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Ariyoshi C, Sant’ana GC, Felicio MS, Sera GH, Nogueira LM, Rodrigues LMR, Ferreira RV, da Silva BSR, de Resende MLV, Destéfano SAL, Domingues DS, Pereira LFP. Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica. Front Plant Sci 2022; 13:989847. [PMID: 36330243 PMCID: PMC9624508 DOI: 10.3389/fpls.2022.989847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Bacteria halo blight (BHB), a coffee plant disease caused by Pseudomonas syringae pv. garcae, has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most Coffea arabica cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in C. arabica Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of C. arabica, we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C. arabica Ethiopian accessions from a historical FAO collection, 11 C. arabica cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to g000 (Chr_0_434_435) and g010741 genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a C. arabica susceptible cultivar and in a C. arabica cultivar with quantitative resistance, when infected with P. syringae pv. garcae. However, peaks of upregulation were observed in a C. arabica cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in C. arabica. In addition, the findings contribute to increasing understanding of the C. arabica domestication history.
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Affiliation(s)
- Caroline Ariyoshi
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | - Mariane Silva Felicio
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
- Programa de pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista “Júlio de Mesquita Filho“ (UNESP), Instituto de Biociências, Campus de Botucatu, Botucatu, Brazil
| | - Gustavo Hiroshi Sera
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | - Livia Maria Nogueira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | - Rafaelle Vecchia Ferreira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | - Bruna Silvestre Rodrigues da Silva
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | | | - Douglas Silva Domingues
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba, Brazil
| | - Luiz Filipe Protasio Pereira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA-Café), Brasília, Brazil
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Siciliano RF, Gualandro DM, Felicio MS, Paixao MR, Marcondes-Braga FG, Oliveira Jr MT, Soeiro A, Tarasoutch F, Caramelli B, Strunz C, Pacanaro AP, Bittencourt MS, Mansur AJ, Pereira-Barretto AC, Strabelli TMV. P4195Biomarkers for the prediction of mortality in patients with infective endocarditis. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy563.p4195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- R F Siciliano
- Heart Institute (InCor), University of São Paulo Medical School, Infection Control Team, São Paulo, Brazil
| | - D M Gualandro
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - M S Felicio
- Heart Institute (InCor), University of São Paulo Medical School, Infection Control Team, São Paulo, Brazil
| | - M R Paixao
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - F G Marcondes-Braga
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - M T Oliveira Jr
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - A Soeiro
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - F Tarasoutch
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - B Caramelli
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - C Strunz
- Heart Institute (InCor), University of São Paulo Medica School, Laboratory, Sao Paulo, Brazil
| | - A P Pacanaro
- Heart Institute (InCor), University of São Paulo Medica School, Laboratory, Sao Paulo, Brazil
| | - M S Bittencourt
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - A J Mansur
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - A C Pereira-Barretto
- Heart Institute (InCor), University of São Paulo Medical School, Cardiology, São Paulo, Brazil
| | - T M V Strabelli
- Heart Institute (InCor), University of São Paulo Medical School, Infection Control Team, São Paulo, Brazil
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dos Santos TB, Lima JE, Felicio MS, Soares JDM, Domingues DS. Genome-wide identification, classification and transcriptional analysis of nitrate and ammonium transporters in Coffea. Genet Mol Biol 2017; 40:346-359. [PMID: 28399192 PMCID: PMC5452133 DOI: 10.1590/1678-4685-gmb-2016-0041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 02/21/2017] [Indexed: 11/21/2022] Open
Abstract
Nitrogen (N) is quantitatively the main nutrient required by coffee plants, with acquisition mainly by the roots and mostly exported to coffee beans. Nitrate (NO3-) and ammonium (NH4+) are the most important inorganic sources for N uptake. Several N transporters encoded by different gene families mediate the uptake of these compounds. They have an important role in source preference for N uptake in the root system. In this study, we performed a genome-wide analysis, including in silico expression and phylogenetic analyses of AMT1, AMT2, NRT1/PTR, and NRT2 transporters in the recently sequenced Coffea canephora genome. We analyzed the expression of six selected transporters in Coffea arabica roots submitted to N deficiency. N source preference was also analyzed in C. arabica using isotopes. C. canephora N transporters follow the patterns observed for most eudicots, where each member of the AMT and NRT families has a particular role in N mobilization, and where some of these are modulated by N deficiency. Despite the prevalence of putative nitrate transporters in the Coffea genome, ammonium was the preferential inorganic N source for N-starved C. arabica roots. This data provides an important basis for fundamental and applied studies to depict molecular mechanisms involved in N uptake in coffee trees.
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Affiliation(s)
- Tiago Benedito dos Santos
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná,
Londrina, PR, Brazil
- Programa de pós-graduação em Agronomia, Universidade do Oeste
Paulista (UNOESTE), Presidente Prudente, SP, Brazil
| | - Joni Esrom Lima
- Departamento de Botânica, Instituto de Ciências Biológicas,
Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Centro de Energia Nuclear na Agricultura (CENA), Escola Superior de
Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), Piracicaba.
SP, Brazil
| | - Mariane Silva Felicio
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná,
Londrina, PR, Brazil
| | | | - Douglas Silva Domingues
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná,
Londrina, PR, Brazil
- Departamento de Botânica, Instituto de Biociências de Rio Claro,
Universidade Estadual Paulista “Júlio Mesquita Filho” (UNESP), Rio Claro, SP,
Brazil
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