Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems

Abstract

One of the greatest problems in Coffea arabica breeding is identifying precisely any inbred line, based only on botanical and agronomical descriptors, because of the reduced genetic variability of the species, close pedigree origin, which results in small phenotypic variation. Recently, molecular markers have been used for plant germplasm characterization and identification in several commercial species. This work evaluates the reliability of three marker systems: RAPD, AFLP and SSR, to characterize the genetic variability of commercially-used Coffea inbred lines developed by the Instituto Agronômico (IAC), and their potential for cultivar identification. All methods identified polymorphisms among the cultivars. The genetic diversity recognized by the methods is very similar, although is very narrow. RAPD and SSR marker systems grouped more efficiently the evaluated cultivars according to parental origin. None of the methods allowed inbred line identification. Therefore for varietal protection, it would be necessary using a combination of botanical, agronomical and molecular markers descriptors for precise cultivar identification. Key words: coffee, cultivar identification, molecular markers CARACTERIZAÇÃO DA DIVERSIDADE GENÉTICA DE LINHAGENS COMERCIAIS DE Coffea arabica ATRAVÉS DE MARCADORES MOLECULARES DO TIPO RAPD, AFLP E SSRRESUMO: A identificação de linhagens de Coffea arabica a partir de descritores botânicos e agronômicos é um problema para o desenvolvimento de cultivares. Basicamente, a limitada variação fenotípica observada em cultivares é o resultado de uma estreita variabilidade genética em C. arabica associada com uma origem genealógica próxima. Recentemente, os uso de marcadores moleculares tem contribuído para a caracterização e identificação de várias espécies de interesse comercial. O objetivo deste trabalho foi comparar a confiabilidade de três tipos de marcadores moleculares, RAPD, AFLP e SSR, para a caracterização da variabilidade genética e uma possível identificação de linhagens comerciais de Coffea desenvolvidas pelo IAC. Os métodos avaliados permitiram identificar polimorfismos entre cultivares. A variabilidade genética detectada por eles é muito semelhante, ainda que reduzida. Marcadores do tipo RAPD e SSR foram mais eficientes em análises de parentesco, e o agrupamento das linhagens correspondeu à sua origem genealógica. No entanto, nenhum dos métodos testados permitiu a identificação individual de linhagens. Neste caso, a utilização conjunta de descritores botânicos, agronômicos e marcadores moleculares é recomendada para a identificação precisa de linhagens, visando processos de proteção legal de cultivares de Coffea.

Analisis Kekerabatan Genetik Kultivar Kopi Arabika Berbuah Kuning dan Berbuah Merah Berdasarkan Marka SSR

“…Nilai rata-rata jumlah alel per lokus dan jumlah total alel yang diperoleh pada penelitian ini lebih tinggi dibandingkan dengan penelitian sebelumnya yang dilakukan oleh Teressa et al (2010), yaitu 6,5 alel per lokus dengan jumlah total 200 alel pada 133 aksesi kopi Arabika dengan menggunakan 32 marka SSR. Sementara, Maluf et al (2005) yang melakukan penelitian pada 28 kultivar kopi Arabika menggunakan 23 marka SSR mendapatkan jumlah total 65 alel dengan rata-rata 2,87 alel per lokus. Perbedaan nilai rata-rata jumlah alel per lokus dan jumlah total alel tersebut diduga dipengaruhi oleh perbedaan jumlah dan jenis kultivar, serta perbedaan jumlah marka SSR yang digunakan.…”

“…Oleh sebab itu, perlu dianalisis kekerabatan genetik kultivar AGK-1 dengan kultivar lain yang diduga sebagai tetuanya. Pendekatan yang dapat digunakan untuk menganalisis kekerabatan genetik kultivar kopi Arabika adalah melalui pemanfaatan teknologi marka molekuler, seperti marka random amplified polymorphic DNA (RAPD) dan simple sequence repeat (SSR) yang diketahui dapat mengelompokkan kultivar kopi Arabika sesuai dengan asal-usul genetiknya (Maluf et al, 2005).…”

Genetic diversity among commercial coffee varieties, advanced selections and museum collections in Kenya using molecular markers

“…Considering that the coffee genotypes evaluated in this study originated from diferent countries (Kenya, Puerto Rico, Tanzania, Ethiopia, Reunion, Portugal, Yemen, Guatemala and Colombia), the similarities observed among Arabica genotypes, attests to the narrow genetic diversity among cultivated Arabica coffee reported in other studies (Lashermes et al, 1993). Comparatively, higher genetic diversity has been reported among wild coffee populations than within cultivated genotypes Aga et al, 2003;Masumbuko et al, 2003;Masumbuko and Bryngelsson 2006;Maluf et al, 2005). Close genetic proximity was observed among the existing traditional commercial varieties in Kenya, namely SL28, SL34 and K7.…”

Genetic diversity and population structure of Chinese ginseng accessions using SSR markers

“…Whether this difference was due to the number of tested samples or the actual genetic diversity of the cultivars needs to be examined with a larger number of cultivars. However, Maluf et al (2005) reported that SSR markers are more effective in detecting genetic diversity than other markers, indicating that the findings in the present study may be used effectively in the future for analyzing the diversity of ginseng genetic resources.…”