Capillary electrophoresis as a tool for genotyping SH3 mediated coffee leaf rust resistance

Savina A.  Gutiérrez-Calle; Rosa A.  Sánchez-Díaz; Yolanda B.  Delgado-Silva; Juan D.  Montenegro; Dina L.  Gutiérrez; Jorge L.  Maicelo-Quintana; Juan C.  Guerrero-Abad

doi:10.17268/sci.agropecu.2021.011

Authors

Savina A. Gutiérrez-Calle Centro Experimental La Molina. Dirección de Recursos Genéticos y Biotecnología. Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima
Rosa A. Sánchez-Díaz Departamento de Fitotecnia. Facultad de Agronomía. Universidad Nacional Agraria La Molina, La Molina. Av. La Molina s/n, 15024 Lima.
Yolanda B. Delgado-Silva Centro Experimental La Molina. Dirección de Recursos Genéticos y Biotecnología. Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima
Juan D. Montenegro Centro Experimental La Molina. Dirección de Recursos Genéticos y Biotecnología. Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima.
Dina L. Gutiérrez Centro Experimental La Molina. Dirección de Recursos Genéticos y Biotecnología. Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima
Jorge L. Maicelo-Quintana Centro Experimental La Molina. Dirección de Recursos Genéticos y Biotecnología. Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima.
Juan C. Guerrero-Abad Centro Experimental La Molina. Dirección de Recursos Genéticos y Biotecnología. Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima.

DOI:

https://doi.org/10.17268/sci.agropecu.2021.011

Keywords:

coffee, capillary, electrophoresis;, Hemileia vastatrix, SH3

Abstract

Coffee is an important agricultural commodity in the world. However, it is susceptible to Hemileia vastatrix (Hv), an obligatory biotrophic fungus that causes coffee leaf rust (CLR). Natural resistance to rust has been identified in the wild species Coffea canephora and Coffea liberica. These species have been used in breeding programs where interspecific resistant hybrids have been generated. The S_H3 gene, derived from C. liberica, has been shown to confer extreme and long-lasting resistance to Hv. A total of 167 accessions of the INIA’s Coffee Germplasm Collection of Peru (INIA-CGC) were screened with 4 markers linked to the S_H3 gene. As positive controls, EA67 (C. liberica) and the hybrid S.288 (C. arabica x C. liberica) were used. Separation of PCR products was done by capillary electrophoresis, which allow to discriminate the alleles of each marker. For three markers, specific alleles for either C. arabica or C. liberica species were found. In all cases, S.288 exhibited specific alleles for both species; whereas the INIA-CGC accessions had exclusively C. arabica alleles and EA67 had C. liberica alleles. The BA-48-21O-f marker did not produce PCR fragments for any of the positive controls, suggesting that this marker is not as predictive as the other three to determine the presence of S_H3. This work reports the existence of multiple alleles for the Sat244 marker; however, the collection does not have the S_H3 mediated-resistance gene. Finally, the utility of capillary electrophoresis as a tool to identify alleles linked to S_H3 was demonstrated.

References

Alkimim, E. R., Caixeta, E. T., Sousa, T. V., Pereira, A. A., de Oliveira, A. C. B., Zambolim, L., & Sakiyama, N. S. 2017. Marker-assisted selection provides arabica coffee with genes from other Coffea species targeting on multiple resistance to rust and coffee berry disease. Molecular Breeding, 37, 6.

Andrianasolo, D. N., Davis, A. P., Razafinarivo, N. J., Hamon, S., Rakotomalala, J. J., Sabatier, S. A., & Hamon, P. 2013. High genetic diversity of in situ and ex situ populations of Madagascan coffee species: Further implications for the management of coffee genetic resources. Tree Genetics & Genomes, 9, 1295-1312.

Avelino, J., Cristancho, M., Georgiou, S., Imbach, P., Aguilar, L., Bornemann, G., Läderach, P., Anzueto, F., Hruska, A. J., & Morales, C. 2015. The coffee rust crises in Colombia and Central America (2008–2013): Impacts, plausible causes and proposed solutions. Food Security, 7, 303-321.

Azmat, M. A., Khan, I. A., Cheema, H. M. N., Rajwana, I. A., Khan, A. S., & Khan, A. A. 2012. Extraction of DNA suitable for PCR applications from mature leaves of Mangifera indica L. Journal of Zhejiang University. Science B, 13, 239-243.

