1
|
Campa A, Geffroy V, Bitocchi E, Noly A, Papa R, Ferreira JJ. Screening for resistance to four fungal diseases and associated genomic regions in a snap bean diversity panel. FRONTIERS IN PLANT SCIENCE 2024; 15:1386877. [PMID: 38919821 PMCID: PMC11196787 DOI: 10.3389/fpls.2024.1386877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024]
Abstract
Anthracnose, white mold, powdery mildew, and root rot caused by Colletotrichum lindemuthianum, Scletorinia sclerotiorum, Erysiphe spp., and Pythium ultimum, respectively, are among the most frequent diseases that cause significant production losses worldwide in common bean (Phaseolus vulgaris L.). Reactions against these four fungal diseases were investigated under controlled conditions using a diversity panel of 311 bean lines for snap consumption (Snap bean Panel). The genomic regions involved in these resistance responses were identified based on a genome-wide association study conducted with 16,242 SNP markers. The highest number of resistant lines was observed against the three C. lindemuthianum isolates evaluated: 156 lines were resistant to CL124 isolate, 146 lines resistant to CL18, and 109 lines were resistant to C531 isolate. Two well-known anthracnose resistance clusters were identified, the Co-2 on chromosome Pv11 for isolates CL124 and CL18, and the Co-3 on chromosome Pv04 for isolates CL124 and C531. In addition, other lesser-known regions of anthracnose resistance were identified on chromosomes Pv02, Pv06, Pv08, and Pv10. For the white mold isolate tested, 24 resistant lines were identified and the resistance was localized to three different positions on chromosome Pv08. For the powdery mildew local isolate, only 12 resistant lines were identified, and along with the two previous resistance genes on chromosomes Pv04 and Pv11, a new region on chromosome Pv06 was also identified. For root rot caused by Pythium, 31 resistant lines were identified and two main regions were located on chromosomes Pv04 and Pv05. Relevant information for snap bean breeding programs was provided in this work. A total of 20 lines showed resistant or intermediate responses against four or five isolates, which can be suitable for sustainable farm production and could be used as resistance donors. Potential genes and genomic regions to be considered for targeted improvement were provided, including new or less characterized regions that should be validated in future works. Powdery mildew disease was identified as a potential risk for snap bean production and should be considered a main goal in breeding programs.
Collapse
Affiliation(s)
- Ana Campa
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), Villaviciosa, Asturias, Spain
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, Ancona, Italy
| | - Alicia Noly
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, Ancona, Italy
| | - Juan José Ferreira
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), Villaviciosa, Asturias, Spain
| |
Collapse
|
2
|
Lovatto M, Vidigal Filho PS, Gonçalves-Vidigal MC, Vaz Bisneta M, Calvi AC, Gilio TAS, Nascimento EA, Melotto M. Alterations in Gene Expression during Incompatible Interaction between Amendoim Cavalo Common Bean and Colletotrichum lindemuthianum. PLANTS (BASEL, SWITZERLAND) 2024; 13:1245. [PMID: 38732460 PMCID: PMC11085365 DOI: 10.3390/plants13091245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 05/13/2024]
Abstract
Anthracnose, caused by the fungus Colletotrichum lindemuthianum, poses a significant and widespread threat to the common bean crop. The use of plant genetic resistance has proven to be the most effective strategy for managing anthracnose disease. The Amendoim Cavalo (AC) Andean cultivar has resistance against multiple races of C. lindemuthianum, which is conferred by the Co-AC gene. Fine mapping of this resistance gene to common bean chromosome Pv01 enabled the identification of Phvul.001G244300, Phvul.001G244400, and Phvul.001G244500 candidate genes for further validation. In this study, the relative expression of Co-AC candidate genes was assessed, as well as other putative genes in the vicinity of this locus and known resistance genes, in the AC cultivar following inoculation with the race 73 of C. lindemuthianum. Gene expression analysis revealed significantly higher expression levels of Phvul.001G244500. Notably, Phvul.001G244500 encodes a putative Basic Helix-Loop-Helix transcription factor, suggesting its involvement in the regulation of defense responses. Furthermore, a significant modulation of the expression of defense-related genes PR1a, PR1b, and PR2 was observed in a time-course experiment. These findings contribute to the development of improved strategies for breeding anthracnose-resistant common bean cultivars, thereby mitigating the impact of this pathogen on crop yields and ensuring sustainable bean production.
