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.





Figure 2: Genetic and genomic distribution of the Coffee8.5K array SNPs. (a) Genome distribution of the 8580 single‐nucleotide polymorphisms (SNPs) synthesized for the array along the 11 pseudo‐chromosomes and the virtual pseudo‐chromosome 0 of unanchored sequences. For each pseudo‐chromosome, we determined: the number of SNPs markers according to their source (C. arabica, Ara or C. canephora, Can), the mean distance between markers and their density related to the estimated size of the pseudo‐chromosome. (b) C. canephora high‐density genetic map of BP409xQ121 progeny, with 11 linkage groups. SNP markers (1307) obtained from the Coffee8.5K array are indicated in red.