Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica
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 sour...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.989847/full |
| _version_ | 1811182100249837568 |
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| author | Caroline Ariyoshi Caroline Ariyoshi Gustavo César Sant’ana Mariane Silva Felicio Mariane Silva Felicio Gustavo Hiroshi Sera Livia Maria Nogueira Livia Maria Nogueira Lucas Mateus Rivero Rodrigues Rafaelle Vecchia Ferreira Rafaelle Vecchia Ferreira Bruna Silvestre Rodrigues da Silva Bruna Silvestre Rodrigues da Silva Mário Lúcio Vilela de Resende Suzete Aparecida Lanza Destéfano Douglas Silva Domingues Luiz Filipe Protasio Pereira Luiz Filipe Protasio Pereira Luiz Filipe Protasio Pereira |
| author_facet | Caroline Ariyoshi Caroline Ariyoshi Gustavo César Sant’ana Mariane Silva Felicio Mariane Silva Felicio Gustavo Hiroshi Sera Livia Maria Nogueira Livia Maria Nogueira Lucas Mateus Rivero Rodrigues Rafaelle Vecchia Ferreira Rafaelle Vecchia Ferreira Bruna Silvestre Rodrigues da Silva Bruna Silvestre Rodrigues da Silva Mário Lúcio Vilela de Resende Suzete Aparecida Lanza Destéfano Douglas Silva Domingues Luiz Filipe Protasio Pereira Luiz Filipe Protasio Pereira Luiz Filipe Protasio Pereira |
| author_sort | Caroline Ariyoshi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T09:26:23Z |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T09:26:23Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-f889eff7857b44a593e4ecb27433809e2022-12-22T04:32:01ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-10-011310.3389/fpls.2022.989847989847Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabicaCaroline Ariyoshi0Caroline Ariyoshi1Gustavo César Sant’ana2Mariane Silva Felicio3Mariane Silva Felicio4Gustavo Hiroshi Sera5Livia Maria Nogueira6Livia Maria Nogueira7Lucas Mateus Rivero Rodrigues8Rafaelle Vecchia Ferreira9Rafaelle Vecchia Ferreira10Bruna Silvestre Rodrigues da Silva11Bruna Silvestre Rodrigues da Silva12Mário Lúcio Vilela de Resende13Suzete Aparecida Lanza Destéfano14Douglas Silva Domingues15Luiz Filipe Protasio Pereira16Luiz Filipe Protasio Pereira17Luiz Filipe Protasio Pereira18Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, BrazilÁrea de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, BrazilTropical Melhoramento & Genética (TMG), Londrina, BrazilÁrea de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, BrazilPrograma de pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista “Júlio de Mesquita Filho“ (UNESP), Instituto de Biociências, Campus de Botucatu, Botucatu, BrazilÁrea de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, BrazilPrograma de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, BrazilÁrea de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, BrazilCentro de Café Alcides Carvalho, Instituto Agronômico (IAC), Campinas, BrazilPrograma de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, BrazilÁrea de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, BrazilPrograma de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, BrazilÁrea de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, BrazilDepartamento de Fitopatologia, Universidade Federal de Lavras (UFLA), Lavras, BrazilInstituto Biológico (IB), Campinas, BrazilDepartamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba, BrazilPrograma de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, BrazilÁrea de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, BrazilEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA-Café), Brasília, BrazilBacteria 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.https://www.frontiersin.org/articles/10.3389/fpls.2022.989847/fullcoffee domesticationbacterial halo blightplant diseasesingle-locus genome-wide associationmulti-locus genome-wide association |
| spellingShingle | Caroline Ariyoshi Caroline Ariyoshi Gustavo César Sant’ana Mariane Silva Felicio Mariane Silva Felicio Gustavo Hiroshi Sera Livia Maria Nogueira Livia Maria Nogueira Lucas Mateus Rivero Rodrigues Rafaelle Vecchia Ferreira Rafaelle Vecchia Ferreira Bruna Silvestre Rodrigues da Silva Bruna Silvestre Rodrigues da Silva Mário Lúcio Vilela de Resende Suzete Aparecida Lanza Destéfano Douglas Silva Domingues Luiz Filipe Protasio Pereira Luiz Filipe Protasio Pereira Luiz Filipe Protasio Pereira Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica Frontiers in Plant Science coffee domestication bacterial halo blight plant disease single-locus genome-wide association multi-locus genome-wide association |
| title | Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica |
| title_full | Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica |
| title_fullStr | Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica |
| title_full_unstemmed | Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica |
| title_short | Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica |
| title_sort | genome wide association study for resistance to pseudomonas syringae pv garcae in coffea arabica |
| topic | coffee domestication bacterial halo blight plant disease single-locus genome-wide association multi-locus genome-wide association |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.989847/full |
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