scholarly journals Analysis of The Open Reading Frame (ORF) 29-TrnC (GCA) Sequence to Detect Indica and Japonica Sub Species on Upland Rice of Situ Bagendit and Inbred Rice of Ciherang

2018 ◽  
Vol 10 (1) ◽  
pp. 153-159
Author(s):  
Rohma Istiana ◽  
Hermin Pancasakti Kusumaningrum ◽  
Rejeki Siti Ferniah
Keyword(s):  
Plant Breeding ◽  
Upland Rice ◽  
Pcr Amplification ◽  
Breeding Program ◽  
Abiotic Factor ◽  
Reading Frame ◽  
Plant Breeding Program ◽  
Pcr Products

The identification and the characterization of genetic diversity of rice was the first step in the rice plant breeding program. This study aimed to detect indica or japonica sub-species on upland rice Situ Bagendit and inbred rice Ciherang using molecular markers ORF 29-TrnC (GCA) on the chloroplast genome. Rice was included to the indica sub-species if the 32 bp insertion on ORF 29-TrnC (GCA) sequence was found, on the contrary, if the deletion 32 bp on ORF 29-TrnC (GCA) was found then it was included to the japonica sub-species. DNA isolation was examined from the leaves of the rice plants, and then it tested quantitatively to determine the transparency and DNA concentration from the isolation results. PCR amplification was performed using a pair of primers CP2 and it was followed by agarose gel electrophoresis. The visualization of the DNA bands used the gel documentation. Sequencing of PCR products produced a long base 390 bp in Situ Bagendit rice and 390 bp in Ciherang rice. Analysis of the sequences showed that the insertions occurred throughout the 32 bp in Situ Bagendit rice and the insertions occurred throughout the 32 bp in Ciherang rice. The results showed that upland rice Situ Bagendit and inbred rice Ciherang were included in the indica sub-species. The knowledge of variety of genetics of rice can be used as bio-information in the plant breeding program. Further, the knowledge can be used to protect in genetic power source, the selection and the composing of superior varieties of rice which is tolerant with kinds of biotic and abiotic factor.

scholarly journals Molecular Characterization of a Novel Cathepsin L in Macrobrachium nipponense and Its Function in Ovary Maturation

2022 ◽  
Vol 12 ◽  
Author(s):  
Sufei Jiang ◽  
Yiwei Xiong ◽  
Wenyi Zhang ◽  
Junpeng Zhu ◽  
Dan Cheng ◽  
...  
Keyword(s):  
Cathepsin L ◽  
Cysteine Proteases ◽  
Macrobrachium Nipponense ◽  
Reading Frame ◽  
Physiological Processes ◽  
Gonad Somatic Index ◽  
Oriental River Prawn ◽  
Ovary Maturation

Cathepsin L genes, which belonged to cysteine proteases, were a series of multifunctional protease and played important roles in a lot of pathological and physiological processes. In this study, we analyzed the characteristics a cathepsin L (named Mn-CL2) in the female oriental river prawn, Macrobrachium nipponense which was involved in ovary maturation. The Mn-CL2 was1,582 bp in length, including a 978 bp open reading frame that encoded 326 amino acids. The Mn-CL2 was classified into the cathepsin L group by phylogenetic analysis. Real-time PCR (qPCR) analysis indicated that Mn-CL2 was highly expressed in the hepatopancreas and ovaries of female prawns. During the different ovarian stages, Mn-CL2 expression in the hepatopancreas and ovaries peaked before ovarian maturation. In situ hybridization studies revealed that Mn-CL2 was localized in the oocyte of the ovary. Injection of Mn-CL2 dsRNA significantly reduced the expression of vitellogenin. Changes in the gonad somatic index also confirmed the inhibitory effects of Mn-CL2 dsRNA on ovary maturation. These results suggest that Mn-CL2 has a key role in promoting ovary maturation.

scholarly journals Identification and Characterization of a Novel Bacterial Sulfite Oxidase with No Heme Binding Domain from Deinococcus radiodurans

2006 ◽  
Vol 188 (2) ◽  
pp. 694-701 ◽  
Author(s):  
Giovanni D'Errico ◽  
Anna Di Salle ◽  
Francesco La Cara ◽  
Mosè Rossi ◽  
Raffaele Cannio
Keyword(s):  
Gene Expression ◽  
Deinococcus Radiodurans ◽  
Heterologous Gene Expression ◽  
Pcr Amplification ◽  
Sulfite Oxidase ◽  
Physical Parameters ◽  
Reading Frame ◽  
Significant Amino Acid Sequence ◽  
Chromosome Ii

