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.

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. euge- nioides (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.

Auteurs: Merot-L’anthoene, V., Tournebize, R., Darracq, O., Rattina, V., Lepelley, M., Bellanger, L., Tranchant-Dubreuil, C., Coulee, M., Pegard, M., Metairon,  S., Fournier, C., Stoffelen, P., Janssens, S. B., Kiwuka, C., Musoli, P., Sumirat, U., Legnate, H., Kambale, J.-L., Ferreira da Costa Neto, J., Revel, C., De Kochko, A., Descombes, P., Crouzillat, D. and Poncet