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Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian, Jl. Tentara Pelajar 3A, Bogor 16111

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Inheritance of Blast Resistance (Pyricularia grisea Sacc.) on Interspecific Crossing between IR64 and Oryza rufipogon Griff UTAMI, DWINITA WIKAN; ASWIDINNOOR, HAJRIAL; MOELJOPAWIRO, SUGIONO; HANARIDA, IDA; REFLINUR, REFLINUR
HAYATI Journal of Biosciences Vol 13, No 3 (2006): September 2006
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Blast disease affected by Pyricularia grisea causes high percentage of yield losses in rice production. The improvement of durable Blast resistance is difficult due to the complexity of the inheritance of this trait. This study was conducted to evaluate the genetic control and inheritance of Blast resistance trait in interspesific population between IR 64 (accepted Indonesian rice type, medium resistant to Indonesian Blast pathogen) and Oryza rufipogon (AA genome; acc. No.IRGC#105491; donor for Blast resistance). Six populations, i.e. P1, P2, F1, F2, BCP1, and BCP2, were inoculated with three Indonesian races of Blast pathogen. The disease intensity was determined on the basis of disease leaf area (DLA). The three types of gene interactions (additive, dominance, and epistatis) were significantly involved in this trait. Among the digenic epistasis interactions, all of the additive x additive [i], additive x dominance (j) and dominance x dominance (l) contributed to the trait. Broad-sense heritability ranged from 50.30 up to 91.20%, while the narrow heritability ranged from 16.98 up to 73.20%. The presence of additive gene effect indicated that selection of this trait is promising. Key words: inheritance, Blast resistance, wild rice, Oryza rufipogon
PENENTUAN LOKUS GEN DALAM KROMOSOM TANAMAN DENGAN BANTUAN MARKA DNA Reflinur, Reflinur; Lestari, Puji
Jurnal Penelitian dan Pengembangan Pertanian Vol 34, No 4 (2015): Desember 2015
Publisher : Pusat Perpustakaan dan Penyebaran Teknologi Pertanian

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Abstract

Kemajuan teknik marka molekuler memberikan kemudahan bagi pemulia tanaman dalam penentuan lokasi gen yang mengendalikan karakter yang diinginkan. Penentuan gen yang mengendalikan sejumlah karakter penting dengan menggunakan marka genetik telah berhasil dilakukan pada berbagai jenis tanaman. Sebelum pemetaan suatu marka molekuler terhadap karakter yang diinginkan, diperlukan pemetaan genetik yang dikonstruksi dari sejumlah marka molekuler. Pemetaan daerah dalam kromosom yang mengendalikan karakter kualitatif dan kuantitatif mendapat perhatian yang sangat besar dalam program pemuliaan. Penentuan gen yang mengendalikan karakter kualitatif maupun kuantitatif memerlukan populasi pemetaan. Metode umum yang digunakan dalam penentuan lokasi gen yang mengendalikan karakter kualitatif ialah bulk segregant analysis (BSA). Pendekatan tersebut terbukti mampu mempercepat penentuan lokasi gen dengan biaya yang relatif rendah. Sebaliknya, penentuan lokasi gen yang mengen-dalikan sifat kuantitatif dilakukan melalui pemetaan  quantitative trait loci (QTL). Dibandingkan penentuan lokasi gen pengendali sifat kualitatif, pemetaan QTL lebih kompleks dan membutuhkan kemampuan analisis statistik untuk menentukan daerah kromosom yang terkait dengan karakter kuantitatif tersebut. Tulisan ini membahas metode penentuan lokasi gen di dalam kromosom yang bertanggung jawab terhadap karakter penting tanaman dengan memanfaatkan marka molekuler dalam pemetaan genetik dan analisis QTL.
Manfaat Sekuen Genom Lengkap dalam Identifikasi Gen: Peranan Kelompok Gen Actin-myosin dalam Sistem Pertahanan Tanaman Reflinur, Reflinur; Utami, Dwinita Wikan
Jurnal AgroBiogen Vol 1, No 1 (2005): April
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

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Abstract

Complete genome sequencing of Arabidopsis thaliana and rice (Oryza sativa) were accomplished in 2000 and 2004, respectively. The availability of high quality genome sequences of A. thaliana and rice amenable for identification and understanding of the structure and functional genes in the plant genome. One of the genes family that have been investigated is the actin-myosin genes. This genes family contributes to signalling process of the plant defence mechanism. This paper focuses on phylogenetic characterization and activation of actin-myosin genes family with emphasis on involvement on the plant defence mechanism.
Keragaman Genetik Isolat Cendawan Pyricularia oryzae Menggunakan Primer Pot-2 (Rep-PCR) Tasliah, Tasliah; Reflinur, Reflinur; Bustamam, Masdiar
Jurnal AgroBiogen Vol 4, No 2 (2008): Oktober
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

