Assessment of EST-SSR markers for genetic analisys on coffee

Abstract

EST-SSR markers were used to investigate the genetic diversity among and within coffee populations, to explore the possibility of their use for fingerprinting of cultivars and to assist breeding programs. Seventeen markers, developed from ESTs (Expressed Sequence Tags) from the Brazilian Coffee Genome Project, were used. All markers showed polymorphism among the genotypes assessed. The average number of allele per primer was 5.1. The highest polymorphisms were found within C. canephora (88.2%) and rust-resistant varieties (35.3%). About 29.4% of the markers differentiated C. arabica from Híbrido de Timor; it was also possible to identify those closest and farthest from C. arabica . The analysis of population-grouped genotypes revealed a 64.0% genetic diversity among and a 36.0% genetic diversity within populations. The differentiation index was 0.637. Six markers distinguished four rust-resistance varieties, showing their fingerprinting potential. These results demonstrate the usefulness of EST-SSR markers for cross orientation, in diversity and introgression studies, and in genetic mapping.

Polymorphic information content of SSR markers for Coffea spp.

“…These primers may be useful for genetic fingerprinting and certification of clonal commercial varieties derived from C. canephora (Missio et al 2009a). The SSRCa 068 and 018 primer differentiated the IAPAR 59 cultivar among the others leaf rust resistant cultivar of arabica (Catiguá MG2, Oeiras MG6851, Sacramento MG1, Catucai Amarelo 2SL and Obatã Amarelo IAC 4932) indicating the potential of this SSR markers in variety identification studies and in genetic fingerprinting (Figure 1).…”

“…Previous studies using different molecular markers showed low levels of polymorphism among C. arabica accessions (Poncet et al 2006, Aggarwal et al 2007, Missio et al 2009a, hindering further genetic research in this species. Simple Sequence Repeats (SSRs) or microsatellite markers are potentially useful in this situation, especially for exploring highly variable regions of the genome among individuals or populations of the same species.…”

Genetic characterization of an elite coffee germplasm assessed by gSSR and EST-SSR markers

“…The first, containing 17 primer pairs, was obtained from C. arabica ESTs of the Brazilian Coffee Genome Project (Missio et al, 2009b). The second, containing 18 primer pairs, was obtained from an enriched genomic library of the C. arabica genotype Bourbon Amarelo UFV 570 (Missio et al, 2009a).…”

“…The level of polymorphism was 88.2% within C. canephora accessions and 11.8% within C. arabica accessions. The known narrow genetic base and autogamy were probably responsible for the low level of polymorphism in C. arabica (Missio et al, 2009b). It was previously reported that because EST-SSR markers are originated from highly conserved genomic regions, they may show a lower level of polymorphism compared to gSSR markers, which have a wider distribution in the genome (Varshney et al, 2005).…”

Molecular characterization of edible pea through EST-SSR markers

“…EST-SSRs have several fundamental advantages over traditional genomic SSR markers, such as being embedded in functional gene sequences, in direct association with transcribed genes, less costly, and highly transferable between related species (Varshney et al, 2005). EST-SSR markers have been used in several studies, such as evaluation of genetic diversity in grapevine, coffee, and sugar cane and in genetic map integration in soybean and genetic mapping of wheat, potato, and cotton (Missio et al, 2009). In pea, EST-SSR markers have been used to determine genetic diversity (Burstin et al, 2001).…”