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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.
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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
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2
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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.
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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
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Arriagada O, Arévalo B, Cabeza RA, Carrasco B, Schwember AR. Meta-QTL Analysis for Yield Components in Common Bean ( Phaseolus vulgaris L.). PLANTS (BASEL, SWITZERLAND) 2022; 12:117. [PMID: 36616246 PMCID: PMC9824219 DOI: 10.3390/plants12010117] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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Taboada G, Abán CL, Mercado Cárdenas G, Spedaletti Y, Aparicio González M, Maita E, Ortega-Baes P, Galván M. Characterization of fungal pathogens and germplasm screening for disease resistance in the main production area of the common bean in Argentina. FRONTIERS IN PLANT SCIENCE 2022; 13:986247. [PMID: 36161011 PMCID: PMC9490223 DOI: 10.3389/fpls.2022.986247] [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: 07/04/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet, mainly in Africa and Latin America. Argentina is one of the five major producers of the common bean in the world, and the main cultivation areas are concentrated in the northwestern provinces of this country. Crop production of the common bean is often affected by biotic factors like some endemic fungal diseases, which exert a major economic impact on the region. The most important fungal diseases affecting the common bean in Argentina are white mold caused by Sclerotinia sclerotiorum, angular leaf spot caused by Pseudocercospora griseola, web blight and root rot caused by Rhizoctonia solani, which can cause production losses of up to 100% in the region. At the present, the most effective strategy for controlling these diseases is the use of genetic resistance. In this sense, population study and characterization of fungal pathogens are essential for developing cultivars with durable resistance. In this review we report diversity studies carried out on these three fungal pathogens affecting the common bean in northwestern Argentina, analyzing more than 200 isolates by means of molecular, morphological and pathogenic approaches. Also, the screening of physiological resistance in several common bean commercial lines and wild native germplasm is reviewed. This review contributes to the development of sustainable management strategies and cultural practices in bean production aimed to minimize yield losses due to fungal diseases in the common bean.
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Affiliation(s)
- Gisel Taboada
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Carla L. Abán
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | | | - Yamila Spedaletti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Mónica Aparicio González
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Efrain Maita
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Laboratorio de Investigaciones Botánicas (LABIBO), Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Pablo Ortega-Baes
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Laboratorio de Investigaciones Botánicas (LABIBO), Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Marta Galván
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
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5
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Nadeem MA, Yeken MZ, Shahid MQ, Habyarimana E, Yılmaz H, Alsaleh A, Hatipoğlu R, Çilesiz Y, Khawar KM, Ludidi N, Ercişli S, Aasim M, Karaköy T, Baloch FS. Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1920462] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, PR China
| | | | - Hilal Yılmaz
- Department of Plant and Animal Production, Izmit Vocational School, Kocaeli University, Kocaeli, Turkey
| | - Ahmad Alsaleh
- Department of Food and Agriculture, Insitutue of Hemp Research, Yozgat Bozok University, 66200, Yozgat, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Khalid Mahmood Khawar
- Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Ndiko Ludidi
- Department of Biotechnology and DSI-NRF Center of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
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de Almeida CP, de Carvalho Paulino JF, Bonfante GFJ, Perseguini JMKC, Santos IL, Gonçalves JGR, Patrício FRA, Taniguti CH, Gesteira GDS, Garcia AAF, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Angular Leaf Spot Resistance Loci Associated With Different Plant Growth Stages in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:647043. [PMID: 33927738 PMCID: PMC8078856 DOI: 10.3389/fpls.2021.647043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Angular leaf spot (ALS) is a disease that causes major yield losses in the common bean crop. Studies based on different isolates and populations have already been carried out to elucidate the genetic mechanisms of resistance to ALS. However, understanding of the interaction of this resistance with the reproductive stages of common bean is lacking. The aim of the present study was to identify ALS resistance loci at different plant growth stages (PGS) by association and linkage mapping approaches. An BC2F3 inter-gene pool cross population (AND 277 × IAC-Milênio - AM population) profiled with 1,091 SNPs from genotyping by sequencing (GBS) was used for linkage mapping, and a carioca diversity panel (CDP) genotyped by 5,398 SNPs from BeadChip assay technology was used for association mapping. Both populations were evaluated for ALS resistance at the V2 and V3 PGSs (controlled conditions) and R8 PGS (field conditions). Different QTL (quantitative trait loci) were detected for the three PGSs and both populations, showing a different quantitative profile of the disease at different plant growth stages. For the three PGS, multiple interval mapping (MIM) identified seven significant QTL, and the Genome-wide association study (GWAS) identified fourteen associate SNPs. Several loci validated regions of previous studies, and Phg-1, Phg-2, Phg-4, and Phg-5, among the 5 loci of greatest effects reported in the literature, were detected in the CDP. The AND 277 cultivar contained both the Phg-1 and the Phg-5 QTL, which is reported for the first time in the descendant cultivar CAL143 as ALS10.1UC. The novel QTL named ALS11.1AM was located at the beginning of chromosome Pv11. Gene annotation revealed several putative resistance genes involved in the ALS response at the three PGSs, and with the markers and loci identified, new specific molecular markers can be developed, representing a powerful tool for common bean crop improvement and for gain in ALS resistance.