Collapse
Affiliation(s)
- Maike Lovatto
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | | | | | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | - Alexandre Catto Calvi
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | | | - Eduardo A. Nascimento
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| |
Collapse
|
3
|
Badiyal A, Dhiman S, Singh A, Rathour R, Pathania A, Katoch S, Padder BA, Sharma PN. Mapping of adult plant recessive resistance to anthracnose in Indian common bean landrace Baspa/KRC 8. Mol Biol Rep 2024; 51:254. [PMID: 38302755 DOI: 10.1007/s11033-023-09160-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/14/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND The common bean (Phaseolus vulgaris) has become the food of choice owing to its wealthy nutritional profile, leading to a considerable increase in its cultivation worldwide. However, anthracnose has been a major impediment to production and productivity, as elite bean cultivars are vulnerable to this disease. To overcome barriers in crop production, scientists worldwide are working towards enhancing the genetic diversity of crops. One way to achieve this is by introducing novel genes from related crops, including landraces like KRC 8. This particular landrace, found in the North Western Himalayan region, has shown adult plant resistance against anthracnose and also possesses a recessive resistance gene. METHODS AND RESULTS In this study, a population of 179 F2:9 RIL individuals (Jawala × KRC 8) was evaluated at both phenotypic and genotypic levels using over 830 diverse molecular markers to map the resistance gene present in KRC 8. We have successfully mapped a resistance gene to chromosome Pv01 using four SSR markers, namely IAC 238, IAC 235, IAC 259, and BM 146. The marker IAC 238 is closely linked to the gene with a distance of 0.29 cM, while the other markers flank the recessive resistance gene at 10.87 cM (IAC 259), 17.80 cM (BM 146), and 25.22 cM (IAC 235). Previously, a single recessive anthracnose resistance gene (co-8) has been reported in the common bean accession AB 136. However, when we performed PCR amplification with our tightly linked marker IAC 238, we got different amplicons in AB 136 and KRC 8. Interestingly, the susceptible cultivar Jawala produced the same amplicon as AB 136. This observation indicated that the recessive gene present in KRC 8 is different from co-8. As the gene is located far away from the Co-1 locus, we suggest naming the recessive gene co-Indb/co-19. Fine mapping of co-Indb in KRC 8 may provide new insights into the cloning and characterization of this recessive gene so that it can be incorporated into future bean improvement programs. Further, the tightly linked marker IAC 238 can be utilized in marker assisted introgression in future bean breeding programs. CONCLUSION The novel co-Indb gene present in Himalayan landrace KRC 8, showing adult plant resistance against common bean anthracnose, is independent from all the resistance genes previously located on chromosome Pv01.
Collapse
Affiliation(s)
- Anila Badiyal
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Shiwali Dhiman
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Amar Singh
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Anju Pathania
- Faculty of Agriculture, DAV University, Jalandhar, 144001, Punjab, India
| | - Shabnam Katoch
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-K Srinagar, Srinagar, 190025, J&K, India.
| | - Prem N Sharma
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India.
