HABIB RIJZAANI
Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

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Konstruksi Pustaka Genom Kakao (Theobroma cacao L.) untuk Sekuensing Genom Total Menggunakan Next Generation Sequencing HiSeq2000 Tasma, I Made; Satyawan, Dani; Rijzaani, Habib; Rubiyo, Rubiyo
Jurnal Tanaman Industri dan Penyegar Vol 3, No 2 (2012): Buletin Riset Tanaman Rempah Dan Aneka Tanaman Industri
Publisher : Pusat Penelitian dan Pengembangan Perkebunan

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

Abstract

Pemuliaan kakao secara konvensional memerlukan waktu panjang (10-15 tahun). Pemanfaatan marka DNA akan memperpendek siklus pemuliaan kakao. Tujuan penelitian ini adalah mengkonstruksi pustaka genom tiga genotipe kakao yang dapat digunakan untuk sekuensing genom total kakao menggunakan NGS HiSeq2000 dan mendapatkan data resekuen genom total tiga genotipe kakao.  Bahan tanaman terdiri dari tiga klon unggul kakao (ICCR02, ICCR04, dan SUL02) diperoleh dari Balittri, Pakuwon.  DNA genomik diisolasi dari daun muda sebagai bahan konstruksi pustaka genom total. Sekuensing pustaka dilakukan pada mesin HiSeq2000 mengikuti protokol dari Illumina. Pustaka genom yang telah berhasil dikonstruksi berukuran 300 pasang basa (bp) masing-masing dengan konsentrasi 14,70 ng/µL (ICCR02), 15,20 ng/µL (ICCR04), dan 12,90 ng/µL (SUL02). Ukuran dan konsentrasi pustaka genom yang dihasilkan sangat ideal untuk sekuensing menggunakan HiSeq2000. Sekuensing ketiga genom menghasilkan data sekuen 52,9 x 109 bp.  Klaster DNA pustaka genom memiliki nilai Q scores>30 (75,0%) dengan tingkat kesalahan pembacaan basa rendah (1,47%).  Nilai densitas klaster, persen klaster PF, intensitas basa, persen phasing, dan persen prephasing menunjukkan kualitas klaster pustaka genom ketiga genotipe kakao termasuk kategori pustaka ideal. Data sekuen yang dihasilkan juga sangat ideal untuk identifikasi marka SNP genom kakao. Koleksi marka SNP digunakan untuk identifikasi gen pengendali karakter penting kakao dan pemuliaan berbasis marka DNA untuk memperpendek siklus pemuliaan kakao. Genomic Library Construction Of Cocoa (Theobroma Cacao L.) For Whole Genome Sequensing Using A Next Generation Sequencer Hiseq2000Conventional cocoa breeding is slow and takes about 10-15 years to complete a breeding cycle. Applying genomic technology using DNA markers will significantly decrease cocoa breeding cycle. The objectives of this study were to construct cocoa whole genome genomic libraries to be used for resequencing the whole genome of cocoa and obtain whole genome resequence data of three cocoa genotypes. Three Indonesian cocoa genotypes (ICCR02, ICRR04, and SUL02) were used. DNA genomic was isolated from young leaf and used to construct genomic DNA libraries and generate DNA clusters. DNA clusters were sequenced using a HiSeq2000 platform. The whole genome libraries of the cocoa genotypes were successfully constructed. The library size was 300 bp with concentrations of 14.70 ng/µL (ICCR02), 15.20 ng/µL (ICCR04), and 12.90 ng/µL (SUL02), respectively. The genomic library size and concentrations are suitable for sequencing study using the NGS HiSeq2000. Total sequencing output obtained was 52.9 x 109 bp. The genomic library clusters resulted during the sequencing process demonstrated the Q scores > 30 of 75.0% with low error sequencing rate of 1.47%. Cluster densities, percentage of cluster PF, base intensity, and percentage of phasing and prephasing indicated the cluster quality of the genomic libraries is classified as an ideal one to be used for resequencing study using NGS HiSeq2000. The resequence data were ideal for SNP marker discovery. SNP markers are used to identify economically important genes of cocoa and marker-aided cocoa breeding to decrase the cocoa breeding cycle.
Konstruksi Pustaka Genom Kakao (Theobroma cacao L.) untuk Sekuensing Genom Total Menggunakan Next Generation Sequencing HiSeq2000 Tasma, I Made; Satyawan, Dani; Rijzaani, Habib; Rubiyo, Rubiyo
Jurnal Tanaman Industri dan Penyegar Vol 3, No 2 (2012): Buletin Riset Tanaman Rempah Dan Aneka Tanaman Industri
Publisher : Pusat Penelitian dan Pengembangan Perkebunan