Byrne, M., Macdonald, B., & Francki, M. 2001. Incorporation of Sodium Sulfite into Extraction Protocol Minimizes Degradation of Acacia DNA. BioTechniques, 30, 742-748.

Cabral, P. G. C., Maciel-Zambolim, E., Oliveira, S. A. S., Caixeta, E. T., & Zambolim, L. 2016. Genetic diversity and structure of Hemileia vastatrix populations on Coffea spp. Plant Pathology, 65, 196-204.

Cámara Peruana del Café y Cacao: Café - Datos. 2020. Available in: https://camcafeperu.com.pe/ES/cafe-datos.php

Cueva-Agila, A., Vélez-Mora, D., Arias, D., Curto, M., Meimberg, H., & Brinegar, C. 2019. Genetic characterization of fragmented populations of Cinchona officinalis L. (Rubiaceae), a threatened tree of the northern Andean cloud forests. Tree Genetics & Genomes, 15(6), 81.

Doyle, J. J., & Doyle, J. L. 1987. A rapid DNA isolation procedure from small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11-15.

Durney, B. C., Crihfield, C. L., & Holland, L. A. 2015. Capillary electrophoresis applied to DNA: Determining and harnessing sequence and structure to advance bioanalyses (2009–2014). Analytical and Bioanalytical Chemistry, 407, 6923-6938.

Galili, T. 2015. Dendextend: An R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics, 31, 3718-3720.

Genetic resources, Instituto Superior de Agronomia. 2020. Available in: https://www.isa.ulisboa.pt/en/cifc/genetic-resources

González-Martínez, L. F., Cortina-Guerrero, H. A., & Herrera-Pinilla, J. C. 2009. Validación de Marcadores Moleculares Ligados al Gen SH3 de Resistencia contra la Roya en Introducciones de la Colección Colombiana de Café. Cenicafé, 60, 375-389.

Herrera, S. 2019. Caracterización de la diversidad genética de variedades de albaricoquero mediante marcadores microsatélites (SSR). Thesis Máster Bioinformática y Bioestadística, Universitat Oberta de Catalunya. España. 42 pp.

Inglis, P. W., Pappas, M. de C. R., Resende, L. V., & Grattapaglia, D. 2018. Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications. PLOS ONE, 13(10), e0206085.

International Coffee Organization-Historical Data on the Global Coffee Trade. 2020. [Data Base]. Available in: http://www.ico.org/new_historical.asp

Jombart, T. 2008. Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403-1405.

Junta Nacional del Café. 2019. La caficultura peruana está en riesgo por bajos precios y altos costos de producción. El Cafetalero, 62, 10-12.

Lashermes, P., Combes, M.C., Ribas, A., Cenci, A., Mahé, L., & Etienne, H. 2010. Genetic and physical mapping of the SH3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.). Tree Genetics & Genomes, 6, 973-980.

Lashermes, P., Andrzejewski, S., Bertrand, B., Combes, M. C., Dussert, S., Graziosi, G., Trouslot, P., & Anthony, F. 2000. Molecular analysis of introgressive breeding in coffee (Coffea arabica L.). Theoretical and Applied Genetics, 100, 139-146.

Lee, J. 2019. Development and Evolution of Molecular Markers and Genetic Maps in Capsicum Species. N. Ramchiary & C. Kole (Eds.), The Capsicum Genome. Springer International Publishing. Pp. 85-103.

Mahé, L., Combes, M. C., Várzea, V. M., Guilhaumon, C., & Lashermes, P. 2008. Development of sequence characterized DNA markers linked to leaf rust (Hemileia vastatrix) resistance in coffee (Coffea arabica L.). Molecular Breeding, 21(1), 105-113.

Mahé, L. 2007. Contribution à l'amélioration génétique de la résistance des caféiers (Coffea arabica L.) à la rouille (Hemileia vastatrix): De l'étude des hybrides interspécifiques naturels de Nouvelle-Calédonie à la cartographie d'un locus de résistance. Tesis Doctoral. École nationale supérieure agronomique (Montpellier). Francia. 135 pp.

McCook, S., & Vandermeer, J. 2015. The Big Rust and the Red Queen: Long-Term Perspectives on Coffee Rust Research. Phytopathology, 105, 1164-1173.

Mishra, M. K. 2020. Genetic Resources and Breeding of Coffee (Coffea spp.) | SpringerLink. En Advances in Plant Breeding Strategies: Nut and Beverage Crops (Al-Khayri J.; Jain S.; Johnson D. (Eds). Springer. Pp. 475-515.