| |
Collapse
|
4
|
Meziadi C, Alvarez-Diaz JC, Thareau V, Gratias A, Marande W, Soler-Garzon A, Miklas PN, Pflieger S, Geffroy V. Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:8. [PMID: 38092992 DOI: 10.1007/s00122-023-04513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE R-BPMV is located within a recently expanded TNL cluster in the Phaseolus genus with suppressed recombination and known for resistance to multiple pathogens including potyviruses controlled by the I gene. Bean pod mottle virus (BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the R-BPMV resistance gene conferring resistance to BPMV and linked with the I resistance gene. To fine map R-BPMV, 182 recombinant inbred lines (RILs) derived from the cross BAT93 × JaloEEP558 were genotyped with polymerase chain reaction (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned R-BPMV to a target region containing at least 16 TIR-NB-LRR (TNL) sequences in BAT93. Because the I cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as R-BPMV candidate gene. The evolutionary history of the TNLs for the I cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family. A single I TNL was present in Medicago truncatula and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the I cluster predates the divergence of the Phaseolus species, in agreement with the emergence of R-BPMV before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of R-BPMV resistance gene in order to transfer the resistance into soybean.
Collapse
Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Juan-Camilo Alvarez-Diaz
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | | | - Alvaro Soler-Garzon
- Irrigated Agriculture Research and Extension Center, Washington State Univ, Prosser, WA, USA
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, USDA ARS, Prosser, WA, USA
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France.
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France.
| |
Collapse
|
5
|
Lovatto M, Gonçalves-Vidigal MC, Vaz Bisneta M, Calvi AC, Mazucheli J, Vidigal Filho PS, Miranda EGR, Melotto M. Responsiveness of Candidate Genes on CoPv01CDRK/PhgPv01CDRK Loci in Common Bean Challenged by Anthracnose and Angular Leaf Spot Pathogens. Int J Mol Sci 2023; 24:16023. [PMID: 38003212 PMCID: PMC10671028 DOI: 10.3390/ijms242216023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 11/26/2023] Open
Abstract
Anthracnose (ANT) and angular leaf spot (ALS) are significant diseases in common bean, leading to considerable yield losses under specific environmental conditions. The California Dark Red Kidney (CDRK) bean cultivar is known for its resistance to multiple races of both pathogens. Previous studies have identified the CoPv01CDRK/PhgPv01CDRK resistance loci on chromosome Pv01. Here, we evaluated the expression levels of ten candidate genes near the CoPv01CDRK/PhgPv01CDRK loci and plant defense genes using quantitative real-time PCR in CDRK cultivar inoculated with races 73 of Colletotrichum lindemuthianum and 63-39 of Pseudocercospora griseola. Gene expression analysis revealed that the Phvul.001G246300 gene exhibited the most elevated levels, showing remarkable 7.8-fold and 8.5-fold increases for ANT and ALS, respectively. The Phvul.001G246300 gene encodes an abscisic acid (ABA) receptor with pyrabactin resistance, PYR1-like (PYL) protein, which plays a central role in the crosstalk between ABA and jasmonic acid responses. Interestingly, our results also showed that the other defense genes were initially activated. These findings provide critical insights into the molecular mechanisms underlying plant defense against these diseases and could contribute to the development of more effective disease management strategies in the future.
Collapse
Affiliation(s)
- Maike Lovatto
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Alexandre Catto Calvi
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Josmar Mazucheli
- Departamento de Estatística, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | | | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| |
Collapse
|
6
|
Campa A, Rodríguez Madrera R, Jurado M, García-Fernández C, Suárez Valles B, Ferreira JJ. Genome-wide association study for the extractable phenolic profile and coat color of common bean seeds (Phaseolus vulgaris L.). BMC PLANT BIOLOGY 2023; 23:158. [PMID: 36959530 PMCID: PMC10035135 DOI: 10.1186/s12870-023-04177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND A large variation in seed coat colors and seed phenolic metabolites is present in common bean (Phaseolus vulgaris L.). The study of the relationships between seed coat color phenotype and the phenolic profile is an important step in the elucidation of the gene network involved in the phenylpropanoid biosynthetic pathway. However, this relationship is still poorly understood in this species. RESULTS A genome-wide association study (GWAS) was used to investigate the genomic regions associated with the synthesis of 10 flavonoids (5 anthocyanins and 5 flavonols) and with 10 seed coat color traits using a set of 308 common bean lines of the Spanish Diversity Panel (SDP) which have been genotyped