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All Journal Indonesian Journal of Mathematics and Natural Sciences
A. Retnoningsih
Jurusan Biologi, Fakultas MIPA, Universitas Negeri Semarang, Indonesia
Mathematics

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ANALISIS KEANEKARAGAMAN KULTIVAR PISANG MENGGUNAKAN PENANDA PCR-RFLP PADA INTERNAL TRANSCRIBED SPACER (ITS) DNA RIBOSOM Ekasari, T.W.D.; Retnoningsih, A.; Widianti, T.
Jurnal MIPA Vol 35, No 1 (2012): April 2012
Publisher : Jurnal MIPA

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Abstract

Pisang merupakan bahan makanan pokok keempat terpenting di negara berkembang yang memiliki keanekaragaman sangat tinggi. Penanda DNA mikrosatelit dapat membedakan kultivar pisang yang memiliki genom A dengan kultivar pisang bergenom B. Namun penanda mikrosatelit memiliki beberapa keterbatasan, yaitu membutuhkan primer spesifik dan membutuhkan preparasi yang lebih rumit, sehingga membutuhkan waktu dan biaya yang cukup mahal. Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) terhadap DNA internal transcribed spacer (ITS) ribosom mampu mengklasifikasikan kultivar-kultivar pisang berdasarkan pita restriksi daerah ITS yang dipotong dengan enzim RsaI. Koleksi DNA dari 15 kultivar pisang di Laboratorium Genetika dan Molekular Jurusan Biologi UNNES sudah diklasifikasikan genomnya berdasarkan mikrosatelit. DNA kultivar pisang diamplifikasi menggunakan primer ITS L dan ITS 4 menghasilkan fragmen ITS sebesar 700 pb. Pemotongan fragmen ITS DNA ribosom dengan enzim RsaI menghasilkan fragmen  530 pb yang spesifik untuk genom A, fragmen 350 pb dan 180 pb spesifik untuk genom B. Hasil perbandingan klasifikasi genomik berdasarkan mikrosatelit dan PCR-RFLP dari daerah ITS DNA ribosom menunjukkan bahwa klasifikasi genomnya serupa. Banana is the fourth most important staple foods in developing countries which has very high diversity. Microsatellite markers can be able to differentiate bananas cultivars which have A and B genomes, but this marker has restrictions. It requires a specific primer which is takes time and the costs expensive enough. Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) of the ribosomal DNA internal transcribed spacer (ITS) was able to classify banana cultivars based on the restriction band ITS regions cut by RsaI enzyme. The DNA collection from 15 banana cultivars from the Laboratory of Genetics and Molecular Biology Department of Biological Science UNNES have been classified its genome based on microsatellite. Banana cultivar amplified using the primers ITS L and ITS 4 produce ITS fragment at 700 bp. The cutting of ribosomal DNA ITS fragments by RsaI enzyme produce 530 bp fragment that was unique for the A genome, the other fragment 350 bp and 180 bp genome are unique for the B genome. Comparison result of genomic classification based on microsatellite and PCR-RFLP of ribosomal DNA ITS regions showed that the genome classification was similar.
KERAGAMAN DURIAN BERDASARKAN FRAGMEN INTERNAL TRANSCRIBED SPACERS (ITS) DNA RIBOSOMAL MELALUI ANALISIS PCR-RFLP Hikmah, R. U.; Retnoningsih, A.; Habibah, N. A.