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Affiliation(s)
| | | | | | | | - Isabella Laporte Santos
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico - IAC, Campinas, Brazil
| | | | | | - Cristiane Hayumi Taniguti
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriel de Siqueira Gesteira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Antônio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, United States
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7
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de Almeida CP, Paulino JFDC, Morais Carbonell SA, Chiorato AF, Song Q, Di Vittori V, Rodriguez M, Papa R, Benchimol-Reis LL. Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding. Genes (Basel) 2020; 11:E1298. [PMID: 33143347 PMCID: PMC7694079 DOI: 10.3390/genes11111298] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/29/2022] Open
Abstract
Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 'diagnostic SNPs' that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.
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Affiliation(s)
- Caléo Panhoca de Almeida
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
| | - Jean Fausto de Carvalho Paulino
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
| | | | - Alisson Fernando Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (S.A.M.C.); (A.F.C.)
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture–Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA;
| | - Valerio Di Vittori
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica dele Marche, 60131 Ancona, Italy; (V.D.V.); (R.P.)
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy;
- Centro per la Cobservazione e Valorizzazione della Biodiversità Vegetale (CBV), Università degli Studi di Sassari, 07040 Alghero, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica dele Marche, 60131 Ancona, Italy; (V.D.V.); (R.P.)
| | - Luciana Lasry Benchimol-Reis
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
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8
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Gonçalves-Vidigal MC, Gilio TAS, Valentini G, Vaz-Bisneta M, Vidigal Filho PS, Song Q, Oblessuc PR, Melotto M. New Andean source of resistance to anthracnose and angular leaf spot: Fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar. PLoS One 2020; 15:e0235215. [PMID: 32598372 PMCID: PMC7323968 DOI: 10.1371/journal.pone.0235215] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Anthracnose (ANT) and angular leaf spot (ALS) caused by Colletotrichum lindemuthianum and Pseudocercospora griseola, respectively, are devastating diseases of common bean around the world. Therefore, breeders are constantly searching for new genes with broad-spectrum resistance against ANT and ALS. This study aimed to characterize the genetic resistance of California Dark Red Kidney (CDRK) to C. lindemuthianum races 73, 2047, and 3481 and P. griseola race 63-39 through inheritance, allelism testing, and molecular analyses. Genetic analysis of response to ANT and ALS in recombinant inbred lines (RILs) from a CDRK × Yolano cross (CY) showed that the resistance of CDRK cultivar is conferred by a single dominant loci, which we named CoPv01CDRK/PhgPv01CDRK. Allelism tests performed with race 3481showed that the resistance gene in CDRK is independent of the Co-1 and Co-AC. We conducted co-segregation analysis in genotypes of 110 CY RILs and phenotypes of the RILs in response to different races of the ANT and ALS pathogens. The results revealed that CoPv01CDRK and PhgPv01CDRK are coinherited, conferring resistance to all races. Genetic mapping of the CY population placed the CoPv01CDRK/PhgPv01CDRK loci in a 245 Kb genomic region at the end of Pv01. By genotyping 19 RILs from the CY population using three additional markers, we fine-mapped the CoPv01CDRK/PhgPv01CDRK loci to a smaller genomic region of 33 Kb. This 33 Kb region harbors five predicted genes based on the common bean reference genome. These results can be applied in breeding programs to develop bean cultivars with ANT and ALS resistance using marker-assisted selection.
