Microsatellite-based analysis of genetic diversity in 91 commercial Brassica oleracea L. cultivars belonging to six varietal groups

Izzah, Nur; Lee, Jonghoon; Perumal, Sampath; Park, Jee Young; Ahn, Kyounggu; Fu, Donghui; Kim, Goon-Bo; Nam, Young‐Woo; Yang, Tae-Jin

doi:10.1007/s10722-013-9966-3

Cited by 50 publications

(39 citation statements)

References 41 publications

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“…The same results were reported in various other studies where SSR markers were compared to other molecular markers (Jain et al, 2014). Therefore, SSRs have increasingly become the marker set of choice for genetic studies as they are abundant, highly polymorphic, codominant in nature, and genome-specific (Cuevas and Prom, 2013;Izzah et al, 2013). Being so important, SSR markers were previously used for assessing genetic diversity in pea (Taran et al, 2005;Nasiri et al, 2009), but anonymous SSRs are more costly and time-consuming to develop from genomic libraries (Ramu et al, 2013).…”

Section: Introductionsupporting

confidence: 77%

Molecular characterization of edible pea through EST-SSR markers

Nisar¹,

Khan²,

Wadood³

et al. 2017

Turk J Bot

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Section: Introductionsupporting

confidence: 77%

Molecular characterization of edible pea through EST-SSR markers

Nisar¹,

Khan²,

Wadood³

et al. 2017

Turk J Bot

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“…Penentuan kekerabatan genetik kultivar kopi Arabika berbuah kuning (AGK-1) dengan 11 kultivar kopi Arabika berbuah merah yang banyak dikembangkan di Garut dilakukan dengan menggunakan program NTSYS. Nilai koefisien kesamaan genetik 66% digunakan sebagai ambang untuk mengelompokkan semua kultivar yang dievaluasi, seperti yang dilakukan oleh Jain, Jain, & McCouch (2004) dan Izzah et al, (2013). Hasil dendrogram memperlihatkan semua kultivar kopi Arabika terbagi menjadi tiga kelompok utama (Gambar 3).…”

Section: Kekerabatan Genetikunclassified

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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“…In which, 20 out of 22 broccoli cultivars were clustered together in group I. This result indicates that the broccoli cultivars which originated from different seed companies demonstrated close relatedness, which may be because those seed companies shared their breeding materials or they used common elite lines with different names (Izzah et al 2013;Zhao et al 2014). In general, the clustering of 22 broccoli cultivars did not reflect their main phenotypic characters.…”

Section: Discussionmentioning

confidence: 91%

“…For instance, Wen et al (2010) had been successfully used 36 EST-SSR markers for classifying 45 Jatropha curcas accessions into six groups, which showed correlation with geographic origin. A recent study reported a set of EST-SSR and gSSR markers which clearly separated 91 commercial B. oleracea cultivars belonging to six subspecies including cabbage, broccoli, cauliflower, kohlrabi, kale and kailan into six different clusters with a tendency to cluster into its subspecies (Izzah et al 2013). Moreover, another research done by Zhao et al (2014) also exhibited the power of SSR markers in dividing 49 cauliflower genotypes into three major groups based on their curd types.…”

Section: Introductionmentioning

confidence: 98%

Development of Est-SSR Markers to Assess Genetic Diversity of Broccoli and Its Related Species

Izzah¹,

Reflinur²,

Yang³

2017

Indones. J. Agric. Sci.

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Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.[Keywords: Broccoli, cauliflower, kohlrabi, EST-SSR markers, genetic diversity] ABSTRAK

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Microsatellite-based analysis of genetic diversity in 91 commercial Brassica oleracea L. cultivars belonging to six varietal groups

Cited by 50 publications

References 41 publications

Molecular characterization of edible pea through EST-SSR markers

Molecular characterization of edible pea through EST-SSR markers

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

Development of Est-SSR Markers to Assess Genetic Diversity of Broccoli and Its Related Species

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