MoccaDB 2.0, an Interactive Coffee SNP Database

RATIONALE. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms (SNPs) that may be used by breeders to identify and trace genes when breeding new varieties. Next-generation sequencing technology has accelerated the whole genome sequencing of Coffea canephora¹ and C. arabica as well as the re-sequencing of diverse coffee accessions and the discovery of genome-wide SNPs. To enhance the potential utility of genome-wide SNPs for geneticists and breeders, we updated MoccaDB²with a new web-based query interface to search and browse SNPs in addition to other genetic markers (SSR, RFLP,CAPS,etc..).

METHODS. The information on a large number of SNPs was collectively acquired from the research projects of the Coffea canephora Sequencing Consortium^1, and the Arabica Coffee Genome Consortium (ACGC). We implemented new modules in MoccaDB²to include information and search tools related to SNPs, which allows access and visualization of the SNP information and locations both on linkage maps and reference genomes.

RESULTS. Molecular markers and genetic maps are stored in the MoccaDB database. Six Coffea genetic maps are currently recorded, including the high-density C. canephora consensus map used for the anchoring of scaffolds¹. For the latter, among the 3230 loci distributed on 11 linkage groups, 2564 markers have been anchored. The new C. arabicagenetic map was added to the database increasing the number of anchored SNP markers to 2600 validated ones. The query results can be visualized as text format in tables displayed on interfaces, the maps can be viewed and compared as graphics using the CMap and in a genome browser.

CONCLUSIONS & PERSPECTIVES. Genome-wide SNP analysis is a promising tool to examine the genetic diversity of Coffee populations and genetic traits of scientific and economic importance. By combining information including SNPs and other genetic markers MoccaDB is an integrative web-portal providing a database of large-scale genome variation across coffee useful for both breeders and researchers.

REFERENCES

¹Denoeud, F., et al. (2014) The Coffee Genome Provides Insight into the Convergent Evolution of Caffeine Biosynthesis. Science, 345, 1181-1184.

²Plechakova, O., Tranchant-Dubreuil, C., Benedet, F., Couderc, M., Tinaut, A., Viader, V., De Block, P., Hamon, P., Campa, C., de Kochko, A., Hamon, S. & Poncet, V. (2009) MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family. BMC Plant Biology, 9, 123.

³Dereeper, A., Bocs, S., Rouard, M., Guignon, V., Ravel, S., Tranchant-Dubreuil, C., Poncet, V., Garsmeur, O., Lashermes, P. & Droc, G. (2015) The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res, 43, D1028-35.