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Affiliation(s)
- M. C. Gonçalves-Vidigal
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo, Maringá, Paraná, Brazil
| | - T. A. S. Gilio
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo, Maringá, Paraná, Brazil
| | - G. Valentini
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo, Maringá, Paraná, Brazil
| | - M. Vaz-Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo, Maringá, Paraná, Brazil
| | - P. S. Vidigal Filho
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo, Maringá, Paraná, Brazil
| | - Q. Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, BARC-West, Beltsville, Maryland, United States of America
| | - P. R. Oblessuc
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - M. Melotto
- Department of Plant Sciences, University of California, Davis, California, United States of America
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9
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Nay MM, Mukankusi CM, Studer B, Raatz B. Haplotypes at the Phg-2 Locus Are Determining Pathotype-Specificity of Angular Leaf Spot Resistance in Common Bean. FRONTIERS IN PLANT SCIENCE 2019; 10:1126. [PMID: 31572421 PMCID: PMC6753878 DOI: 10.3389/fpls.2019.01126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/15/2019] [Indexed: 05/11/2023]
Abstract
Angular leaf spot (ALS) is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) and causes serious yield losses worldwide. ALS resistance is reportedly pathotype-specific, but little is known about the efficacy of resistance loci against different pathotypes. Here, we report on ALS resistance evaluations of 316 bean lines under greenhouse and field conditions at multiple sites in Colombia and Uganda. Surprisingly, genome-wide association studies revealed only two of the five previously described resistance loci to be significantly associated with ALS resistance. Phg-2 on chromosome eight was crucial for ALS resistance in all trials, while the resistance locus Phg-4 on chromosome 4 was effective against one particular pathotype. Further dissection of Phg-2 uncovered an unprecedented diversity of functional haplotypes for a resistance locus in common bean. DNA sequence-based clustering identified eleven haplotype groups at Phg-2. One haplotype group conferred broad-spectrum ALS resistance, six showed pathotype-specific effects, and the remaining seven did not exhibit clear resistance patterns. Our research highlights the importance of ALS pathotype-specificity for durable resistance management strategies in common bean. Molecular markers co-segregating with resistance loci and haplotypes will increase breeding efficiency for ALS resistance and allow to react faster to future changes in pathogen pressure and composition.
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Affiliation(s)
- Michelle M. Nay
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Clare M. Mukankusi
- Bean Program, International Center for Tropical Agriculture (CIAT), Kampala, Uganda
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bodo Raatz
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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10
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Nay MM, Souza TLPO, Raatz B, Mukankusi CM, Gonçalves-Vidigal MC, Abreu AFB, Melo LC, Pastor-Corrales MA. A Review of Angular Leaf Spot Resistance in Common Bean. CROP SCIENCE 2019; 59:1376-1391. [PMID: 33343018 PMCID: PMC7680949 DOI: 10.2135/cropsci2018.09.0596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/05/2019] [Indexed: 05/05/2023]
Abstract
Angular leaf spot (ALS), caused by Pseudocercospora griseola, is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) in tropical and subtropical production areas. Breeding for ALS resistance is difficult due to the extensive virulence diversity of P. griseola and the recurrent appearance of new virulent races. Five major loci, Phg-1 to Phg-5, conferring ALS resistance have been named, and markers tightly linked to these loci have been reported. Quantitative trait loci (QTLs) have also been described, but the validation of some QTLs is still pending. The Phg-1, Phg-4, and Phg-5 loci are from common bean cultivars of the Andean gene pool, whereas Phg-2 and Phg-3 are from beans of the Mesoamerican gene pool. The reference genome of common bean and high-throughput sequencing technologies are enabling the development of molecular markers closely linked to the Phg loci, more accurate mapping of the resistance loci, and the comparison of their genomic positions. The objective of this report is to provide a comprehensive review of ALS resistance in common bean. Furthermore, we are reporting three case studies of ALS resistance breeding in Latin America and Africa. This review will serve as a reference for future resistance mapping studies and as a guide for the selection of resistance loci in breeding programs aiming to develop common bean cultivars with durable ALS resistance.
