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. 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.

Characterization of branching in two Hevea brasiliensis clones

Rubber has been grown for several decades in Africa, notably in Ivory Coast. Although the yields obtained with selected clones are good, some problems with adaptation to edaphic and climatic conditions have yet to be solved. Of these problems, tree breakage due to violent winds during frequent storms is a major handicap. Some clones are more resistant to wind damage. However, this resistance trait remains difficult to measure, and detecting it at an early stage appeared important. As no differences have been found in the physical properties of the wood of different clones, the search for differences between clones displaying resistance and susceptibility to wind damage was switched to architectural structures. Architectural traits were thus studied on two rubber clones with very different resistances to wind. Observations were focused both on young trees and adult trees. Of all the architectural traits observed, a description of branching provided information likely to explain differences in the way the clones being studied developed over time. The clone GT1 which is resistant to wind, developed more lateral branches but they did not grow much in length. On the other hand, fewer axillary branches appeared on the susceptible clone PB235 but they grew longer. Moreover, as some of these traits proved to be similar in both young and adult trees, they could be detected at a sufficiently early stage for use as early prediction traits, if their involvement in susceptibility to wind damage is confirmed.