62 research outputs found
Genetic Diversity of Japonica Rice (Oryza sativa L.) Based on Markers Corresponding to Starch Synthesizing Genes
Full text linkGenes related to starch synthesis and the metabolism contribute to a variety of physicochemical properties that determine the eating/cooking qualities of rice. Our previous study suggested that a set of molecular markers was able to estimate the eating quality of japonica rice. The present study reports the genetic diversity of 22 japonica rice varieties based on markers corresponding to starch synthesizing genes. The mean of the polymorphic information content (PIC: 0.135) value and the diversity index (0.171) indicated a low genetic diversity in these varieties. The phylogenetic tree clearly demonstrated three main clusters: 1) cluster I contained seven varieties with similar physicochemical properties; 2) cluster II only showed a Japanese variety, Koshihikari, and 3) cluster III included the most Korean varieties (14 varieties). This phylogenetic analysis did not completely represent the physicochemical properties differentiation of the japonica varieties, although it did reveal an initial clue to the close relationship between Korean rice and the Japanese and Chinese varieties. Notably, these markers were also able to identify a premium japonica rice. The molecular markers and information concerning the genetic relationship would be useful in improving the japonica rice along with its starch quality of in breeding program
Analisis Molekuler Latar Belakang Genetik Galur-Galur Harapan Padi Ciherang Aromatik (BC5F6)
No full textPadi aromatik lokal Pandan Wangi dan Mentik Wangi telah dikembangkan
sebagai tetua donor dalam pembentukkan varietas unggul padi aromatik dengan
padi Ciherang sebagai tetua pemulih nonaromatik yang memiliki karakterisasi
unggul. Penelitian ini bertujuan menganalisis persentase genome recovery tetua
pemulih dari dua set populasi backcross (BC5F6) melalui seleksi background
genetik dengan bantuan marka molekuler. DNA padi tetua dan galur BC5F6
berhasil diisolasi dan diamplifikasi dengan primer polimorfik terpilih hasil survei
primer. Persentase pemulihan genom alel Ciherang pada galur BC5F6 populasi
Ciherang-Pandan Wangi mencapai 98.95% pada semua kedelapan individu,
kecuali individu nomor 4, 7, dan 8 yang masing-masing bernilai 86.92%, 96.99%,
dan 97.91%. Persentase pemulihan genom tiap sembilan individu galur BC5F6
populasi Ciherang-Mentik Wangi seragam sebesar 80%. Visualisasi data juga
dilakukan menggunakan perangkat lunak Graphical Genotypes (GGT) versi 2.0
Penentuan Lokus Gen dalam Kromosom Tanaman dengan Bantuan Marka Dna
Full text linkKemajuan 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
Identifikasi Marka Molekuler Terpaut Gen Ketahanan Bulai pada Tanaman Jagung (Zea mays L.)
No full textPenyakit bulai adalah adalah penyakit yang disebabkan oleh cendawan Peronosclerospora yang menjadi salah satu penyakit penting pada tanaman jagung serta dapat menimbulkan kerusakan serius di pertanaman seluruh dunia dan berpotensi secara signifikan menyebabkan kehilangan hasil. Identifikasi marka molekuler terpaut lokus tertentu pada tanaman jagung, khususnya penyakit bulai, merupakan langkah strategis dalam meningkatkan ketahanan bulaimelalui program pemuliaan tanaman jagung. Tujuan utama dari penelitian ini adalah mengidentifikasi marka molekuler terpaut karakter ketahanan bulai pada tanaman jagung. Dua set populasi jagung (F3 dan F3:4) masing-masing terdiri dari 198 galur yang berasal dari persilangan R10-4430 (tetua betina) dan Kandora (tetua jantan) digunakan dalam penelitian ini. Populasi F3 digunakan dalam analisis genotipik dan F3:4 digunakan untuk analisis fenotipik. Selain itu kedua tetua persilangan digunakan pada masing-masing analisis. Satu set marka Simple Sequence Repeats (SSR) jagung yang diperoleh dari database tanaman jagung (maizegdb.org) digunakan pada analisis genotipik seluruh populasi dan tetua persilangannya.