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Affiliation(s)
| | | | - Bodo Raatz
- Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
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Diniz AL, Giordani W, Costa ZP, Margarido GRA, Perseguini JMKC, Benchimol-Reis LL, Chiorato AF, Garcia AAF, Vieira MLC. Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans. Genes (Basel) 2018; 10:E5. [PMID: 30583474 PMCID: PMC6356217 DOI: 10.3390/genes10010005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 12/15/2018] [Accepted: 12/18/2018] [Indexed: 01/05/2023] Open
Abstract
Phaseolus vulgaris is an important grain legume for human consumption. Recently, association mapping studies have been performed for the species aiming to identify loci underlying quantitative variation of traits. It is now imperative to know whether the linkage disequilibrium (LD) reflects the true association between a marker and causative loci. The aim of this study was to estimate and analyze LD on a diversity panel of common beans using ordinary r² and r2 extensions which correct bias due to population structure (rS²), kinship (rV²), and both (rVS²). A total of 10,362 single nucleotide polymorphisms (SNPs) were identified by genotyping by sequencing (GBS), and polymorphisms were found to be widely distributed along the 11 chromosomes. In terms of r2, high values of LD (over 0.8) were identified between SNPs located at opposite chromosomal ends. Estimates for rV² were lower than those for rS². Results for rV² and rVS² were similar, suggesting that kinship may also include information on population structure. Over genetic distance, LD decayed to 0.1 at a distance of 1 Mb for rVS². Inter-chromosomal LD was also evidenced. This study showed that LD estimates decay dramatically according to the population structure, and especially the degree of kinship. Importantly, the LD estimates reported herein may influence our ability to perform association mapping studies on P. vulgaris.
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Affiliation(s)
- Augusto Lima Diniz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Willian Giordani
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Zirlane Portugal Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Gabriel R A Margarido
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Juliana Morini K C Perseguini
- Universidade Tecnológica Federal do Paraná, Dois Vizinhos, Paraná 85660-000, Brazil.
- Centro de Recursos Genéticos, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil.
| | - Luciana L Benchimol-Reis
- Centro de Recursos Genéticos, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil.
| | - Alisson F Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil.
| | - Antônio Augusto F Garcia
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
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Tock AJ, Fourie D, Walley PG, Holub EB, Soler A, Cichy KA, Pastor-Corrales MA, Song Q, Porch TG, Hart JP, Vasconcellos RCC, Vicente JG, Barker GC, Miklas PN. Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen. FRONTIERS IN PLANT SCIENCE 2017; 8:1170. [PMID: 28736566 PMCID: PMC5500643 DOI: 10.3389/fpls.2017.01170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/19/2017] [Indexed: 05/11/2023]
Abstract
Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).
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Affiliation(s)
- Andrew J. Tock
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
- Department of Plant Sciences, Faculty of Biology, University of CambridgeCambridge, United Kingdom
| | - Deidré Fourie
- ARC-Grain Crops InstitutePotchefstroom, South Africa
| | - Peter G. Walley
- Functional and Comparative Genomics, Institute of Integrative Biology, University of LiverpoolLiverpool, United Kingdom
| | - Eric B. Holub
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Alvaro Soler
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
| | - Karen A. Cichy
- Sugarbeet and Bean Research Unit, Agricultural Research Service, US Department of AgricultureEast Lansing, MI, United States
| | - Marcial A. Pastor-Corrales
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Timothy G. Porch
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | - John P. Hart
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | | | - Joana G. Vicente
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Guy C. Barker
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
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Bassi D, Briñez B, Rosa JS, Oblessuc PR, Almeida CPD, Nucci SM, Silva LCDD, Chiorato AF, Vianello RP, Camargo LEA, Blair MW, Benchimol-Reis LL. Linkage and mapping of quantitative trait loci associated with angular leaf spot and powdery mildew resistance in common beans. Genet Mol Biol 2017; 40:109-122. [PMID: 28222201 PMCID: PMC5409766 DOI: 10.1590/1678-4685-gmb-2015-0314] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/20/2016] [Indexed: 11/23/2022] Open
Abstract
Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases
causing significant yield losses in common beans. In this study, a new genetic
linkage map was constructed using single sequence repeats (SSRs) and single
nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277
x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were
performed in the greenhouse to identify quantitative trait loci
(QTLs) associated with resistance by means of the composite interval mapping
analysis. Four QTLs were identified for ALS resistance. The QTL ALS11AS,
linked on the SNP BAR 5054, mapped on chromosome Pv11, showed the greatest effect
(R2 = 26.5%) on ALS phenotypic variance. For PWM resistance, two QTLs
were detected, PWM2AS and PWM11AS, on Pv2 and Pv11, explaining
7% and 66% of the phenotypic variation, respectively. Both QTLs on Pv11 were mapped
on the same genomic region, suggesting that it is a pleiotropic region. The present
study resulted in the identification of new markers closely linked to ALS and PWM
QTLs, which can be used for marker-assisted selection, fine mapping and positional
cloning.
