Development and Evaluation of a 8K SNP Genotyping Array for Coffea canephora and Coffea arabica

Genotyping arrays are now becoming an usual tool for plant genetics and breeding. Over the last few years, the sequencing of various species by next-generation sequencing technologies (NGS) has led to the discovery of numerous genome-wide SNPs. This approach has allowed the design of a Coffee 8K genotyping array for the two main cultivated species: Coffea canephora and Coffea arabica.

For genome-wide SNP discovery, 12 Coffea canephora and 4 Coffea arabica genotypes representing the genetic diversity of the species (Gomez et al. 2009, Musoli et al. 2009) were re-sequenced using the Illumina technology. Following the mapping of these sequences to the Coffea canephora reference genome (Denoeud et al. 2014), a subset of 8,000 high-quality SPs were selected for the design of an Illumina Infinium SNP array, including 65 % and 35 % of SNPs from Coffea canephora and Coffea Arabica, respectively. The array contained evenly distributed markers among the 11 linkage groups, 58 % of which are located within genic regions as annotated in the Coffea canephora reference genome.

The usefulness of this genotyping tool to address specific questions related to genetic diversity and to linkage mapping has been demonstrated. In terms of genetic diversity, the Coffee 8K array allowed the characterization of seven genetic groups for Coffea canephora in accordance with previous results obtained with a set of 19 SSR markers. The array was also used to generate high-density genetic maps for the two species Coffea canephora and Coffea arabica, consisting of 3048 and 1842 markers, respectively. These two high-resolution genetic maps have already been used to improve the Robusta and Arabica reference genome assemblies and QTL detection.

The Coffee 8K array will definitely provide a valuable additional resource for coffee research, which will significantly accelerate various genomic studies as well as breeding programs.

[1] Gomez C. et al. (2009) Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evol Biol 9:167

[2] Musoli, P et al. (2009) Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome, 52, 634-46

[3] Denoeud F. et al. (2014) The Coffee Genome Provides Insight into Convergent Evolution of Caffeine Biosynthesis. Science 345(6201):1181