Analysis of genetic structure in a sample of coffee (Coffea arabica L.) using fluorescent SSR markers

Abstract

The knowledge of population structure is important to determine the degree of linkage disequilibrium, which allows the selection of genotypes for association mapping. Using 47 SSR markers, the genetic variability and population structure of 68 accessions of C. arabica (wild and cultivated) and of three diploid species used as reference were evaluated. The analysis was done with the distance method and the structure model. The structure analysis inferred nine subpopulations (k=9), for which the greatest values of probability were obtained. Three of the groups corresponded to the three diploid species as expected. There were six groups identified within C. arabica. The genetic subdivisions within C. arabica were based on geographical origin, degree of domestication, and dispersal history of coffee. One group consisted entirely of cultivated genotypes, where intense population bottleneck were associated with a founder effect. This was the most homogeneous group, as demonstrated by the reduced distance between cultivars in the dendrogram. Three of the cultivated genotypes, originating from Sudan, were separated into an independent group, presumably due to selective adaptation to a different set of environmental conditions. Another group consisted of genotypes of the type "ennarea" that were grown and cultivated in isolation on the shores of the Tana lake. The semi-wild genotypes clustered into three different groups. This type of analysis provides a strong evidence of population structure in C. arabica. Based on these findings, it is possible to better identify a balanced sample of diverse plants in germplasm.

Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

“…Most of the accessions derived from the same plant by seed propagation grouped together with a shared ancestral probability > 0.80. López-Gartner et al (2009) also proved the efficiency of the model based Bayesian clustering analysis for studying the genetic diversity and structure of arabic coffee originating from Ethiopia.…”

Genetic variation and risks of introgression in the wild Coffea arabica gene pool in south‐western Ethiopian montane rainforests

“…So far, coffee breeding in Ethiopia has been less intensive than other crops such as maize, which underwent a rigorous process of breeding and selection, yielding elite breeding pools with very little of the genetic diversity found in the maize wild relatives (Ortiz et al 2010). In general, genetic domestication bottlenecks seem to be more limited in perennial fruit crops than in annual crops (Miller and Gross 2011), although commercial coffee cultivars grown in central America or Asia show important losses of genetic diversity (Lashermes et al 1996;Ló pez-Gartner et al 2009). Our results show the striking presence of alleles from the CBD-resistant gene pool in all SFC populations, and to a much lesser extent in some FC populations.…”

Processos evolutivos e a origem das plantas cultivadas

“…Diversos exemplos de alopoliplóides são descritos na literatura, entre eles o caso do trigo (Triticum aestivum), formado por três genomas distintos (AABBDD), originário do cruzamento entre T. monococcum (AA), T. searssi (BB), sendo que o híbrido F1 teve o seu número de cromossomos duplicados, formando o T. turgidum (AABB) que se hibridizou com o T. tauschii (DD) (BRAMMER et al, 2001). Outras espécies de plantas cultivadas que sofreram o mesmo mecanismo é o algodão tetraplóide (Gossypium hirsutum e G. barbadense), formado a partir do cruzamento de uma espécie diplóide (genoma A) originária da Ásia com outra espécie diplóide (genoma D) originária do Novo Mundo (KIMBER, 1961); e também o café tetraplóide (Coffea arabica), originário do cruzamento entre as espécies Coffea eugenioides e C. canephora (LÓPEZ-GARTNER et al, 2009), entre outros (Tabela 1).…”

“…Várias são as culturas que demonstram perda de diversidade genética devido a sucessivos gargalos de garrafa, tais como café (Coffea arabica) (LÓPEZ-GARTNER et al, 2009), algodão (Gossypium hirsutum) (IQBAL et al, 2001), tomateiro (Solanum lycopersicum) (SAN-SAN-YI et al, 2008), grão-de-bico (Cicer arietinum) (ABBO et al, 2003), entre outras (Tabela 1). Tal processo também foi importante na domesticação de espécies arbóreas como a teca (Tectona grandis) (VARGHESE et al, 2006) e de plantas daninhas que coevoluiram com as plantas cultivadas, como é o caso de Lythrum salicaria, a qual foi introduzida nos EUA a partir da Europa (ECKERT et al, 1996).…”