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Affiliation(s)
- Denis Bassi
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas (IAC), Campinas, SP, Brazil
| | - Boris Briñez
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas (IAC), Campinas, SP, Brazil
| | - Juliana Santa Rosa
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas (IAC), Campinas, SP, Brazil
| | - Paula Rodrigues Oblessuc
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas (IAC), Campinas, SP, Brazil
| | - Caléo Panhoca de Almeida
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas (IAC), Campinas, SP, Brazil
| | - Stella Maris Nucci
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas (IAC), Campinas, SP, Brazil
| | | | | | | | - Luis Eduardo Aranha Camargo
- Departamento de Fitopatologia, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, SP, Brazil
| | - Matthew Wohlgemuth Blair
- Department of Agriculture and Environmental Sciences, Tennessee State University, Nashville, TN, USA
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Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.). PLoS One 2016; 11:e0150506. [PMID: 26930078 PMCID: PMC4773255 DOI: 10.1371/journal.pone.0150506] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 02/14/2016] [Indexed: 12/27/2022] Open
Abstract
The common bean (Phaseolus vulgaris L.) is the world’s most important legume for human consumption. Anthracnose (ANT; Colletotrichum lindemuthianum) and angular leaf spot (ALS; Pseudocercospora griseola) are complex diseases that cause major yield losses in common bean. Depending on the cultivar and environmental conditions, anthracnose and angular leaf spot infections can reduce crop yield drastically. This study aimed to estimate linkage disequilibrium levels and identify quantitative resistance loci (QRL) controlling resistance to both ANT and ALS diseases of 180 accessions of common bean using genome-wide association analysis. A randomized complete block design with four replicates was performed for the ANT and ALS experiments, with four plants per genotype in each replicate. Association mapping analyses were performed for ANT and ALS using a mixed linear model approach implemented in TASSEL. A total of 17 and 11 significant statistically associations involving SSRs were detected for ANT and ALS resistance loci, respectively. Using SNPs, 21 and 17 significant statistically associations were obtained for ANT and angular ALS, respectively, providing more associations with this marker. The SSR-IAC167 and PvM95 markers, both located on chromosome Pv03, and the SNP scaffold00021_89379, were associated with both diseases. The other markers were distributed across the entire common bean genome, with chromosomes Pv03 and Pv08 showing the greatest number of loci associated with ANT resistance. The chromosome Pv04 was the most saturated one, with six markers associated with ALS resistance. The telomeric region of this chromosome showed four markers located between approximately 2.5 Mb and 4.4 Mb. Our results demonstrate the great potential of genome-wide association studies to identify QRLs related to ANT and ALS in common bean. The results indicate a quantitative and complex inheritance pattern for both diseases in common bean. Our findings will contribute to more effective screening of elite germplasm to find resistance alleles for marker-assisted selection in breeding programs.
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Keller B, Manzanares C, Jara C, Lobaton JD, Studer B, Raatz B. Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:813-26. [PMID: 25740562 PMCID: PMC4544502 DOI: 10.1007/s00122-015-2472-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/31/2015] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE A major QTL for angular leaf spot resistance in the common bean accession G5686 was fine-mapped to a region containing 36 candidate genes. Markers have been developed for marker-assisted selection. Common bean (Phaseolus vulgaris L.) is an important grain legume and an essential protein source for human nutrition in developing countries. Angular leaf spot (ALS) caused by the pathogen Pseudocercospora griseola (Sacc.) Crous and U. Braun is responsible for severe yield losses of up to 80%. Breeding for resistant cultivars is the most ecological and economical means to control ALS and is particularly important for yield stability in low-input agriculture. Here, we report on a fine-mapping approach of a major quantitative trait locus (QTL) ALS4.1(GS, UC) for ALS resistance in a mapping population derived from the resistant genotype G5686 and the susceptible cultivar Sprite. 180 F3 individuals of the mapping population were evaluated for ALS resistance and genotyped with 22 markers distributed over 11 genome regions colocating with previously reported QTL for ALS resistance. Multiple QTL analysis identified three QTL regions, including one major QTL on chromosome Pv04 at 43.7 Mbp explaining over 75% of the observed variation for ALS resistance. Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes. Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance. Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.