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

Abstract

Pemuliaan kakao secara konvensional memerlukan waktu panjang (10-15 tahun). Pemanfaatan marka DNA akan memperpendek siklus pemuliaan kakao. Tujuan penelitian ini adalah mengkonstruksi pustaka genom tiga genotipe kakao yang dapat digunakan untuk sekuensing genom total kakao menggunakan NGS HiSeq2000 dan mendapatkan data resekuen genom total tiga genotipe kakao.  Bahan tanaman terdiri dari tiga klon unggul kakao (ICCR02, ICCR04, dan SUL02) diperoleh dari Balittri, Pakuwon.  DNA genomik diisolasi dari daun muda sebagai bahan konstruksi pustaka genom total. Sekuensing pustaka dilakukan pada mesin HiSeq2000 mengikuti protokol dari Illumina. Pustaka genom yang telah berhasil dikonstruksi berukuran 300 pasang basa (bp) masing-masing dengan konsentrasi 14,70 ng/µL (ICCR02), 15,20 ng/µL (ICCR04), dan 12,90 ng/µL (SUL02). Ukuran dan konsentrasi pustaka genom yang dihasilkan sangat ideal untuk sekuensing menggunakan HiSeq2000. Sekuensing ketiga genom menghasilkan data sekuen 52,9 x 109 bp.  Klaster DNA pustaka genom memiliki nilai Q scores>30 (75,0%) dengan tingkat kesalahan pembacaan basa rendah (1,47%).  Nilai densitas klaster, persen klaster PF, intensitas basa, persen phasing, dan persen prephasing menunjukkan kualitas klaster pustaka genom ketiga genotipe kakao termasuk kategori pustaka ideal. Data sekuen yang dihasilkan juga sangat ideal untuk identifikasi marka SNP genom kakao. Koleksi marka SNP digunakan untuk identifikasi gen pengendali karakter penting kakao dan pemuliaan berbasis marka DNA untuk memperpendek siklus pemuliaan kakao. Genomic Library Construction Of Cocoa (Theobroma Cacao L.) For Whole Genome Sequensing Using A Next Generation Sequencer Hiseq2000Conventional cocoa breeding is slow and takes about 10-15 years to complete a breeding cycle. Applying genomic technology using DNA markers will significantly decrease cocoa breeding cycle. The objectives of this study were to construct cocoa whole genome genomic libraries to be used for resequencing the whole genome of cocoa and obtain whole genome resequence data of three cocoa genotypes. Three Indonesian cocoa genotypes (ICCR02, ICRR04, and SUL02) were used. DNA genomic was isolated from young leaf and used to construct genomic DNA libraries and generate DNA clusters. DNA clusters were sequenced using a HiSeq2000 platform. The whole genome libraries of the cocoa genotypes were successfully constructed. The library size was 300 bp with concentrations of 14.70 ng/µL (ICCR02), 15.20 ng/µL (ICCR04), and 12.90 ng/µL (SUL02), respectively. The genomic library size and concentrations are suitable for sequencing study using the NGS HiSeq2000. Total sequencing output obtained was 52.9 x 109 bp. The genomic library clusters resulted during the sequencing process demonstrated the Q scores > 30 of 75.0% with low error sequencing rate of 1.47%. Cluster densities, percentage of cluster PF, base intensity, and percentage of phasing and prephasing indicated the cluster quality of the genomic libraries is classified as an ideal one to be used for resequencing study using NGS HiSeq2000. The resequence data were ideal for SNP marker discovery. SNP markers are used to identify economically important genes of cocoa and marker-aided cocoa breeding to decrase the cocoa breeding cycle.
KARAKTERISASI KERAGAMAN GENETIK 27 GENOTIPE CABAI BERDASARKAN MARKA SSR (SIMPLE SEQUENCE REPEAT) Terryana, Rerenstradika Tizar; Nugroho, Kristianto; Rijzaani, Habib; Lestari, Puji
BERITA BIOLOGI Vol 17, No 2 (2018)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/beritabiologi.v17i2.3313