with 11,763 SNP markers.. A total of 31 significant SNP-trait associations (QTNs) were identified, grouped in 20 chromosome regions: 6 for phenolic metabolites on chromosomes Pv01, Pv02, Pv04, Pv08, and Pv09, 13 for seed coat color on chromosomes Pv01, Pv02, Pv06, Pv07, and Pv10, and 1 including both types of traits located on chromosome Pv08. In all, 58 candidate genes underlying these regions have been proposed, 31 of them previously described in the phenylpropanoid pathway in common bean, and 27 of them newly proposed in this work based on the association study and their homology with Arabidopsis anthocyanin genes. CONCLUSIONS Chromosome Pv08 was identified as the main chromosome involved in the phenylpropanoid pathway and in consequence in the common bean seed pigmentation, with three independent chromosome regions identified, Phe/C_Pv08(2.7) (expanding from 2.71 to 4.04 Mbp), C_Pv08(5.8) (5.89-6.59 Mbp), and Phe_Pv08(62.5) (62.58 to 63.28 Mbp). Candidate genes previously proposed by other authors for the color genes V and P were validated in this GWAS. Candidate genes have been tentatively proposed from this study for color genes B and Rk on Pv02, Asp on Pv07, and complex C on Pv08. These results help to clarify the complex network of genes involved in the genetic control of phenolic compounds and seed color in common bean and provide the opportunity for future validation studies.
Collapse
Affiliation(s)
- Ana Campa
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain.
| | - Roberto Rodríguez Madrera
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - María Jurado
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Carmen García-Fernández
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Belén Suárez Valles
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Juan José Ferreira
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| |
Collapse
|
7
|
Aono AH, Pimenta RJG, Dambroz CMDS, Costa FCL, Kuroshu RM, de Souza AP, Pereira WA. Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization. Gene 2023; 855:147127. [PMID: 36563714 DOI: 10.1016/j.gene.2022.147127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.
Collapse
Affiliation(s)
- Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil.
| | | | | | | | - Reginaldo Massanobu Kuroshu
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, Brazil.
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil; Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil.
| | | |
Collapse
|
8
|
Simons KJ, Schröder S, Oladzad A, McClean PE, Conner RL, Penner WC, Stoesz DB, Osorno JM. Modified screening method of middle american dry bean genotypes reveals new genomic regions on Pv10 associated with anthracnose resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:1015583. [PMID: 36457529 PMCID: PMC9705789 DOI: 10.3389/fpls.2022.1015583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib., is one of the most devastating diseases in dry bean (Phaseolus vulgaris L.) with seed yield losses up to 100%. Most anthracnose resistance genes thus far identified behave in a dominant manner and were identified by seedling screening. The Middle American Diversity Panel (MDP; n=266) was screened with a modified greenhouse screening method to evaluate the response to anthracnose race 73. Thirty MDP genotypes exhibited resistance to the race of which 16 genotypes were not known to contain anthracnose resistance genes to race 73. GWAS with ~93,000 SNP markers identified four genomic regions, two each on Pv01 and Pv10, associated race 73 resistance. A likelihood-ratio-based R2 analysis indicated the peak four SNP markers are responsible for 26% of the observed phenotypic variation, where one SNP, S10_072250, explains 23% of the total variation. SNP S10_072250 is associated with a new region of anthracnose resistance and is in an intron of a ZPR1-like gene. Further greenhouse testing of the 16 resistant lines without previously known resistance to race 73 revealed various levels of resistance under various levels of disease pressure. Disease resistance was further characterized in the field using four representative genotypes. GTS-900 and Remington exhibited field resistance while Merlot and Maverick were susceptible. Field testing with two different fungicide regimes revealed the resistant genotypes had no significant disease differences. The results suggest resistance to anthracnose may differ at various growth stages and that breeders have been selecting for major genes at early seedling stages while ignoring the effect of alternative genes that may be active at later stages. The newly identified resistant lines may be related to Age Related Resistance (ARR) and could be exploited as parental sources of anthracnose resistance in addition to already known major genes. The physical localization of the multiple regions of resistance confirms the presence of two clusters of disease resistance genes on Pv01 and identifies two new regions of anthracnose resistance on Pv10 possibly associated with ARR. Future research should look at the mode of inheritance of this resistance and its effect when combined with other anthracnose resistance loci.
