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Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Record number 552056
Title Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.
Author(s) Merot-L'anthoene, Virginie; Tournebize, Rémi; Darracq, Olivier; Rattina, Vimel; Lepelley, Maud; Bellanger, Laurence; Tranchant-Dubreuil, Christine; Coulée, Manon; Pégard, Marie; Metairon, Sylviane; Fournier, Coralie; Stoffelen, Piet; Janssens, Steven B.; Kiwuka, Catherine; Musoli, Pascal; Sumirat, Ucu; Legnaté, Hyacinthe; Kambale, Jean Léon; Ferreira da Costa Neto, João; Revel, Clara; Kochko, Alexandre de; Descombes, Patrick; Crouzillat, Dominique; Poncet, Valérie
Source Plant Biotechnology Journal 17 (2019)7. - ISSN 1467-7644 - p. 1418 - 1430.
DOI https://doi.org/10.1111/pbi.13066
Department(s) Centre for Crop Systems Analysis
Publication type Refereed Article in a scientific journal
Publication year 2019
Keyword(s) C. canephora - C. eugenioides - Coffea arabica origin - genetic map - single-nucleotide polymorphism - SNP array
Abstract

Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.

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