Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers

Abstract

Information about population structure and genetic relationships within and among wild and brazilian Coffea arabica L. genotypes is highly relevant to optimize the use of genetic resources for breeding purposes. In this study, we evaluated genetic diversity, clustering analysis based on Jaccard's coefficient and population structure in 33 genotypes of C. arabica and of three diploid Coffea species (C. canephora, C. eugenioides and C. racemosa) using 30 SSR markers. A total of 206 alleles were identified, with a mean of 6.9 over all loci. The set of SSR markers was able to discriminate all genotypes and revealed that Ethiopian accessions presented higher genetic diversity than commercial varieties. Population structure analysis indicated two genetic groups, one corresponding to Ethiopian accessions and another corresponding predominantly to commercial cultivars. Thirty-four private alleles were detected in the group of accessions collected from West side of Great Rift Valley. We observed a lower average genetic distance of the C. arabica genotypes in relation to C. eugenioides than C. canephora. Interestingly, commercial cultivars were genetically closer to C. eugenioides than C. canephora and C. racemosa. The great allelic richness observed in Ethiopian Arabica coffee, especially in Western group showed that these accessions can be potential source of new alleles to be explored by coffee breeding programs.

Coffee (Coffea arabica L.): Methods, Objectives, and Future Strategies of Breeding in Ethiopia—Review

“…On the other hand, several DNA-based techniques were used in different studies about coffee genetics. These include RAPD, AFLP, ISSR, and microsatellite (SSR) markers [68,69,[83][84][85][86][87][88][89]. Among the several types of molecular markers, microsatellites (SSR) are most commonly used in genetic diversity studies because they offer several advantages, including the high degree of polymorphism, repeatability, reproducibility, codominance, technical simplicity, speed, and multiallelism [90].…”

Validating South Sudan as a Center of Origin for Coffea arabica: Implications for Conservation and Coffee Crop Improvement

“…Former studies (Anthony et al, 2002;da Silva et al, 2019;Benti et al, 2020) had proven the efficiency of SSR markers to study the genetic diversity of Arabica. In our study, we confirm that the reduced set of SSR markers established by Pruvot-Woehl et al (2020) are efficient to describe a new genetic group in Yemen (Montagnon et al, 2021) is again efficient to describe a new genetic group in this species: the South Sudan group.…”

Combining Ability and Molecular Marker Approach Identified Genetic Resources to Improve Agronomic Performance in Coffea arabica Breeding

“…In this study, the DNA of 22 coffee cultivars and accession, with the potential to be used in breeding, showed low diversity (mean: 2.3 bands/primer). The narrow genetic base of C. arabica has been reported worldwide, which is explained by the recent origin of the species with a single polyploidization event, autogamous reproduction system, and poor initial global distribution (Missio et al, 2011;Sousa et al, 2017a;da Silva et al, 2019;Jingade et al, 2019;Merot-L'anthoene et al, 2019;Sánchez et al, 2020;Scalabrin et al, 2020). Moreover, its genetic resources have been conserved in the field and, therefore, may be quickly eroded due to local hazards and global climatic change, worsening the genetic variability reduction (Legesse, 2020).…”