Penelitian ini berhasil memetakan sebanyak 44 pasang marka SSR ke dalam 10 grup pautan dengan total jarak genetik yang dapat dicakup pada penelitian ini sebesar 460.3 cM (39.75% dari total genom tanaman jagung) dengan jarak rata-rata antar marker sejauh 26.85 cM. Sebanyak tujuh lokus karakter kuantitatif (QTLs) untuk sifat ketahanan bulai berhasil diidentifikasi pada empat kromosom jagung, dengan rincian tiga QTL pada kromosom satu (qDM-Pp1a, qDM-Pp1b1 dan qDM-Pp1b2), satu QTL pada kromosom 5 (qDM-Pp5), dua QTL pada kromosom 6 (qDM-Pp6b1 dan qDM-Pp6b2), dan satu QTL pada kromosom 10 (qDM-Pp10). Efek gen aditif (gen ketahanan) terhadap penyakit bulai dari seluruh QTL sebesar 43.35% sampai dengan 53.71 %.Efek ini erat kaitannya dengan kontribusi alel-alel tetua donor yang diwariskan ke galur anakan secara poligenik terhadap karakter ketahanan tertentu. Pengaruh QTL terhadap fenotip ditunjukkan dengan nilai PVE. Berdasarkan penelitian ini, masing-masing QTL menunjukkan pengaruh yang besar terhadap fenotip dengan nilai PVE-nya lebih dari 10%. Penelitian ini menunjukkan tujuh QTL diidentifikasi terpaut dengan karakter ketahanan bulai, yaitu pada kromosom qDM-Pp1a (marka umc2225), qDM-Pp1b1 (marka bnlg1564), qDM-Pp1b2 (marka bnlg1884), qDM-Pp5 (marka phi048), qDM-Pp6b1 (marka nc010), qDM-Pp6b2 (marka bnlg1443) dan qDM-Pp10 (marka bnlg2190). Penelitian ini berhasil mengidentifikasi beberapa marka molecular yang terpaut sifat resisensi terhadap penyakit bulai pada jagung populasi F3:4 hasil persilangan jagung varietas R10-4430 dan Kandora
Manfaat Sekuen Genom Lengkap Dalam Identifikasi Gen: Peranan Kelompok Gen Actin-myosin Dalam Sistem Pertahanan Tanaman
Full text linkComplete 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
Seleksi Marka Molekuler Tahan Cekaman Fe Menggunakan Tanaman Bc1f1 Ciherang-Siam Arjuna.
No full textIdentifikasi marka molekuler yang terkait sifat tahan cekaman Fe tinggi merupakan penelitan awal untuk memperoleh varietas unggul toleran terhadap keracunan Fe. Penelitian ini bertujuan menentukan marka molekuler yang terkait dengan sifat tahan cekaman Fe pada tanaman padi BC1F1 Ciherang-Siam Arjuna, serta mengukur ketahanan galur-galur padi BC1F1 hasil persilangan tanaman padi unggul nasional (Ciherang) dengan tanaman padi rawa (Siam Arjuna) tahan cekaman Fe pada kondisi terkontrol menggunakan larutan Yoshida Fe 300 ppm. Seleksi marka molekuler dilakukan dengan teknik PCR dan elektroforesis terhadap DNA tetua, galur tahan, dan rentan menggunakan metode bulk segregant analysis. Survei terhadap 127 marka molekuler (STS dan SSR) menghasilkan 30 makra molekuler polimorfik. Marka S06096 dapat membedakan pola pita DNA galur tahan mengikuti pola pita DNA tetua tahan (Siam Arjuna), dan pola pita DNA galur rentan mengikuti pola pita DNA tetua rentan (Ciherang). Ada 12 galur tahan cekaman Fe 300 ppm, yaitu galur nomor 5, 6, 22, 23, 30, 39, 68, 93, 119, 120, 123, 130
Comparison of detergent and CTAB method for isolation of DNA from Salak ( Salacca zalacca (Gaert.) Voss. ‘Pondoh’)
Full text linkThis 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 µg/ml. There is no difference between the quality of genomic DNA isolated by CTAB and detergent methods
Keragaman Genetik Isolat Cendawan Pyricularia oryzae Menggunakan Primer Pot-2 (Rep-PCR)