Collapse
Affiliation(s)
- Kristin J. Simons
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Stephan Schröder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Atena Oladzad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Robert L. Conner
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Waldo C. Penner
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Dennis B. Stoesz
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| |
Collapse
|
9
|
Jurado M, Campa A, Ferreira JJ. Differentially expressed genes against Colletotrichum lindemuthiamum in a bean genotype carrying the Co-2 gene revealed by RNA-sequencing analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:981517. [PMID: 36311094 PMCID: PMC9615912 DOI: 10.3389/fpls.2022.981517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
Anthracnose is responsible for large yield losses in common bean crops. RNA-sequencing was used to investigate the differentially expressed genes (DEGs) in response to race 38 of Colletotrichum lindemuthianum in two near-isogenic lines (A25 and A4804) that differ in the presence of a resistance gene located in the cluster Co-2. Their responses were analyzed at different hours after inoculation (0, 24, and 48) and within and between genotypes. In all, 2,850 DEGs were detected, with 2,373 assigned to at least one functional GO term. Enriched GO terms in the resistant genotype were mainly related to functions as a response to stimulus, hormone signaling, cellular component organization, phosphorylation activities, and transcriptional regulation. The region containing the Co-2 cluster was delimited at the end of chromosome Pv11 (46.65-48.65 Mb) through a comparison with the SNP genotypes, obtained using 'Genotyping by Sequencing,' among seven resistant lines harboring the Co-2 gene and the susceptible line A25. The delimited region contained 23 DEGs, including 8 typical R genes, that showed higher expression levels in the resistant genotype and non-changes in the susceptible genotype after inoculation. Six R genes encoding protein kinases and an LRR domain formed a cluster in a core region between 46.98 and 47.04 Mb. The alignment of the raw transcriptome reads in the core region revealed structural changes that were used to design four potential breeder-friendly DNA markers, and it revealed some alignments with the intergenic regions, suggesting the presence of genes in addition to those annotated in the reference genome.
Collapse
|
10
|
Alvarez-Diaz JC, Laugé R, Delannoy E, Huguet S, Paysant-Le Roux C, Gratias A, Geffroy V. Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean. PLANTS 2022; 11:plants11151995. [PMID: 35956473 PMCID: PMC9370732 DOI: 10.3390/plants11151995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022]
Abstract
Bean anthracnose caused by the hemibiotrophic fungus Colletotrichum lindemuthianum is one of the most important diseases of common bean (Phaseolus vulgaris) in the world. In the present study, the whole transcriptome of common bean infected with C. lindemuthianum during compatible and incompatible interactions was characterized at 48 and 72 hpi, corresponding to the biotrophy phase of the infection cycle. Our results highlight the prominent role of pathogenesis-related (PR) genes from the PR10/Bet vI family as well as a complex interplay of different plant hormone pathways including Ethylene, Salicylic acid (SA) and Jasmonic acid pathways. Gene Ontology enrichment analysis reveals that infected common bean seedlings responded by down-regulation of photosynthesis, ubiquitination-mediated proteolysis and cell wall modifications. In infected common bean, SA biosynthesis seems to be based on the PAL pathway instead of the ICS pathway, contrarily to what is described in Arabidopsis. Interestingly, ~30 NLR were up-regulated in both contexts. Overall, our results suggest that the difference between the compatible and incompatible reaction is more a question of timing and strength, than a massive difference in differentially expressed genes between these two contexts. Finally, we used RT-qPCR to validate the expression patterns of several genes, and the results showed an excellent agreement with deep sequencing.