Mohamed, A., García-Martínez, S., Loumerem, M., Carbonell, P., Ruiz, J. J., & Boubaker, M. 2019. Assessment of genetic diversity among local pea (Pisum sativum L.) accessions cultivated in the arid regions of Southern Tunisia using agro-morphological and SSR molecular markers. Genetic Resources and Crop Evolution, 66(6), 1189-1203.

Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 23, 341-369.

Nolte, G. E. 2020. Peru: Coffee Annual [USDA Agency]. The Foreign Agricultural Service (FAS) - United States Department of Agriculture. Available in: https://www.fas.usda.gov/data/peru-coffee-annual-4

Nsabiyera, V., Qureshi, N., Bariana, H. S., Wong, D., Forrest, K. L., Hayden, M. J., & Bansal, U. K. 2016. Molecular markers for adult plant leaf rust resistance gene Lr48 in wheat. Molecular Breeding, 36(6), 65.

Prakash, N. S., Marques, D. V., Varzea, V. M. P., Silva, M. C., Combes, M. C., & Lashermes, P. 2004. Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into C. arabica L. Theoretical and Applied Genetics, 109, 1311-1317.

Prakash, N.S., Combes, M. C., Somanna, N., & Lashermes, P. 2002. AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid. Euphytica, 124, 265-271.

Pruvot-Woehl, S., Krishnan, S., Solano, W., Schilling, T., Toniutti, L., Bertrand, B., & Montagnon, C. 2020. Authentication of Coffea arabica Varieties through DNA Fingerprinting and its Significance for the Coffee Sector. Journal of AOAC INTERNATIONAL, 103(2), 325-334.

Ribas, A. F., Cenci, A., Combes, M. C., Etienne, H., & Lashermes, P. 2011. Organization and molecular evolution of a disease-resistance gene cluster in coffee trees. BMC Genomics, 12, 240.

Romero, G., Vásquez, L. M., Lashermes, P., & Herrera, J. C. 2014. Identification of a major QTL for adult plant resistance to coffee leaf rust (Hemileia vastatrix) in the natural Timor hybrid (Coffea arabica x C. canephora). Plant Breeding, 133, 121-129.

Sánchez, E., Solano, W., Gatica-Arias, A., Chavaría, M., & Araya-Valverde, E. 2020. Microsatellite DNA fingerprinting of Coffea sp. Germplasm conserved in Costa Rica through singleplex and multiplex PCR. Crop Breeding and Applied Biotechnology, 20(1), e27812013.

Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18, 233-234.

Silva, D. N., Várzea, V., Paulo, O. S., & Batista, D. 2018. Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust. Molecular Plant Pathology, 19, 1742-1753.

Sousa, T. V., Caixeta, E. T., Alkimim, E. R., Oliveira, A. C. B., Pereira, A. A., Sakiyama, N. S., Zambolim, L., & Resende, M. D. V. 2019. Early Selection Enabled by the Implementation of Genomic Selection in Coffea arabica Breeding. Frontiers in Plant Science, 9, 1934.

Souza, H. A. V., Muller, L. A. C., Brandão, R. L., & Lovato, M. B. 2012. Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado. Genetics and Molecular Research, 11, 756-764.

Talhinhas, P.; Batista, D.; Diniz, I.; Vieira, A.; Silva, D. N.; Loureiro, A.; Tavares, S.; Pereira, A. P.; Azinheira, H. G.; Guerra-Guimarães, L.; Várzea, V. & Silva, M. D. C. 2017. The coffee leaf rust pathogen Hemileia vastatrix: One and a half centuries around the tropics. Molecular Plant Pathology 18: 1039-1051.

Tornincasa, P. 2008. Marcatori genetici per l´analisi, la caratterizzazione e la tracciabilità del caffè e delle due specie vegetali Coffea arabica L. e Coffea canephora. PhD Thesis Genetica, Università degli Studi di Trieste. Italia. 110 pp.

Valencia, A., Morales, A. Y., del Pilar Moncada, M. I., Cortina, H. A., & Herrera, J. C. 2017. Introgresion of the SH3 gene resistant to rust (Hemileia vastatrix) in improved lines of CASTILLO variety (Coffea arabica L.). Journal of Plant Breeding and Crop Science, 9, 130-138.

Wickham, H. 2016. ggplot2: elegant graphics for data analysis. Springer.

Zambolim, L. 2016. Current status and management of coffee leaf rust in Brazil. Tropical Plant Pathology, 41, 1-8.