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Diversity and structure of Coffea canephora from old seminal crops in Espírito Santo, Brazil: genetic resources for coffee breeding

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Abstract

The Coffea canephora germplasm, found in old seed crops in southern Espírito Santo, Brazil, represents a valuable genetic resource for coffee breeding programs. However, the renewal of these crops by clonal cultivars can narrow down the genetic base. Thus, this study aims to characterize the genetic diversity and population structure of 280 C. canephora genotypes from selected matrices in old (15–46-year-old) seed crops from southern Espírito Santo using Single Nucleotide Polymorphism (SNP) markers. Out of the 9491 SNPs retrieved from the Diversity Array Technology™ sequencing, 2542 high-quality SNPs were used for diversity and population STRUCTURE analyses, which detected two genetic pools. Cluster analysis revealed six clusters, some of which showed a high frequency of expected heterozygotes (HE), an indicative of the genetic diversity (GD) within this population. Clusters 4, 5, and 6, especially, harbor an abundance of heterozygous loci. High FST values were detected between clusters 4 and 2 (0.60), 2 and 5 (0.60), and 4 and 3 (0.50) and between the two genetic pools (0.59). This population’s higher GD indices demonstrate that the old seed crops from southern Espírito Santo constitute a noticeably rich germplasm bank. This valuable source must be maintained and conserved to ensure coffee crop sustainability since it can broaden the genetic base once reduced by the replacement of crops with clonal cultivars.

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Acknowledgements

The authors are grateful to the producers who allowed the collection of seeds on their farms and to everyone who helped execute this experiment.

Funding

This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico [National Council for Scientific and Technological Development] (CNPq, Brasília, DF, Brazil, grant number 311950/2016-7), Fundação de Amparo à Pesquisa e Inovação do Espírito Santo [Research Support Foundation of Espírito Santo] (FAPES, Vitória, ES, Brazil), and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior [Coordination for the Improvement of Higher Education Personnel] (CAPES, Brasília, DF, Brazil)–Finance Code 001, for the financial support.

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Authors and Affiliations

  1. Laboratório de Genética e Melhoramento Vegetal, Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, ZIP: 29.500-000, Alegre, ES, Brazil

    Iasmine Ramos Zaidan, Adésio Ferreira, Luina Ribeiro Noia, Jônatas Gomes Santos, Valderson Cabral de Arruda, Diego Pereira do Couto, Ramon Azevedo Braz & Marcia Flores da Silva Ferreira

  2. Departamento de Ciências Agrárias e Biológicas, Centro Universitário do Norte do Espírito Santo, Universidade Federal do Espírito Santo, ZIP: 29, São Mateus, ES, 932-540, Brazil

    Fábio Luiz Partelli

  3. Departamento de Estatística, Universidade Federal de Viçosa, ZIP: 36.570-900, Viçosa, MG, Brazil

    Camila Ferreira Azevedo

  4. Incaper-Centro de Pesquisa Desenvolvimento e Inovação Sul, ZIP: 29.323-000, Cachoeiro de Itapemirim, ES, Brazil

    João Felipe de Brites Senra

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  1. Iasmine Ramos Zaidan
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Contributions

Zaidan I.R. designed the research and data analysis and wrote the manuscript. Ramon A.B. coordinated sampling. Arruda V.C., Santos J.G., and Senra J.F.B. contributed in experimental implementation and plant selection. Noia L.R. and Santos J.G. helped in performing molecular biology and provided assistance with genotyping and experimentation design. Partelli F.L. helped with interpretation and discussion. Azevedo C.F. helped with the conception of the project and helped with interpretation and discussion. Ferreira A. contributed in conception and design of the project and data analysis, secured funding, and wrote the manuscript. Ferreira M.F.S. contributed in conception and design of the project, secured funding, and wrote the manuscript.

Corresponding author

Correspondence to Marcia Flores da Silva Ferreira.

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Zaidan, I.R., Ferreira, A., Noia, L.R. et al. Diversity and structure of Coffea canephora from old seminal crops in Espírito Santo, Brazil: genetic resources for coffee breeding. Tree Genetics & Genomes 19, 19 (2023). https://doi.org/10.1007/s11295-023-01594-x

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