Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties

Risliawati, Andari; Riyanti, Eny Ida; Lestari, Puji; Utami, Dwinita Wikan; Silitonga, Tiur S.

doi:10.21082/jbio.v11n2.2015.p49-58

Cited by 11 publications

(19 citation statements)

References 19 publications

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“…The two digital codes were started from "01" for each SSR motif observed on each primer. This digital code transformation would be done for total SSR in the formulated marker set and the digital codes represented the ID of each mungbean variety (Risliawati et al 2015).…”

Section: Discussionmentioning

confidence: 99%

The Potential Use of SSR Markers to Support the Morphological Identification of Indonesian Mungbean Varieties

Reflinur¹,

Lestari²,

Lee³

2017

Indones. J. Agric. Sci.

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Mungbean varieties were mainly characterized based on morphological traits. Molecular genetic approach is expected to help the breeder in identification of mungbean varieties in more detail and to protect intellectual property right. This study aimed to identify Indonesian mungbean varieties based on DNA fingerprint profile using a marker set to support morphological characters. A total of 22 Indonesian mungbean accessions were characterized based on 21 morphological traits and 55 simple sequence repeats (SSRs) primers. Of the total 22 mungbean varieties used in the present study, 16 varieties were improved varieties and remaining six varieties were local varieties originated from Java, Nusa Tenggara and Sulawesi collected in GeneBank of ICABIOGRAD. The results showed that the 21 morphological characters were not sufficient to differentiate 22 mungbean varieties, while SSR analysis revealed that eight multi-alleles markers and high polymorphic information content (PIC) values have been successfully selected for varietal identification. The selected markers enabled to differentiate each mungbean variety according to their genetic marker with the lowest distance of 0.125, demonstrating the robustness of the selected marker set as a tool to identify a specific DNA fingerprint profile as a varietal identity (ID). The genetic identity of a variety was shown by digital barcoding which represented a series of alleles produced by corresponding markers. The DNA fingerprint profile of each variety would be beneficial as reference identities of a mungbean variety.

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Section: Discussionmentioning

confidence: 99%

The Potential Use of SSR Markers to Support the Morphological Identification of Indonesian Mungbean Varieties

Reflinur¹,

Lestari²,

Lee³

2017

Indones. J. Agric. Sci.

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“…Seleksi varietas padi berdasarkan karakter morfologi juga kurang terpercaya mengingat karakter utama yang diinginkan biasanya penurunan sifatnya rendah secara genetik (Joshi et al, 2000). Sementara itu karakterisasi secara molekuler melalui penggunaan marka molekuler memberikan hasil yang lebih presisi karena tidak dipengaruhi lingkungan (Ram, 2007;Risliawati et al, 2015). Pemanfaatan marka molekuler merupakan pendekatan efisien untuk analisis keragaman genetik dan dapat dimanfaatkan secara luas diberbagai studi biologi.…”

Section: P E N D a H U L U A Nunclassified

KERAGAMAN GENETIK 24 VARIETAS PADI SAWAH DAN PADI GOGO (Oryza sativa L.) INDONESIA BERDASARKAN MARKA SSR

2017

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A B S T R A C TThe use of molecular marker is an efficient approach to analyze the genetic diversity and it can be used widely in biological studies. The characterization of rice germplasms by using molecular markers technique is more precise because it is not influenced by environmental factors. The purpose of this study was to analyze the genetic diversity of 24 varieties of lowland and upland rice by using 15 SSR markers. The results showed as many as 86 alleles were detected in 24 rice varieties, with the average number of alleles per marker was 5.73 and the range of alleles per locus was 2-10. The average of major allele frequency was 43% with the lowest score was 26% on RM6997 and RM536 markers and the highest score was 65% on RM60 marker. A total of 14 SSR markers were able to discriminate heterozygous alleles within a range between 0.17 (RM105) to 1.00 (RM201, RM263, RM416, RM518 and RM223). The value of gene diversity ranged from 0.48 (RM60) to 0.81 (RM536) with an average of 0.70. The value of PIC (Polymorphic Information Content) ranged from 0.38 (RM105) to 0.78 (RM536) with an average of 0.65. The phylogenetic analysis showed that 24 rice varieties separate into two main clusters in the coefficient of 0.63. The first cluster consists of 12 lowland varieties and the second cluster consists of 12 upland varieties. The genetic diversity data in this study were expected could be a valuable information in the rice plant breeding activities in the future.

