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Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, Wang C, Rajaraman S, Rastas P, Zheng C, Muñoz DS, Meidanis J, Paschoal AR, Bawin Y, Krabbenhoft TJ, Wang ZQ, Fleck SJ, Aussel R, Bellanger L, Charpagne A, Fournier C, Kassam M, Lefebvre G, Métairon S, Moine D, Rigoreau M, Stolte J, Hamon P, Couturon E, Tranchant-Dubreuil C, Mukherjee M, Lan T, Engelhardt J, Stadler P, Correia De Lemos SM, Suzuki SI, Sumirat U, Wai CM, Dauchot N, Orozco-Arias S, Garavito A, Kiwuka C, Musoli P, Nalukenge A, Guichoux E, Reinout H, Smit M, Carretero-Paulet L, Filho OG, Braghini MT, Padilha L, Sera GH, Ruttink T, Henry R, Marraccini P, Van de Peer Y, Andrade A, Domingues D, Giuliano G, Mueller L, Pereira LF, Plaisance S, Poncet V, Rombauts S, Sankoff D, Albert VA, Crouzillat D, de Kochko A, Descombes P. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 2024; 56:721-731. [PMID: 38622339 PMCID: PMC11018527 DOI: 10.1038/s41588-024-01695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
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Affiliation(s)
- Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Aditi Rambani
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Zhe Yu
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Susan Strickler
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Maud Lepelley
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Cui Wang
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniella Santos Muñoz
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - João Meidanis
- Institute of Computing, University of Campinas, Campinas, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, The Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Yves Bawin
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Zhen Qin Wang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Rudy Aussel
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille, France
| | | | - Aline Charpagne
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Coralie Fournier
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Mohamed Kassam
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Gregory Lefebvre
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Sylviane Métairon
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Déborah Moine
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Michel Rigoreau
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Jens Stolte
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Perla Hamon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Emmanuel Couturon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | | | - Minakshi Mukherjee
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jan Engelhardt
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Peter Stadler
- Department of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | | | | | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia
| | - Ching Man Wai
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicolas Dauchot
- Research Unit in Plant Cellular and Molecular Biology, University of Namur, Namur, Belgium
| | - Simon Orozco-Arias
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Andrea Garavito
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Catherine Kiwuka
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Pascal Musoli
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Anne Nalukenge
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Erwan Guichoux
- Biodiversité Gènes & Communautés, INRA, Bordeaux, France
| | | | - Martin Smit
- Hortus Botanicus Amsterdam, Amsterdam, the Netherlands
| | | | - Oliveiro Guerreiro Filho
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Masako Toma Braghini
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Lilian Padilha
- Embrapa Café/Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Pierre Marraccini
- CIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501, Montpellier, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Alan Andrade
- Embrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG, Lavras, Brazil
| | - Douglas Domingues
- Group of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Rome, Italy
| | - Lukas Mueller
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Luiz Filipe Pereira
- Embrapa Café/Lab. Biotecnologia, Área de Melhoramento Genético, Londrina, Brazil
| | | | - Valerie Poncet
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | | | - Alexandre de Kochko
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
| | - Patrick Descombes
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
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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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Shigueoka LH, de Batista Fonseca IC, Sera GH, Sera T, Aleandro da Silva S, Dorigo OF, Machado ACZ. Virulence and Reproductive Fitness of Meloidogyne paranaensis Field Populations in Coffee Genotypes. Plant Dis 2022; 106:2618-2624. [PMID: 35442053 DOI: 10.1094/pdis-01-22-0247-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The aim of this study was to characterize Meloidogyne paranaensis populations collected from infested coffee crops. Methodologies used to characterize the 11 studied populations from municipalities in Paraná and Minas Gerais States involved the morphological analysis of perineal patterns, biochemical analysis by isozyme electrophoresis, sequencing of internal transcribes spacer 1 (ITS-1) and D2/D3 ribosomal DNA (rDNA) regions, reproductive fitness, and virulence characterization in coffee genotypes. Morphological evaluations showed the existence of variation between populations, although the majority of them showed typical perineal patterns. The biochemical identification was based on α-esterase isozyme analyses and resulted in the appearance of three distinct profiles: P1 (typical), P2 (atypical), and a nondescribed profile, P2b. BLAST of the ITS-1 and D2/D3 rDNA regions indicated homology (>95%) with other sequences deposited in GenBank. For reproductive fitness and virulence characterization, 13 coffee genotypes (5 Coffea arabica and 8 C. canephora) were inoculated with 11 M. paranaensis populations. Variation in the reproductive fitness of populations was observed for cultivar Mundo Novo, a genotype without resistance genes, and variation in the virulence of populations was observed in genotypes carrying resistance genes. Three populations exhibited virulence combined with high reproductive fitness, while one showed virulence with low reproductive fitness. Some hosts were resistant to 11 populations, while one of the hosts was resistant to only one population, indicating the presence of different resistance genes. Nevertheless, no relationship was observed between the origin of population and their variations in perineal patterns, esterase profiles, phylogeny, or reproductive fitness in coffee genotypes, or between the different characterizations, although differences were observed within each characteristic.
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Affiliation(s)
| | | | - Gustavo Hiroshi Sera
- Instituto de Desenvolvimento Rural do Paraná-IAPAR-EMATER, 86047-902, Londrina, PR, Brazil
| | - Tumoru Sera
- Instituto de Desenvolvimento Rural do Paraná-IAPAR-EMATER, 86047-902, Londrina, PR, Brazil
| | | | - Orazília França Dorigo
- Instituto de Desenvolvimento Rural do Paraná-IAPAR-EMATER, 86047-902, Londrina, PR, Brazil
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