Collapse
Affiliation(s)
- Juan C. Alvarez-Diaz
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Richard Laugé
- Université Paris-Saclay, INRAE UR 1290 BIOGER, Av. Lucien Bretignières, BP 01, 78850 Thiverval Grignon, France;
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
| |
Collapse
|
11
|
Jiang L, Zhang S, Su J, Peck SC, Luo L. Protein Kinase Signaling Pathways in Plant- Colletotrichum Interaction. FRONTIERS IN PLANT SCIENCE 2022; 12:829645. [PMID: 35126439 PMCID: PMC8811371 DOI: 10.3389/fpls.2021.829645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Anthracnose is a fungal disease caused by members of Colletotrichum that affect a wide range of crop plants. Strategies to improve crop resistance are needed to reduce the yield losses; and one strategy is to manipulate protein kinases that catalyze reversible phosphorylation of proteins regulating both plant immune responses and fungal pathogenesis. Hence, in this review, we present a summary of the current knowledge of protein kinase signaling pathways in plant-Colletotrichum interaction as well as the relation to a more general understanding of protein kinases that contribute to plant immunity and pathogen virulence. We highlight the potential of combining genomic resources and phosphoproteomics research to unravel the key molecular components of plant-Colletotrichum interactions. Understanding the molecular interactions between plants and Colletotrichum would not only facilitate molecular breeding of resistant cultivars but also help the development of novel strategies for controlling the anthracnose disease.
Collapse
Affiliation(s)
- Lingyan Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Shizi Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jianbin Su
- Division of Plant Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Scott C. Peck
- Division of Biochemistry, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lijuan Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| |
Collapse
|
12
|
Nabi A, Lateef I, Nisa Q, Banoo A, Rasool RS, Shah MD, Ahmad M, Padder BA. Phaseolus vulgaris-Colletotrichum lindemuthianum Pathosystem in the Post-Genomic Era: An Update. Curr Microbiol 2022; 79:36. [PMID: 34982236 DOI: 10.1007/s00284-021-02711-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022]
Abstract
Phaseolus vulgaris-Colletotrichum lindemuthianum is one among the oldest host and pathogen interface. Researchers have taken painstaking efforts across the world for understanding the dialogue during early and late phases of interaction. Collectively, these efforts resulted in the deluge of information that helped the researchers to underpin the interface. The latest molecular biology techniques furnished novel detection methods for the anthracnose pathogen, refined the understanding of pathogen population dynamics, and provided the insights on co-evolutionary common bean resistance and C. lindemuthianum virulence dynamics. One of the important breakthroughs came when the Phaseolus vulgaris and its corresponding anthracnose pathogen (C. lindemuthianum) genomes were decoded in 2014 and 2017, respectively. Availability of both the genomes yielded a significant genomic information that helped bean communities to fine map the economically important traits and to identify the pathogenicity determinants and effector molecules. The interface is in a continuous development as knowledge of the anthracnose resistance genes, their precise physical locations, and the identification of effector proteins; the fungus arsenals are being routinely updated. Hence, we revisited the interface and tried to provide an overview of host pathogen dialogue in the genomic era. Additionally, we compiled the sporadic information on this pathosystem from India and provided its futuristic road map to shape its research in the world and northern India, the major dry bean area in the country.
Collapse
Affiliation(s)
- Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aqleema Banoo
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rovidha S Rasool
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - M D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Mushtaq Ahmad
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
| |
Collapse
|
13
|
Alvarez-Diaz JC, Richard MMS, Thareau V, Teano G, Paysant-Le-Roux C, Rigaill G, Pflieger S, Gratias A, Geffroy V. Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection. Genes (Basel) 2021; 13:genes13010064. [PMID: 35052407 PMCID: PMC8774654 DOI: 10.3390/genes13010064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB) proteins, RNA-dependent RNA polymerase (RDR), and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant, taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRBs, 5 PvRDRs, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization, and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.