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Abstract

Rice blast (Pyriculariaoryzae) is one of the most important diseases of rice. It canbe very destructive in the field, when the environmentalconditions are favourable. Information on genetic diversity ofthis pathogen could assist plant breeders in determiningstrategy for a successful control of the disease. This studywas conducted to analyze genetic diversity in P. oryzaeisolates by a pair of Pot-2 primers using the rep-PCRtechnique. These primers were designed from a transposonelement of the entire blast fungus genomic DNA. DNAsamples were extracted from 212 isolates of P. oryzaecollected from two endemic areas of the disease inIndonesia, i.e., Tamanbogo, Lampung, and Sukabumi, WestJava, as well as from some non-endemic areas in NorthSumatra and West Sumatra). Results of the study indicatedthat the 212 isolates could clustered into 21 haplotypes. Themost dominant haplotypes as indicated by their highestfrequency of haplotypes were haplotype Pot 2-019 (54.46%)followed by haplotype Pot 2-021 (14.73%) and haplotipe Pot2-016 (6.25%). Regardless of origins of the P. oryzae isolates,we found 6 haplotypes from Tamanbogo (out of 117samples), 13 haplotypes from Sukabumi (out of 77 samples),and 11 haplotypes from North Sumatra and West Sumatra(out of 18 isolates). It seems that genetic diversity of the P.oryzae isolates was not affected by the total number ofsamples/isolates, but rather by place of the origin and ricegenotypes from which the isolates were collected.
Genetic Diversity Analysis Using Resistance Gene Analog-Based Markers to Support Morphological Characterization of Shallots Herlina, Lina; Reflinur, Reflinur; Nugroho, Kristianto; Terryana, Rerenstradika T.; Sobir, Sobir; Maharijaya, Awang; Wiyono, Suryo
Jurnal AgroBiogen Vol 14, No 2 (2018): December
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

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Abstract

Shallot (Allium cepa var. aggregatum) is one of the most important vegetable crops grown in Indonesia. The limited knowledge available on the genetic diversity and the threat of plant disease have been major problems to maintain high shallot production in Indonesia. Development of molecular markers linked to disease resistance is required for molecular breeding activity in this crop. This study aimed to assess the genetic diversity at conserved domain of resistance gene analog (RGA) in a set of 36 Indonesian shallot genotypes to complement morphological characterization. Twelve morphological and fifteen molecular markers traits were investigated in an attempt to characterize and to discriminate the Indonesian shallots genotypes. Characterization at orphological level indicated that phenotypic variance was highest for total bulb weight (TWB, cv = 99.39%) and the least for the plant height (PH, cv = 28.16%). The correlation analysis between traits showed that TWB and number of bulb (NB), TWB and bulb weight per plant (WB), NB and WB, and WB and PH were positively correlated. Molecular analysis revealed a total of 1,512 alleles with an average of 1.946 alleles per locus. The Polymorphism Information Content (PIC) values ranged from 0.253 to 0.676 and six out of 15 RGA markers were highly informative with PIC values ≥0.50. Based on cluster analysis, the 36 Indonesian shallot genotypes were clearly discriminated into six major groups. These results revealed that the RGA-based markers could support the morphological characterization in evaluating the genetic diversity of shallots. 
KERAGAMAN GENETIK VARIETAS PADI japonica DAN indica BERDASARKAN MARKA DNA TERKAIT MUTU RASA Lestari, Puji; Reflinur, Reflinur; Handoko, Dody Dwi; Mastur, Mastur
Scripta Biologica Vol 5, No 1 (2018)
Publisher : Fakultas Biologi | Universitas Jenderal Soedirman

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Abstract

PCR-based markers and evaluation of physicochemical properties should be addressed for the improvement of rice varieties with good eating dan eating quality (EQ). This study aimed to examine the genetic diversity of rice varieties based on DNA markers related to physicochemical properties determining EQ. A total of 46 rice varieties consisting of 22 japonica varieties and 24 indica varieties were examined using 43 PCR-based markers. The results showed that polymorphic information content (PIC) ranged from 0.04 to 0.38, in support of genetic diversity indices which ranged from 0.04 to 0.50 across total markers. Pairwise genetic similarity matrix ranged from 0.40 to 0.98 with the closest genetic distance was observed between two japonica varieties (Dongjin and Hwaseong) and the most distant one was between japonica and indica (Onnuri/Manmi with Cigeulis/Fatmawati). The unweighted neighbor-joining tree clustered the rice varieties into two major clades, indica and japonica, and subsequent subclades were differentiating according to the individual genetic background. The genetic diversity of rice from different subspecies and DNA markers for EQ can effectively be utilized for basic information and marker-assisted selection (MAS) for the development of improved varieties with good EQ in rice breeding program.
GENETIC DIVERSITY OF INDONESIAN SHALLOTS BASED ON BULB-TUNIC PATTERNS AND MORPHOLOGICAL CHARACTERS Herlina, Lina; Reflinur, Reflinur; Sobir, Sobir; Maharijaya, Awang; Wiyono, Suryo; Istiaji, Bonjok
Indonesian Journal of Agricultural Science Vol 20, No 1 (2019): June 2019
Publisher : Indonesian Agency for Agricultural Research and Development

