Development of microsatellite markers for identifying Brazilian Coffea arabica varieties

Abstract

Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of nineteen commercially important Brazilians and six interspecific hybrids of Coffea arabica, Coffea canephora and Coffealiberica. The set used comprised 52 newly developed SSR markers derived from microsatellite enriched libraries, 56 designed on the basis of coffee SSR sequences available from public databases, 6 already published, and 13 universal chloroplast microsatellite markers. Only 22 were polymorphic, these detecting 2-7 alleles per marker, an average of 2.5. Based on the banding patterns generated by polymorphic SSR loci, the set of twenty-five coffee varieties were clustered into two main groups, one composed of only Brazilian varieties, and the other of interspecific hybrids, with a few Brazilians. Color mutants could not be separated. Clustering was in accordance with material genealogy thereby revealing high similarity.

Molecular markers useful to discriminate Coffea arabica cultivars with high genetic similarity

“…In 34 C. arabica cultivars, a mean of 2.35 alleles per primer was obtained using 20 polymorphic markers. Similar to this result, a mean of 2.5 alleles per microsatellite primer has been reported in a study on 19 C. arabica cultivars (Vieira et al 2010); indicating a narrow genetic base between the cultivars/progenies. This can be explained by the low number of plants that were initially introduced in Brazil, which constitute the genetic base of the current cultivars (Setotaw et al 2013).…”

“…These results demonstrate the low genetic variability of this species, since the studied population originated from a contrasting cross in the F 2 generation. In several studies, a small number of polymorphic loci was observed for C. arabica (Combes et al 2000;Anthony et al 2001;Anthony et al 2002;Sera et al 2003;Diniz et al 2005;Vieira et al 2010).…”

Research Article Genetic diversity among 16 genotypes of Coffea arabica in the Brazilian cerrado.

“…Specific area crown (mm) = SAS, diameter of the crown base = DCB, length of the orthotropic branch = LOB, diameter of the orthotropic branch = DOB, root volume (mm 3 ) = RV, root surface area (mm 2 /cm 3 ) = RSA, root weighted diameter (mm) = RWD, and productivity = P. The results reported by Vieira et al, (2010) have most of the Brazilian varieties in a single group with a high initialization value (81.7). Intraspecific hybrids and two Brazilian varieties (Tupi and Icatu Vermelho) were placed in groups with bootstrap values below 50%, which indicates that the observed clustering of varieties in the dendrogram accurately represents the genetic similarity estimates.…”

Molecular characterization of arabica and Conilon coffee plants genotypes by SSR and ISSR markers

“…This strategy allowed the performance of a statistical analysis of diversity between the species of different ploidy and of dominant and multi-allelic markers (Powell et al 1996;Souza et al 2008;Vieira 2010). The genetic similarity values were estimated by the complement of the Jaccard similarity index and clustering analysis by the Unweighted Pair Group Method Arithmetic Mean (UPGMA).…”