Jurnal MIPA Vol 39, No 1 (2016): April 2016
Publisher : Jurnal MIPA

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Durian adalah salah satu jenis buah-buahan tropis yang memiliki nilai ekonomi tinggi. Durian memiliki bermacam-macam kultivar dengan morfologi yang sulit untuk membedakan. jaminan identitas penting bagi informasi mendasar dalam meningkatkan efisiensi pemuliaan dan pengembangan durian. identifikasi molekuler dianggap lebih akurat dibandingkan dengan karakter morfologi. Polymerase Chain Reaction Restriction Fragment Length Polimorfism (PCR-RFLP) adalah metode untuk menganalisis hasil DNA fragmen panjang perbedaan yang mencerna menggunakan enzim restriksi dengan endonuklease. Sampel yang digunakan dalam penelitian ini adalah aksesi durian diambil secara acak di kecamatan Gunungpati, Semarang. Genomik DNA diisolasi berdasarkan protokol Kit nukleon Phytopure dengan modifikasi. ITS wilayah ribosom DNA diamplifikasi menggunakan teknik PCR-RFLP mengeksploitasi primer spesifik L ITS dan ITS 4 menghasilkan ITS panjang fragmen pada 800 bp. Amplikon yang dicerna menggunakan enam enzim restriksi AluI, Eco471, Bsp1431, BsuRI, Mph11301 dan Ade1. Hasil penelitian dari 11 aksesi durian yang diperiksa menunjukkan bahwa enzim Bsp1431 memiliki dua situs tertentu yang dipotong pada ukuran 550 bp dan 120 bp. enzim BsuR1 memiliki luka situs tertentu dalam ukuran 600 bp. Sedangkan enzim Eco471 telah mencerna situs spesifik pada ukuran 450 bp. Kesimpulan dari penelitian ini adalah durian nomor aksesi ke-12, 15, dan 17 memiliki hubungan genetik dekat dan diduga berada di salah satu spesies.Durian is one of the types of tropical fruits that has high economic value. Durian has an assortment of cultivars with morphology that are difficult to distinguish. Identity assurance is important for the fundamental information in increasing the efficiency of breeding and development of durian. Molecular identification is considered to be more accurate than the morphological characters. Polymerase Chain Reaction Restriction Fragment Length Polimorfism (PCR-RFLP) is a method to analyze the results of DNA fragment length difference that digest using restriction enzyme with endonuclease. The sample used in this study was the accession of durian taken randomly in Gunungpati district, Semarang. Genomic DNA was isolated based on Nucleon Phytopure Kit protocol with modification. ITS DNA ribosomal region was amplified using PCR-RFLP technique exploiting specific primers ITS L and ITS 4 produce ITS fragment length at 800 bp. Amplicon was digested using six restriction enzyme AluI, Eco471, Bsp1431, BsuRI, Mph11301 and Ade1. The research result of 11 accessions durian which is examined shows that the Bsp1431 enzyme has two specific sites that is cut on the size 550 bp and 120 bp. BsuR1 enzymes have a specific site cuts in the size of 600 bp. Whereas Eco471 enzyme has digesting sites specifics on size 450 bp. The conclusion of this research is durian accession number 12th, 15th, and 17th have close genetic relation and are alleged to be in one species.
KERAGAMAN DURIAN BERDASARKAN FRAGMEN INTERNAL TRANSCRIBED SPACERS (ITS) DNA RIBOSOMAL MELALUI ANALISIS PCR-RFLP Hikmah, R. U.; Retnoningsih, A.; Habibah, N. A.
Indonesian Journal of Mathematics and Natural Sciences Vol 39, No 1 (2016): April 2016
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Durian adalah salah satu jenis buah-buahan tropis yang memiliki nilai ekonomi tinggi. Durian memiliki bermacam-macam kultivar dengan morfologi yang sulit untuk membedakan. jaminan identitas penting bagi informasi mendasar dalam meningkatkan efisiensi pemuliaan dan pengembangan durian. identifikasi molekuler dianggap lebih akurat dibandingkan dengan karakter morfologi. Polymerase Chain Reaction Restriction Fragment Length Polimorfism (PCR-RFLP) adalah metode untuk menganalisis hasil DNA fragmen panjang perbedaan yang mencerna menggunakan enzim restriksi dengan endonuklease. Sampel yang digunakan dalam penelitian ini adalah aksesi durian diambil secara acak di kecamatan Gunungpati, Semarang. Genomik DNA diisolasi berdasarkan protokol Kit nukleon Phytopure dengan modifikasi. ITS wilayah ribosom DNA diamplifikasi menggunakan teknik PCR-RFLP mengeksploitasi primer spesifik L ITS dan ITS 4 menghasilkan ITS panjang fragmen pada 800 bp. Amplikon yang dicerna menggunakan enam enzim restriksi AluI, Eco471, Bsp1431, BsuRI, Mph11301 dan Ade1. Hasil penelitian dari 11 aksesi durian yang diperiksa menunjukkan bahwa enzim Bsp1431 memiliki dua situs tertentu yang dipotong pada