No full text<p>Rice blast (Pyricularia<br />oryzae) is one of the most important diseases of rice. It can<br />be very destructive in the field, when the environmental<br />conditions are favourable. Information on genetic diversity of<br />this pathogen could assist plant breeders in determining<br />strategy for a successful control of the disease. This study<br />was conducted to analyze genetic diversity in P. oryzae<br />isolates by a pair of Pot-2 primers using the rep-PCR<br />technique. These primers were designed from a transposon<br />element of the entire blast fungus genomic DNA. DNA<br />samples were extracted from 212 isolates of P. oryzae<br />collected from two endemic areas of the disease in<br />Indonesia, i.e., Tamanbogo, Lampung, and Sukabumi, West<br />Java, as well as from some non-endemic areas in North<br />Sumatra and West Sumatra). Results of the study indicated<br />that the 212 isolates could clustered into 21 haplotypes. The<br />most dominant haplotypes as indicated by their highest<br />frequency of haplotypes were haplotype Pot 2-019 (54.46%)<br />followed by haplotype Pot 2-021 (14.73%) and haplotipe Pot<br />2-016 (6.25%). Regardless of origins of the P. oryzae isolates,<br />we found 6 haplotypes from Tamanbogo (out of 117<br />samples), 13 haplotypes from Sukabumi (out of 77 samples),<br />and 11 haplotypes from North Sumatra and West Sumatra<br />(out of 18 isolates). It seems that genetic diversity of the P.<br />oryzae isolates was not affected by the total number of<br />samples/isolates, but rather by place of the origin and rice<br />genotypes from which the isolates were collected.</p></jats:p
THE POTENTIAL USE OF SSR MARKERS TO SUPPORT THE MORPHOLOGICAL IDENTIFICATION OF INDONESIAN MUNGBEAN VARIETIES
Full text link<p>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. <strong></strong></p></jats:p
Evaluation of Mungbean Mutant Lines to Drought Stress and Their Genetic Relationships Using SSR Markers
No full textDevelopment of mungbean cultivarstolerant to drought stress through mutation breeding approach would enable us to anticipate the crop yield-reducing effects of climate changes. The objective of this research was to evaluate the yield performance of mungbean mutant lines that showed tolerance to drought stress, and to analyze their genetic diversity and relationship among mutant lines using SSR markers. The study was conducted during the dry season of 2012 in the Muneng experimental farm, Probolinggo, East Java. The experiment was laid out in a randomized block design with four replications. Five mutant lines and two parental lines as control were tested for evaluation of yield and drought tolerance under twoenvironments of two irrigation systems as treatment. The two environmental conditions consisted of optimal irrigation (at least three times: at planting, flowering and during pod filling) and suboptimal irrigation (two times at planting and flowering). To evaluate genetic variation among selected mutant lines and their discrimination from parental lines in molecular level, a cluster analysis was performed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) in the NTSYS software. The results showed that three mutant lines, including PsJ30, PsJ31, PsJ32 produced the highest grain yields of 1.17, 1.01, and 1.04 ton/ha, respectively, compared to the other mutant lines and the parents Gelatik (0.85 ton/ha) and Perkutut (0.87 ton/ha) as control check. Of those mutant lines, PSJ31 was the most tolerant to drought with sensitivity index value of 0.47. The PSJ31 has now been officially released as a new variety ( 2013), named as Muri which was identified to have high yield and tolerant to drought. Based on 23 SSR markers used for clustering analysis of those 3 selected mutant lines,9SSR markers (MBSS R033; satt137; MBSSR008; MBSSR203; MBSSR013; MBSSR021; MBSSR016; MBSSR136; and DMBSSR013) were successfully identified the three mungbean mutant lines. Taken together, we have succeeded at develop and evaluate three elite mutant breeding lines which are valuable resources for genetic variation in mungbean. The genetic variation information of mungbean at molecular level potentially provides room for recombinants which are essential for the development of a new superior variety in mungbean improvemen
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