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Affiliation(s)
- Beat Keller
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Chloe Manzanares
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Carlos Jara
- Agrobiodiversity Research Area, Bean Program, CIAT Cali-Palmira, A. A. 6713, Cali, Colombia
| | - Juan David Lobaton
- Agrobiodiversity Research Area, Bean Program, CIAT Cali-Palmira, A. A. 6713, Cali, Colombia
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Bodo Raatz
- Agrobiodiversity Research Area, Bean Program, CIAT Cali-Palmira, A. A. 6713, Cali, Colombia
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Oblessuc PR, Matiolli CC, Chiorato AF, Camargo LEA, Benchimol-Reis LL, Melotto M. Common bean reaction to angular leaf spot comprises transcriptional modulation of genes in the ALS10.1 QTL. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 25815001 DOI: 10.3389/fpls.2015.00152/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Genetic resistance of common bean (Phaseolus vulgaris L.) against angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola, is conferred by quantitative trait loci (QTL). In this study, we determined the gene content of the major QTL ALS10.1 located at the end of chromosome Pv10, and identified those that are responsive to ALS infection in resistant (CAL 143) and susceptible (IAC-UNA) genotypes. Based on the current version of the common bean reference genome, the ALS10.1 core region contains 323 genes. Gene Ontology (GO) analysis of these coding sequences revealed the presence of genes involved in signal perception and transduction, programmed cell death (PCD), and defense responses. Two putative R gene clusters were found at ALS10.1 containing evolutionary related coding sequences. Among them, the Phvul.010G025700 was consistently up-regulated in the infected IAC-UNA suggesting its contribution to plant susceptibility to the fungus. We identified six other genes that were regulated during common bean response to P. griseola; three of them might be negative regulators of immunity as they showed opposite expression patterns during resistant and susceptible reactions at the initial phase of fungal infection. Taken together, these findings suggest that common bean reaction to P. griseola involves transcriptional modulation of defense genes in the ALS10.1 locus, contributing to resistance or susceptibility depending on the plant-pathogen interaction.
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Affiliation(s)
- Paula R Oblessuc
- Department of Plant Sciences, University of California, Davis Davis, CA, USA ; Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil ; Centro de Pesquisa e Desenvolvimento em Recursos Genéticos Vegetais, Instituto Agronômico de Campinas-IAC Campinas, Brazil
| | - Cleverson C Matiolli
- Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Alisson F Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico de Campinas-IAC Campinas, Brazil
| | - Luis E A Camargo
- Departamento de Fitopatologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo Piracicaba, Brazil
| | - Luciana L Benchimol-Reis
- Centro de Pesquisa e Desenvolvimento em Recursos Genéticos Vegetais, Instituto Agronômico de Campinas-IAC Campinas, Brazil
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis Davis, CA, USA
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Oblessuc PR, Matiolli CC, Chiorato AF, Camargo LEA, Benchimol-Reis LL, Melotto M. Common bean reaction to angular leaf spot comprises transcriptional modulation of genes in the ALS10.1 QTL. FRONTIERS IN PLANT SCIENCE 2015; 6:152. [PMID: 25815001 PMCID: PMC4357252 DOI: 10.3389/fpls.2015.00152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/25/2015] [Indexed: 05/11/2023]
Abstract
Genetic resistance of common bean (Phaseolus vulgaris L.) against angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola, is conferred by quantitative trait loci (QTL). In this study, we determined the gene content of the major QTL ALS10.1 located at the end of chromosome Pv10, and identified those that are responsive to ALS infection in resistant (CAL 143) and susceptible (IAC-UNA) genotypes. Based on the current version of the common bean reference genome, the ALS10.1 core region contains 323 genes. Gene Ontology (GO) analysis of these coding sequences revealed the presence of genes involved in signal perception and transduction, programmed cell death (PCD), and defense responses. Two putative R gene clusters were found at ALS10.1 containing evolutionary related coding sequences. Among them, the Phvul.010G025700 was consistently up-regulated in the infected IAC-UNA suggesting its contribution to plant susceptibility to the fungus. We identified six other genes that were regulated during common bean response to P. griseola; three of them might be negative regulators of immunity as they showed opposite expression patterns during resistant and susceptible reactions at the initial phase of fungal infection. Taken together, these findings suggest that common bean reaction to P. griseola involves transcriptional modulation of defense genes in the ALS10.1 locus, contributing to resistance or susceptibility depending on the plant-pathogen interaction.