ukuran 550 bp dan 120 bp. enzim BsuR1 memiliki luka situs tertentu dalam ukuran 600 bp. Sedangkan enzim Eco471 telah mencerna situs spesifik pada ukuran 450 bp. Kesimpulan dari penelitian ini adalah durian nomor aksesi ke-12, 15, dan 17 memiliki hubungan genetik dekat dan diduga berada di salah satu spesies.Durian is one of the types of tropical fruits that has high economic value. Durian has an assortment of cultivars with morphology that are difficult to distinguish. Identity assurance is important for the fundamental information in increasing the efficiency of breeding and development of durian. Molecular identification is considered to be more accurate than the morphological characters. Polymerase Chain Reaction Restriction Fragment Length Polimorfism (PCR-RFLP) is a method to analyze the results of DNA fragment length difference that digest using restriction enzyme with endonuclease. The sample used in this study was the accession of durian taken randomly in Gunungpati district, Semarang. Genomic DNA was isolated based on Nucleon Phytopure Kit protocol with modification. ITS DNA ribosomal region was amplified using PCR-RFLP technique exploiting specific primers ITS L and ITS 4 produce ITS fragment length at 800 bp. Amplicon was digested using six restriction enzyme AluI, Eco471, Bsp1431, BsuRI, Mph11301 and Ade1. The research result of 11 accessions durian which is examined shows that the Bsp1431 enzyme has two specific sites that is cut on the size 550 bp and 120 bp. BsuR1 enzymes have a specific site cuts in the size of 600 bp. Whereas Eco471 enzyme has digesting sites specifics on size 450 bp. The conclusion of this research is durian accession number 12th, 15th, and 17th have close genetic relation and are alleged to be in one species.
ANALISIS KEANEKARAGAMAN KULTIVAR PISANG MENGGUNAKAN PENANDA PCR-RFLP PADA INTERNAL TRANSCRIBED SPACER (ITS) DNA RIBOSOM Ekasari, T.W.D.; Retnoningsih, A.; Widianti, T.
Indonesian Journal of Mathematics and Natural Sciences Vol 35, No 1 (2012): April 2012
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Pisang merupakan bahan makanan pokok keempat terpenting di negara berkembang yang memiliki keanekaragaman sangat tinggi. Penanda DNA mikrosatelit dapat membedakan kultivar pisang yang memiliki genom A dengan kultivar pisang bergenom B. Namun penanda mikrosatelit memiliki beberapa keterbatasan, yaitu membutuhkan primer spesifik dan membutuhkan preparasi yang lebih rumit, sehingga membutuhkan waktu dan biaya yang cukup mahal. Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) terhadap DNA internal transcribed spacer (ITS) ribosom mampu mengklasifikasikan kultivar-kultivar pisang berdasarkan pita restriksi daerah ITS yang dipotong dengan enzim RsaI. Koleksi DNA dari 15 kultivar pisang di Laboratorium Genetika dan Molekular Jurusan Biologi UNNES sudah diklasifikasikan genomnya berdasarkan mikrosatelit. DNA kultivar pisang diamplifikasi menggunakan primer ITS L dan ITS 4 menghasilkan fragmen ITS sebesar 700 pb. Pemotongan fragmen ITS DNA ribosom dengan enzim RsaI menghasilkan fragmen  530 pb yang spesifik untuk genom A, fragmen 350 pb dan 180 pb spesifik untuk genom B. Hasil perbandingan klasifikasi genomik berdasarkan mikrosatelit dan PCR-RFLP dari daerah ITS DNA ribosom menunjukkan bahwa klasifikasi genomnya serupa. Banana is the fourth most important staple foods in developing countries which has very high diversity. Microsatellite markers can be able to differentiate bananas cultivars which have A and B genomes, but this marker has restrictions. It requires a specific primer which is takes time and the costs expensive enough. Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) of the ribosomal DNA internal transcribed spacer (ITS) was able to classify banana cultivars based on the restriction band ITS regions cut by RsaI enzyme. The DNA collection from 15 banana cultivars from the Laboratory of Genetics and Molecular Biology Department of Biological Science UNNES have been classified its genome based on microsatellite. Banana cultivar amplified using the primers ITS L and ITS 4 produce ITS fragment at 700 bp. The cutting of ribosomal DNA ITS fragments by RsaI enzyme produce 530 bp fragment that was unique for the A genome, the other fragment 350 bp and 180 bp genome are unique for the B genome. Comparison result of genomic classification based on microsatellite and PCR-RFLP of ribosomal DNA ITS regions showed that the genome classification was similar.
Co-Authors N. A. Habibah, N. A. R. U. Hikmah, R. U. T. Widianti T.W.D. Ekasari