Abstract

Chili pepper (Capsicum annuum) is one of the high economical horticultural comodity in Indonesia and its genetic diversity contributes to the success of breeding programs. Simple sequence repeat (SSR) markers can be used to analyze genetic diversity among chili pepper genotypes. The aim of this research was to analyze the genetic diversity of twenty-seven genotypes of chili pepper by using 24 SSR markers. The collected data was analyzed using cluster analysis and principle coordinate analysis (PCoA). The result showed that high allele variation (4–17 alleles) was observed among chili pepper genotypes tested, with an average allele number and Polymorphism Information Content (PIC) value was 7.708 and 0.758 (0.598–0.920) respectively. All of SSR markers showed PIC value >0.5 which indicated that these markers were suitable for chili pepper diversity studies with a high differentiation and with the average value of genetic diversity was 0.78. The clustering and principle coordinate analysis showed that twenty-seven genotypes of chili pepper were divided into two groups (coefficient of similarity 0.74 in cluster analysis) indicating a high genetic variability among them. Genetic diversity analysis in this study will be useful as an initial basis of selection for appropriate parents with desired traits to assist the breeding program of chili pepper in Indonesia.
CLUSTERING OF BROWN PLANTHOPPER BIOTYPE BASED ON RAPD-PCR BAHAGIAWATI, BAHAGIAWATI; RIJZAANI, HABIB
HAYATI Journal of Biosciences Vol. 12 No. 1 (2005): March 2005
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (717.068 KB) | DOI: 10.4308/hjb.12.1.1

Abstract

Random amplified polymorphic DNA (RAPD) technique was used to differentiate two brown planthopper biotypes, that were multiplied in the greenhouse. Ten selected random decamer RAPD primers produced unique DNA band patterns for each individual brown planthopper. However, no single primer produced DNA band that could differentiate the two brown planthopper biotype populations. Nonetheless, analysis of the DNA band patterns was able to cluster the majority of the individual samples according to their respective biotypes. Molecular data analysis also indicated greater genetic variation within biotype population than among biotypes.
Genetic Stability of Banana Plant Regenerated from Floral Axis Organogenesis Assessed by Newly Developed SSR Markers Lestari, Puji; Roostika, I.; Nugroho, Kristianto; HS, Edison; Rijzaani, Habib; Mastur, Mastur
AGRIVITA, Journal of Agricultural Science Vol 41, No 2 (2019)
Publisher : Faculty of Agriculture University of Brawijaya in collaboration with PERAGI

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17503/agrivita.v41i2.1931

Abstract

Molecular marker is robust to precisely monitor the genetic stability of in vitro-banana plants. This study examined the genetic stability of 8 monthold banana plants of Soka variety derived from floral axis organogenesis using newly developed SSR markers. The results showed that the same qualitative and similar quantitative morphological characters of pseudostem, leaf and fruit were identified between mother plants and culture plants from floral axis regeneration. Both plants types were quite similar in number of tillers, brix percentage, fruit peel/mesocarp thickness and fruit length. Eleven out of 211 good quality of SSR loci showing high homology with important genes were selected for suitable PCR primers and produced unambiguous bands.The number of total bands was 323 for total SSR primers, in range of 20-60 per primer for total individual plants. Most culture plants showed identical with their mother plants, with very minor variation as reflected by genetic similarity coefficient range of 0.9-1.0. A high similar pattern on SSR to support morphological characters of mother plants and culture plants indicated a successful micropropagation using floral axis to encounter off-type clones.The floral axis organogenesis in this study is able to provide sufficient genetic materials of Soka for varietal registration and other applications.
KARAKTERISASI KERAGAMAN GENETIK 27 GENOTIPE CABAI BERDASARKAN MARKA SSR (SIMPLE SEQUENCE REPEAT) Terryana, Rerenstradika Tizar; Nugroho, Kristianto; Rijzaani, Habib; Lestari, Puji
BERITA BIOLOGI Vol 17, No 2 (2018)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/beritabiologi.v17i2.3313

Abstract

Chili pepper (Capsicum annuum) is one of the high economical horticultural comodity in Indonesia and its genetic diversity contributes to the success of breeding programs. Simple sequence repeat (SSR) markers can be used to analyze genetic diversity among chili pepper genotypes. The aim of this research was to analyze the genetic diversity of twenty-seven genotypes of chili pepper by using 24 SSR markers. The collected data was analyzed using cluster analysis and principle coordinate analysis (PCoA). The result showed that high allele variation (4?17 alleles) was observed among chili pepper genotypes tested, with an average allele number and Polymorphism Information Content (PIC) value was 7.708 and 0.758 (0.598?0.920) respectively. All of SSR markers showed PIC value >0.5 which indicated that these markers were suitable for chili pepper diversity studies with a high differentiation and with the average value of genetic diversity was 0.78. The clustering and principle coordinate analysis showed that twenty-seven genotypes of chili pepper were divided into two groups (coefficient of similarity 0.74 in cluster analysis) indicating a high genetic variability among them. Genetic diversity analysis in this study will be useful as an initial basis of selection for appropriate parents with desired traits to assist the breeding program of chili pepper in Indonesia.