Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross‐species amplifications

Abstract

Genetic improvement of coffee ( Coffea arabica L.) is constrained by low genetic diversity and lack of genetic markers, suitable screening tools, information on the genetic makeup of available gene pool and long generation time. In this context, use of DNA markers such as microsatellites that provide high genetic-resolution becomes highly desirable. Here, we report the development of nine new microsatellite markers from partial genomic library of an elite variety of Coffea arabica . The developed microsatellites revealed robust cross-species amplifications in 17 related species of coffee, and their Polymorphic Information Content varied from 0 to 0.6, 0 to 0.78 and 0.67 to 0.90 for the arabica, robusta genotypes and species representatives, respectively. The data thus suggest their potential use as genetic markers for assessment of germplasm diversity and linkage analysis of coffee.

Polymorphic information content of SSR markers for Coffea spp.

“…The highest mean PIC values were found for C. canephora (0.46), while the lowest values were in C. arabica (0.22) and triploid (0.22) accessions. The low polymorphism found for C. arabica is in agreement with Baruah et al (2003) work, and may be explained by the autogamous nature and the narrow genetic base of this species. All SSR primers were able to detect genetic differences between C. arabica and C. canephora populations, as well as among C. canephora and the remaining populations.…”

“…Notwithstanding all the advantages of SSR molecular markers for genetic studies, few SSR primers have been developed for coffee (Combes et al 2000, Baruah et al 2003, Moncada and McCouch 2004, Bhat et al 2005, Poncet et al 2006, Aggarwal et al 2007, Hendre et al 2008, Missio et al 2009b), compared to other crops (http:// www.gramene.org/). In this study, the potential of 33 SSR markers, developed from C. arabica were used for assessed the Polymorphism Information Content (PIC) in 24 accessions of the Coffea genus, including C. arabica.…”

Genetics of coffee quality

“…Development of neutral markers: Although not directly and exclusively linked to the comprehension of the molecular determinism of coffee quality, the efforts provided by the coffee research community towards the development of co-dominant and multiallelic molecular markers spread all over the coffee genome (Combes et al, 2000;Dufour et al, 2001;Baruah et al, 2003;Moncada and Mc Couch, 2004;Poncet et al, 2004;Bhat et al, 2005) will undoubtedly benefit this field of research. Indeed, the availability of these markers will allow the analysis of population structure and the development of genetic maps, two pre-requisites towards the identification of the genes responsible for the natural variation of coffee quality.…”

Microsatellite markers in analysis of resistance to coffee leaf miner in Arabica coffee

“…The search for polymorphic SSR loci associated with a desirable trait is complex due to the limited number of coffee SSRs available. In species with a narrow genetic base, such as C. arabica, the probability of finding polymorphism is low (Baruah et al, 2003;Vieira et al, 2006). Genetic diversity among coffee species identified by EST-SSR markers can be used as a gene source in breeding programs, with potential for other studies of genetic mapping, in the identification of cultivars or in pre-breeding by the genotyping of germplasm bank accessions.…”