Collapse
Affiliation(s)
- Juan C. Alvarez-Diaz
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Manon M. S. Richard
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Vincent Thareau
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Gianluca Teano
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Christine Paysant-Le-Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Laboratoire de Mathématiques et Modélisation d’Evry, Université Paris-Saclay, CNRS, Université Evry, INRAE, 91037 Evry, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
| |
Collapse
|
14
|
Bellucci E, Mario Aguilar O, Alseekh S, Bett K, Brezeanu C, Cook D, De la Rosa L, Delledonne M, Dostatny DF, Ferreira JJ, Geffroy V, Ghitarrini S, Kroc M, Kumar Agrawal S, Logozzo G, Marino M, Mary‐Huard T, McClean P, Meglič V, Messer T, Muel F, Nanni L, Neumann K, Servalli F, Străjeru S, Varshney RK, Vasconcelos MW, Zaccardelli M, Zavarzin A, Bitocchi E, Frontoni E, Fernie AR, Gioia T, Graner A, Guasch L, Prochnow L, Oppermann M, Susek K, Tenaillon M, Papa R. The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:646-660. [PMID: 34427014 PMCID: PMC9293105 DOI: 10.1111/tpj.15472] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 05/14/2023]
Abstract
Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.
Collapse
Affiliation(s)
- Elisa Bellucci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Orlando Mario Aguilar
- Instituto de Biotecnología y Biología MolecularUNLP‐CONICETCCT La PlataLa PlataArgentina
| | - Saleh Alseekh
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Kirstin Bett
- Department of Plant SciencesUniversity of Saskatchewan51 Campus DriveSaskatoonSKS7N 5A8Canada
| | - Creola Brezeanu
- Staţiunea de Cercetare Dezvoltare Pentru LegumiculturăBacău600388Romania
| | - Douglas Cook
- Department of Plant PathologyUniversity of California DavisDavisCA95616‐8680USA
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Massimo Delledonne
- Department of BiotechnologyUniversity of VeronaStrada Le Grazie 15Verona37134Italy
| | - Denise F. Dostatny
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute‐NRIRadzikówBłonie05‐870Poland
| | - Juan J. Ferreira
- Regional Service for Agrofood Research and Development (SERIDA)Ctra AS‐267, PK 19VillaviciosaAsturias33300Spain
| | - Valérie Geffroy
- CNRSINRAEInstitute of Plant Sciences Paris‐Saclay (IPS2)Univ EvryUniversité Paris‐SaclayOrsay91405France
- CNRSINRAEInstitute of Plant Sciences Paris Saclay (IPS2)Université de ParisOrsay91405France
| | | | - Magdalena Kroc
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Shiv Kumar Agrawal
- Genetic Resources SectionInternational Center for Agricultural Research in the Dry AreasICARDAAgdal RabatMorocco
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Mario Marino
- International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA)Food and Agriculture Organization of the United Nations (FAO)Viale delle Terme di CaracallaRome00153Italy
| | - Tristan Mary‐Huard
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Phil McClean
- Department of Plant Sciences, Genomics and Bioinformatics ProgramNorth Dakota State UniversityFargoND58108USA
| | - Vladimir Meglič
- Crop Science DepartmentAgricultural Institute of SloveniaHacquetova ulica 17Ljubljana1000Slovenia
| | - Tamara Messer
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Frédéric Muel
- Terres InoviaInstitut Technique des oléagineux, des protéagineux eu du chanvren1 Av L. BrétignièresThiverval-Grignon78850France
| | - Laura Nanni
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Filippo Servalli
- Comunità del Mais Spinato di Gandino (MASP)Via XX Settembre, 5GandinoBergamo24024Italy
| | - Silvia Străjeru
- Suceava Genebank (BRGV)Bdul 1 Mai, nr. 17Suceava720224Romania
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi- Arid Tropics (ICRISAT)PatancheruIndia
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Marta W. Vasconcelos
- CBQF – Centro de Biotecnologia e Química Fina – Laboratório AssociadoEscola Superior de BiotecnologiaUniversidade Católica PortuguesaRua Diogo Botelho 1327Porto4169-005Portugal
| | - Massimo Zaccardelli
- Council for Agricultural Research and EconomicsResearch Centre for Vegetable and Ornamental CropsVia Cavalleggeri 25Pontecagnano‐FaianoSA84098Italy
| | - Aleksei Zavarzin
- Federal Research CenterThe N.I. Vavilov All‐Russian Institute of Plant Genetic ResourcesSt. Petersburg190031Russia
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Emanuele Frontoni
