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

Maluf, Mirian Perez; Silvestrini, Milene; Ruggiero, Luciana Machado de Campos; Filho, Oliveiro Guerreiro; Colombo, Carlos Augusto

doi:10.1590/s0103-90162005000400010

Cited by 57 publications

(72 citation statements)

References 24 publications

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“…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.…”

Section: Analisis Dataunclassified

“…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).…”

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

Izzah

Randriani

Dani

2015

JTIDP

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ABSTRAKKopi Arabika berbuah kuning (AGK-1) merupakan kultivar lokal yang berpeluang untuk dilepas sebagai varietas unggul. Namun, asal-usul genetiknya (genetic background) belum jelas. Padahal, karakter itu merupakan salah satu syarat dalam pelepasan varietas. Penelitian bertujuan menganalisis kekerabatan genetik kultivar AGK-1 dengan 11 kultivar kopi Arabika berbuah merah berdasarkan marka simple sequence repeats (SSR). Penelitian dilaksanakan di Laboratorium Molekuler Balai Penelitian Tanaman Industri dan Penyegar (Balittri) Sukabumi, dan Laboratorium Biologi Molekuler Balai Besar Litbang Bioteknologi dan Sumber Daya Genetik Pertanian Bogor, mulai Maret sampai Juni 2015. Kedua belas kultivar kopi Arabika yang digunakan berasal dari Kabupaten Garut. Sebanyak 12 primer SSR digunakan untuk menelusuri kekerabatan genetik kultivar kopi Arabika. Kekerabatan genetik dianalisis menggunakan marka SSR untuk melihat polimorfisme dan clustering. Hasil penelitian menunjukkan kedua belas marka SSR yang digunakan mampu mengidentifikasi kekerabatan 12 kultivar kopi Arabika ke dalam tiga kelompok (pada nilai ambang 66%). Pengelompokan secara genetik berkaitan dengan morfologi tanaman, terutama karakter pertumbuhan, yaitu tinggi, semi katai, dan katai. Kultivar AGK-1 secara genetik berkerabat dekat dengan salah satu kultivar berbuah merah, yaitu ABP-2 yang berasal dari Brasil dan keduanya mempunyai tipe pertumbuhan semi katai. Kultivar AGK-1 berbuah kuning diduga merupakan hasil persarian bebas dari tetua berbuah merah, terutama kultivar ABP-2. Dengan demikian, kopi Arabika berbuah kuning AGK-1 merupakan kultivar yang unik dan berpeluang untuk dilepas sebagai varietas unggul lokal. Kata kunci: Coffea arabica, kekerabatan genetik, marka SSR ABSTRACT Yellow berry of Arabica coffee (AGK-1) cultivated in Garut is a local cultivar that potentially could be released as a superior variety. However, its genetic background has not been studied. Information of genetic background is one of the requirement in releasing of a new variety. The objective of this research was to analyze the genetic relationships of AGK-1 cultivar with 11 red berries Arabica coffee cultivars based on simple sequence repeats (SSR) markers to find polymorphisms and clustering. The research was carried out at the Molecular Laboratory of Indonesian Industrial and Beverage Crops Research Institute and Biology Molecular Laboratory of Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and PENDAHULUANKopi Arabika termasuk tanaman yang bernilai ekonomi tinggi dan dikembangkan di lebih dari 60 negara beriklim tropis maupun subtropis, dan jumlah produksinya bisa mencapai 70% dari total produksi kopi dunia (Teressa, Crouzillat, Petiard, & Brouhan, 2010). Di Indonesia, kopi merupakan salah satu komoditas perkebunan yang cukup diperhitungkan dan sebagai sumber devisa negara. Kopi Arabika (Coffea arabica L.)

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Section: Analisis Dataunclassified

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

Izzah

Randriani

Dani

2015

JTIDP

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“…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.…”

Section: Discussionmentioning

confidence: 66%

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

W¹

2012

Int. J. Biodvers. Conserv.

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Molecular markers have effectively been applied to study genetic diversity and as markers of particular traits. This study assessed the diversity of twenty four (24) coffee genotypes using 10 Random Amplified Polymorphic DNA (RAPD) primers and 2 microsatellites (M24 and Sat 235). A total of 35 polymorphic bands were generated by the RAPD primers. The bands were scored for presence (1) and absence (0) of amplified products. The data was subjected to cluster analysis using R statistical software and a dendrogram constructed using Unweighted Pair Group Method with Arithmetic Average (UPGMA). The genotypes separated into three main clusters. C. eugenioides clustered alone in the first cluster while un-introgressed Arabica genotypes dominated the second cluster. The third cluster comprised of Coffea canephora (Robusta) and introgressed genotypes, Ruiru 11, Hibrido de Timor and Catimor. Robusta and C. eugenioides were the most distantly related and generated most of the diversity observed. The similarities observed among un-introgressed Arabica genotypes attest to the narrow genetic diversity within Coffea arabica. The divergence observed among introgressed genotypes could be utilized in future breeding programmes.

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“…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.…”

Section: Ssr Polymorphismmentioning

confidence: 73%

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

Park

Hong

et al. 2017

J Plant Biotechnol

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Abstract The need to preserve and use plant genetic resources is widely recognized, and the prospect of dwindling plant genetic diversity, coupled with increased demands on these resources, has made them a topic of global discussion. In the present study, the genetic diversity and population structure of 73 ginseng accessions collected from six regions in China were analyzed using eight simple sequence repeat (SSR) markers. Major allele frequencies ranged between 0.380 .78, with a mean allele frequency value of 0.571. The number of alleles discovered ranged from 3 to 10 per accession, with a mean number of 7; 56 alleles were discovered in total. Gene diversity (GD) and polymorphic information content (PIC) values were similar to each other, and they ranged from 0.36 0.77 (mean 0.588) and 0.33~0.74 (mean 0.548), respectively. Accessions were divided into three clusters based on their phylogenetic relationships and genetic similarities, and although the populations were similar, they were not classified according to the region. Regional genetic diversity was also similar, with slight differences observed based on the number of accessions per region. It is expected that the findings of the present study can provide basic data for future studies on ginseng genetic diversity and for breeding ginseng cultivars.

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

Cited by 57 publications

References 24 publications

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

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

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

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

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