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SNP markers found in non-coding regions can distinguish among low-variant genotypes of Arabica and other coffee species

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Abstract

Development of efficient and scalable methods for molecular identification of Coffea spp. are necessary to accelerate studies related to the characterization of germplasm for both conservation or breeding purposes, and the validation of coffee germplasm. The low genetic diversity of coffee hinders the establishment of protocols that facilitate the molecular characterization of a given genotype. In this study, nucleotide variability was analyzed at 22 loci in the genome of 19 coffee accessions using de novo primer sets and high-resolution melting (HRM). Single nucleotide polymorphisms (SNPs) variants were studied in coding regions of genes implicated in sucrose accumulation in the seed, Sucrose synthase 2 (SUS2), Ent-kaurene oxidase 1 (CaKO1), and Caffeoyl-coenzyme A 3-O-methyltransferase (CcOAOMT). The non-coding Internal transcribed spacer 2 (ITS2) region was also studied. Variability was shown at 103 positions both at the interspecies level (15 loci) and among varieties of Coffea arabica L. (4 loci). The HMR technique for identification of variants in genes CaKO1, SUS2, CcoAOMT, as well as in the ITS2 region proved to be a robust technique for germplasm characterization. More important this technique can be used for fingerprinting and traceability of coffee grain exports which is an increasing market-consumer demand.

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Availability of data and material

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors would like to thank the “Centro Nacional de Alta Tecnología-Consejo Nacional de Rectores” (CeNAT-CONARE) and “Sistema de Estudios de Posgrado de la Universidad de Costa Rica” (SEP-UCR) for the grant awarded to A.B-G. Moreover, we thank the anonymous reviewers for their helpful comments on this manuscript.

Funding

This research was financed by the University of Costa Rica and the “Ministerio de Ciencia, Tecnología y Telecomunicaciones” (MICITT) (project No. 111-B5-140).

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Authors and Affiliations

  1. Laboratorio Biotecnología de Plantas, Escuela de Biología, Universidad de Costa Rica, San Pedro, Costa Rica

    Alejandro Bolívar-González & Andrés Gatica-Arias

  2. Programa de Posgrado en Ciencias Agrícolas y Recursos Naturales con Énfasis en Biotecnología (PPCARN), Universidad de Costa Rica, San Pedro, Costa Rica

    Alejandro Bolívar-González & Andrés Gatica-Arias

  3. Programa de Biotecnología Vegetal y Recursos Genéticos para el Fitomejoramiento (BIOVERFI), Universidad Nacional, Heredia, Costa Rica

    Ramón Molina-Bravo

  4. CATIE (Centro Agronómico Tropical de Investigación y Enseñanza), Turrialba, Cartago, Costa Rica

    William Solano-Sánchez

  5. Centro Nacional de Innovaciones Biotecnológicas, CENIBiot-CeNAT, San José, Costa Rica

    Emanuel Araya-Valverde

  6. Area of Genetic Improvement and Plant Propagation, Paraná Rural Development Institute, Londrina, Paraná, 86047-902, Brazil

    Suzana T. Ivamoto-Suzuki & Luiz F. P. Pereira

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  1. Alejandro Bolívar-González
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  2. Ramón Molina-Bravo
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  3. William Solano-Sánchez
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  4. Emanuel Araya-Valverde
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  5. Suzana T. Ivamoto-Suzuki
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  6. Luiz F. P. Pereira
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  7. Andrés Gatica-Arias
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Contributions

A.B-G. designed and performed the experiments, analyzed data, and wrote the draft manuscript; A.G-A conceived the project, designed and coordinated the experiments, analyzed data, and edited the final manuscript; E.A-V. provided fundamental feedback of experiments execution, discussed the results, and edited the final manuscript; R.M.-B. provided fundamental feedback of experiments execution, discussed the results, and edited the final manuscript; W.S–S provided the plant material, and edited the final manuscript; S.T.I-S and L.F.P.P revised and edited the final manuscript.

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Correspondence to Andrés Gatica-Arias.

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Bolívar-González, A., Molina-Bravo, R., Solano-Sánchez, W. et al. SNP markers found in non-coding regions can distinguish among low-variant genotypes of Arabica and other coffee species. Genet Resour Crop Evol 70, 1215–1228 (2023). https://doi.org/10.1007/s10722-022-01498-0

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