- Department of Information EngineeringPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Luis Guasch
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Lena Prochnow
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Karolina Susek
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Maud Tenaillon
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| |
Collapse
|
15
|
R-BPMV-Mediated Resistance to Bean pod mottle virus in Phaseolus vulgaris L. Is Heat-Stable but Elevated Temperatures Boost Viral Infection in Susceptible Genotypes. Viruses 2021; 13:v13071239. [PMID: 34206842 PMCID: PMC8310253 DOI: 10.3390/v13071239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/23/2022] Open
Abstract
In the context of climate change, elevated temperature is a major concern due to the impact on plant–pathogen interactions. Although atmospheric temperature is predicted to increase in the next century, heat waves during summer seasons have already become a current problem. Elevated temperatures strongly influence plant–virus interactions, the most drastic effect being a breakdown of plant viral resistance conferred by some major resistance genes. In this work, we focused on the R-BPMV gene, a major resistance gene against Bean pod mottle virus in Phaseolus vulgaris. We inoculated different BPMV constructs in order to study the behavior of the R-BPMV-mediated resistance at normal (20 °C) and elevated temperatures (constant 25, 30, and 35 °C). Our results show that R-BPMV mediates a temperature-dependent phenotype of resistance from hypersensitive reaction at 20 °C to chlorotic lesions at 35 °C in the resistant genotype BAT93. BPMV is detected in inoculated leaves but not in systemic ones, suggesting that the resistance remains heat-stable up to 35 °C. R-BPMV segregates as an incompletely dominant gene in an F2 population. We also investigated the impact of elevated temperature on BPMV infection in susceptible genotypes, and our results reveal that elevated temperatures boost BPMV infection both locally and systemically in susceptible genotypes.
Collapse
|
16
|
Cannon SB, Innes RW. A better mousetrap to guard against anthracnose disease in bean. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3487-3488. [PMID: 33948655 DOI: 10.1093/jxb/erab146] [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: 06/12/2023]
Abstract
This article comments on:
Richard MSM, Gratias A, Alvarez Diaz JC, Thareau V, Pflieger S, Meziadi C, Blanchet S, Marande W, Bitochi E, Papa R, Miklas PN, Geffroy V. 2021. A common bean truncated CRINKLY4 kinase controls gene-for-gene resistance to the fungus Colletotrichum lindemuthianum. Journal of Experimental Botany 72, 3569–3581.
Collapse
Affiliation(s)
- Steven B Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, IN, USA
| |
Collapse
|
17
|
Soler-Garzón A, McClean PE, Miklas PN. Genome-Wide Association Mapping of bc-1 and bc-u Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to Bean Common Mosaic Necrosis Virus in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:699569. [PMID: 34267774 PMCID: PMC8277298 DOI: 10.3389/fpls.2021.699569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 05/17/2023]
Abstract
Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean (Phaseolus vulgaris L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million single-nucleotide polymorphisms (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for bc-1. These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (Glycine max). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for bc-u. bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for bc-1 and bc-u and new markers for I and bc-3 genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F3 families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele bc-1 for the Bc-1 locus, and differential expression of the allele is based on presence vs. absence of bc-u; (ii) bc-1 exhibits dominance and incomplete dominance; (iii) bc-1 alone confers resistance to NL-8; (iv) bc-u was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol bc-u d to reflect this change; (v) bc-u d alone delays susceptible symptoms, and when combined with bc-1 enhanced resistance to NL-3; and (vi) bc-u d is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean.
Collapse
Affiliation(s)
- Alvaro Soler-Garzón
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Prosser, WA, United States
- *Correspondence: Phillip N. Miklas, , orcid.org/0000-0002-6636-454X
| |
Collapse
|