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“…Di Indonesia, marka molekuler juga telah dimanfaatkan untuk karakterisasi kedelai (Arisetyaningsih et al, 2010;Wirnas et al, 2011;Wiradjaja, 2012). Di Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian (BB Biogen), marka mikrosatelit telah dimanfaatkan sejak (Septiningsih et al, 2004Santoso et al, 2006;Chaerani et al, 2011;dan Risliawati et al, 2015).…”

Section: Pendahuluanunclassified

“…Pada penelitian ini diperoleh 6-23 alel/lokus, sedangkan Risliawati et al (2015) memperoleh 4-25 alel/ lokus. Banyaknya jumlah alel pada penelitian ini diduga karena beragamnya kultivar yang digunakan.…”

Section: Polimorfisme Alel Mikrosatelitunclassified

“…Hildebrand et al (1992) membuat kriteria marka dengan PIC>0,7 sangat informatif dan sebaliknya. Marka yang informatif memiliki nilai PIC>0,75 (Chaerani et al, 2011) namun marka informatif sebaiknya dengan PIC>0,80 (Risliawati et al, 2015). Mengacu pada kriteria Botstein et al (1980), seluruh marka yang digunakan dalam penelitian ini dengan PIC>0,5 bersifat informatif dan mampu membedakan kultivar kedelai.…”

Section: Polimorfisme Alel Mikrosatelitunclassified

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Analisis Keragaman Genetik Kedelai Introduksi Menggunakan Marka Mikrosatelit

Nugroho

Terryana²,

Reflinur³

et al. 2017

Informatika Pertanian

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ABSTRAKKedelai merupakan komoditas pangan penting selain padi dan jagung. Perakitan dan pengembangan varietas unggul berperan penting dalam meningkatkan produksi. Salah satu sumber daya genetik kedelai yang dapat digunakan dalam perakitan varietas unggul adalah varietas introduksi. Tujuan penelitian ini adalah untuk menganalisis keragaman genetik 35 kultivar kedelai introduksi yang berasal dari berbagai negara menggunakan 15 marka mikrosatelit. Penelitian dilakukan di laboratorium Biologi Molekuler BB Biogen, Januari-Maret 2016. Hasil analisis polymerase chain reaction (PCR) diberi skor data biner dan dianalisis menggunakan NTSYS dan power marker. Karakter morfologi spesifik setiap kultivar menetukan keragaman genetik. Korelasi positif signifikan diidentifikasi pada beberapa karakter morfologi yang bermanfaat dalam program pemuliaan dengan kombinasi karakter target. Sebanyak 189 alel berhasil dideteksi dengan kisaran 6-23 alel/lokus, rata-rata 12,6 alel/marka. Nilai PIC menunjukkan tingkat polimorfisme berkisar antara 0,76 (GmES1424) hingga 0,95 (Satt100) dengan rata-rata 0,86. Sebanyak 12 marka yang memiliki nilai PIC >0,80 menunjukkan kemampuan dalam mendiskriminasi kultivar kedelai. Frekuensi alel utama rata-rata 21% dengan nilai tertinggi 39% (Satt125) dan terendah 8% (Satt100). Lima marka SSR mampu mendiskriminasi genotipe heterozigot dengan nilai heterozigositas antara 0,41 (SoyF3H) hingga 0,82 (Satt333). Hasil analisis filogenetik menunjukkan 35 kultivar kedelai introduksi memisah menjadi dua klaster utama, masing-masing 13 dan 22 kultivar pada koefisien 0,82 berdasarkan latar belakang genetik. Marka mikrosatelit dan informasi keragaman genetik pada penelitian ini bermanfaat mengarahkan persilangan kedelai dengan memanfaatkan material genetik introduksi.Kata kunci: kedelai, kultivar introduksi, keragaman genetik, marka mikrosatelit ABSTRACT Soybean (Glycine max (L.) Meriil) is an important crop next to rice and corn. The development of improved variety are important to increase national soybean production. The introduced soybean varieties is one of genetic resources that can be used to create improved soybean varieties. The aim of this study was to analyze 35 introduced soybean cultivars using 15 microsatellite markers. The research was conducted in ICABIOGRAD Molecular Biology Laboratory, in January-March 2016. PCR analysis was scored as binary data and the collected data was analyzed using NTSYS and PowerMarker. Specific morphological characters from each soybean cultivar determine the genetic diversity. Significant positive correlations were identified among morphological characters which would be helpful to improve the desired character. The result showed that 189 alleles were detected with average of 12.6 alleles per marker. The polymorphism level (PIC) was 0.86 (0.76-0.95). There were 12 of total markers having PIC>0.80 indicating their robustness to discriminating soybean cultivars. The average major allele frequency was 21% and ranges from 8% (Satt100) to 39% (Satt125). Five SSRs were able to dist...

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Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties

Cited by 11 publications

References 19 publications

The Potential Use of SSR Markers to Support the Morphological Identification of Indonesian Mungbean Varieties

The Potential Use of SSR Markers to Support the Morphological Identification of Indonesian Mungbean Varieties

KERAGAMAN GENETIK 24 VARIETAS PADI SAWAH DAN PADI GOGO (Oryza sativa L.) INDONESIA BERDASARKAN MARKA SSR

Analisis Keragaman Genetik Kedelai Introduksi Menggunakan Marka Mikrosatelit

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