust resistance genes increasing rapidly as a result of ongoing advances in marker and sequencing technologies, breeding programs needing to select and prioritize genes for deployment confront a fundamental question: which genes or gene combinations are more likely to provide durable protection against these evolving pathogens? We argue that a refined classification of partial rust resistance genes is required to start answering this question, one based not merely on disease phenotype but also on gene cloning, molecular functional characterization, and interactions with other host and pathogen proteins. Combined with accurate and detailed disease phenotyping and standard genetic studies, an integrated wheat-rust interactome promises to provide the basis for a functional classification of partial resistance genes and thus a conceptual framework for their rational deployment.
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Affiliation(s)
- Iago Lowe
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Dario Cantu
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
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