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Affiliation(s)
- Paula R. Oblessuc
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
- Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de CampinasCampinas, Brazil
- Centro de Pesquisa e Desenvolvimento em Recursos Genéticos Vegetais, Instituto Agronômico de Campinas—IACCampinas, Brazil
| | - Cleverson C. Matiolli
- Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de CampinasCampinas, Brazil
| | - Alisson F. Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico de Campinas—IACCampinas, Brazil
| | - Luis E. A. Camargo
- Departamento de Fitopatologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloPiracicaba, Brazil
| | - Luciana L. Benchimol-Reis
- Centro de Pesquisa e Desenvolvimento em Recursos Genéticos Vegetais, Instituto Agronômico de Campinas—IACCampinas, Brazil
| | - Maeli Melotto
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
- *Correspondence: Maeli Melotto, Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Perseguini JMKC, Silva GMB, Rosa JRBF, Gazaffi R, Marçal JF, Carbonell SAM, Chiorato AF, Zucchi MI, Garcia AAF, Benchimol-Reis LL. Developing a common bean core collection suitable for association mapping studies. Genet Mol Biol 2014; 38:67-78. [PMID: 25983627 PMCID: PMC4415564 DOI: 10.1590/s1415-475738120140126] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 10/08/2014] [Indexed: 12/17/2022] Open
Abstract
Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the Structure analysis. According to analysis of molecular variance, the most divergent accessions comprised 97.2% of the observed genetic variability present within the base collection, confirming the efficiency of the selection criterion. The 180 selected accessions will be used for association mapping in future studies and could be potentially used by breeders to direct new crosses and generate elite cultivars that meet current and future global market needs.
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Affiliation(s)
- Juliana Morini Küpper Cardoso Perseguini
- Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil . ; Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, Campinas, SP, Brazil
| | | | | | - Rodrigo Gazaffi
- Departamento de Biotecnologia Vegetal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, SP, Brazil
| | - Jéssica Fernanda Marçal
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, Campinas, SP, Brazil
| | | | | | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Centro de Desenvolvimento Tecnológico, Instituto Agronômico, Campinas, SP, Brazil
| | | | - Luciana Lasry Benchimol-Reis
- Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil . ; Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, Campinas, SP, Brazil
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Oblessuc PR, Cardoso Perseguini JMK, Baroni RM, Chiorato AF, Carbonell SAM, Mondego JMC, Vidal RO, Camargo LEA, Benchimol-Reis LL. Increasing the density of markers around a major QTL controlling resistance to angular leaf spot in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2451-65. [PMID: 23832048 DOI: 10.1007/s00122-013-2146-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/14/2013] [Indexed: 05/21/2023]
Abstract
Angular leaf spot (ALS) causes major yield losses in the common bean (Phaseolus vulgaris L.), an important protein source in the human diet. This study describes the saturation around a major quantitative trait locus (QTL) region, ALS10.1, controlling resistance to ALS located on linkage group Pv10 and explores the genomic context of this region using available data from the P. vulgaris genome sequence. DArT-derived markers (STS-DArT) selected by bulk segregant analysis and SCAR and SSR markers were used to increase the resolution of the QTL, reducing the confidence interval of ALS10.1 from 13.4 to 3.0 cM. The position of the SSR ATA220 coincided with the maximum LOD score of the QTL. Moreover, a new QTL (ALS10.2(UC)) was identified at the end of the same linkage group. Sequence analysis using the P. vulgaris genome located ten SSRs and seven STS-DArT on chromosome 10 (Pv10). Coincident linkage and genome positions of five markers enabled the definition of a core region for ALS10.1 spanning 5.3 Mb. These markers are linked to putative genes related to disease resistance such as glycosyl transferase, ankyrin repeat-containing, phospholipase, and squamosa-promoter binding protein. Synteny analysis between ALS10.1 markers and the genome of soybean suggested a dynamic evolution of this locus in the common bean. The present study resulted in the identification of new candidate genes and markers closely linked to a major ALS disease resistance QTL, which can be used in marker-assisted selection, fine mapping and positional QTL cloning.
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Affiliation(s)
- Paula Rodrigues Oblessuc
- Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, 13083-970, Brazil,
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