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Abstract

Variation within bulb tunics has been used to determine the genetic diversity in Allium species, including shallots. However, no such study has been reported for shallots of Indonesia. The study aimed to analyze the genetic diversity of the Indonesian shallots based on the bulb-tunic patterns. Thirty-five shallot genotypes from main production centers in Indonesia were used. The ultrasculptures of the bulb tunics were examined by light microscopy, including the inner surface and cell shape patterns of the bulb tunics. The phenotypic data, i.e. quantitative and qualitative traits were subjected to the descriptive statistics, principal component, correlation, regression, and clustering analyses. The results showed that the bulb-tunic cell patterns were varied, which shared almost identical with 13 Allium species. Total bulb weight per genotype showed the greatest variation (cv = 89.10%) and significant correlation with bulb weight per plant (r = 0.773). The principle component analyses showed the cumulative proportion of 78% of the total morphological variation in all shallot genotypes. Based on clustering analysis, the genetic variation of Indonesian shallots are grouped into twelve clusters with 50% genetic similarity. The study indicates that Indonesian shallots are genetically varied and could be useful for further utilization in their genetic improvement program.
Inheritance of Blast Resistance (Pyricularia grisea Sacc.) on Interspecific Crossing between IR64 and Oryza rufipogon Griff UTAMI, DWINITA WIKAN; ASWIDINNOOR, HAJRIAL; MOELJOPAWIRO, SUGIONO; HANARIDA, IDA; REFLINUR, REFLINUR
HAYATI Journal of Biosciences Vol 13, No 3 (2006): September 2006
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Original Source | Check in Google Scholar

Abstract

Blast disease affected by Pyricularia grisea causes high percentage of yield losses in rice production. The improvement of durable Blast resistance is difficult due to the complexity of the inheritance of this trait. This study was conducted to evaluate the genetic control and inheritance of Blast resistance trait in interspesific population between IR 64 (accepted Indonesian rice type, medium resistant to Indonesian Blast pathogen) and Oryza rufipogon (AA genome; acc. No.IRGC#105491; donor for Blast resistance). Six populations, i.e. P1, P2, F1, F2, BCP1, and BCP2, were inoculated with three Indonesian races of Blast pathogen. The disease intensity was determined on the basis of disease leaf area (DLA). The three types of gene interactions (additive, dominance, and epistatis) were significantly involved in this trait. Among the digenic epistasis interactions, all of the additive x additive [i], additive x dominance (j) and dominance x dominance (l) contributed to the trait. Broad-sense heritability ranged from 50.30 up to 91.20%, while the narrow heritability ranged from 16.98 up to 73.20%. The presence of additive gene effect indicated that selection of this trait is promising. Key words: inheritance, Blast resistance, wild rice, Oryza rufipogon
Comparison of detergent and CTAB method for isolation of DNA from Salak ( Salacca zalacca (Gaert.) Voss. ‘Pondoh’) Arfa, Namira Nur; Daryono, Budi Setiadi; Reflinur, Reflinur
Biology, Medicine, & Natural Product Chemistry Vol 7, No 1 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

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Abstract

This study conducted in Laboratory of Molecular Biology, Balai Besar Bioteknologi dan Sumberdaya Genetik Pertanian (BB- Biogen) Bogor. The aims of this study are to determine and comparing the quantity,? quality and the efficiency of DNA isolation result using detergent method and CTAB method.? The parameters observed in this study are the value of DNA concentration, purity, and visualization result using gel electrophoresis. The samples are the leaves of Salak ?Pondoh? (Salacca zalacca (Gaert.) Voss.). Detergent method is a method which was developed by Faculty of Biology UGM, it has simple method and relatively affordable cost. Meanwhile, CTAB method is one of the commonly used methods of DNA isolation protocol with relatively expensive cost.? Detergent method used detergent in the cell wall separation and protein removal in the sample. The CTAB method used Cetyltrimethyl ammonium bromide (CTAB) for cell membrane separation in the sample. The research methods included DNA isolation with detergent and CTAB methods, PCR analysis and electrophoresis. Data analysis was done quantitatively ?using spectrophotometric method and qualitative used electrophoresis method. The result of the study ?showed that DNA isolation using? CTAB method showed higher purity compared with detergent method with the purity values ranging from 1,3- 1,4 . Meanwhile, the concentration of DNA in the detergent method was higher than that of CTAB with the highest concentration of 1730 ?g/ml. There is no difference between the? quality of genomic DNA isolated by CTAB and detergent methods.