ABSTRACT An open reading frame (draSO) encoding a putative sulfite oxidase (SO) was identified in the sequence of chromosome II of Deinococcus radiodurans; the predicted gene product showed significant amino acid sequence homology to several bacterial and eukaryotic SOs, such as the biochemically and structurally characterized enzyme from Arabidopsis thaliana. Cloning of the Deinococcus SO gene was performed by PCR amplification from the bacterial genomic DNA, and heterologous gene expression of a histidine-tagged polypeptide was obtained in a molybdopterin-overproducing strain of Escherichia coli. The recombinant protein was purified to homogeneity by nickel chelating affinity chromatography, and its main kinetic and chemical physical parameters were determined. Northern blot and enzyme activity analyses indicated that draSO gene expression is constitutive in D. radiodurans and that there is no increase upon exposure to thiosulfate and/or molybdenum(II).

scholarly journals Pengelolaan Plasma Nutfah Tanaman Terintegrasi dengan Program Pemuliaan

2016 ◽  
Vol 14 (2) ◽  
pp. 57 ◽  
Author(s):  
NFN Sumarno ◽  
Nani Zuraida
Keyword(s):  
Plant Breeding ◽  
Genetic Research ◽  
Germplasm Collection ◽  
Breeding Population ◽  
Breeding Program ◽  
Team Work ◽  
Germplasm Management ◽  
Plant Germplasm ◽  
Plant Breeding Program ◽  
Donor Gene

<p>Plant breeding, as an applied of plant genetics, is based and is supported by various subdisciplines of genetic sciences, includeing plant germplasm, classical genetics, molecular genetics, cytogenetics, gene-transformation techniques, etc. Linkage and team work system between plant germplasm management and plant breeding program is most required, since the success of plant breeding maybe obtained from the contribution of gene donor parents, derived from the germplasm management. Without the flow of genes from the germplasm collection, varieties produced by the plant breeder would suffer a narrow genetical based or a bottle-necking genetic based. Plant germplasm research is an integral part of the germplasm management, aimed to (1) evaluate the genetic variation of the germplasm collection, to be readily available for the breeding program and to be used for scientific publications, (2) tracing the origin of plant species, and (3) officially release a selected germplasm, containing new economic gene (s). The linkage between germplasm management and plant breeding research program could be facilitated through the following activities (1) identifying an elit germplasm for varietal release, (2) selection and stabilization of a promising germplasm accession for possible varietal releases, (3) use of germplasm accession as a gene donor parent to incorporate adaptive genes into improved variety, (4) use of germplasm accession for a specific donor gene, (5) use of germplasm to broaden the genetical base of varieties through an introgression and nobilization, (6) use of germplasm to improve the genetic value of the breeding population, and (7) to develop multiple crossess involving many parents to broaden the genetical base of the breeding population. Another important function of the germplasm management is to conserve accessions carrying genes which may be useful in the future, to anticipate the dynamic changing of biological and environmental stresses on crop. Germplasm management is considered successfully conducted when it is continously supplying donor gene parents to breeders for parental crosses on their breeding program, conversely, breeding program in considered successfully managed, when it uses the rich genetic variability available on the germplasm collection. Separating the organizational units among the breeding program, germplasm management and molecular genetic research, is only for enhancing the intensity of the research, but should not separate the linkage program of the research.</p><p> </p><p><strong>Abstrak</strong></p><p>Pemuliaan tanaman merupakan ilmu genetika terapan yang didukung oleh berbagai cabang ilmu kegenetikaan, termasuk plasma nutfah, genetika klasik, genetika molekuler, sitogenetika, dan genetika transformasi. Keterpaduan antara pengelolaan plasma nutfah dengan pemuliaan tanaman tidak dapat ditawar, karena keberhasilan pemuliaan sangat tergantung dari ketersediaan sumber gen yang disediakan oleh pengelola plasma nutfah. Tanpa kontribusi sumber gen dari pengelola plasma nutfah, hasil pemuliaan tanaman mengalami penyempitan kandungan genetik, atau terjadi gejala leher botol genetik. Penelitian plasma nutfah merupakan bagian integral dari pengelolaan materi plasma nutfah, bertujuan untuk (1) menggali kekayaan sifat genetik plasma nutfah guna penyediaan tetua persilangan dan bahan publikasi ilmiah, (2) menelusuri asal-usul spesies tanaman, (3) melepas secara resmi plasma nutfah sebagai sumber gen yang diakui kepemilikannya. Keterkaitan pengelolaan plasma nutfah dengan program pemuliaan dapat dilaksanakan melalui (1) pemanfaatan langsung aksesi plasma nutfah elit untuk dilepas sebagai varietas unggul, (2) pemurnian dan pemantapan populasi aksesi plasma nutfah sebagai calon varietas, (3) pemanfaatan aksesi plasma nutfah sebagai donor gen untuk rekombinasi gen-gen unggul adaptif, (4) plasma nutfah sebagai donor gen spesifik, (5) plasma nutfah sebagai bahan perluasan latar belakang genetik varietas melalui proses introgresi dan nobilisasi, (6) pemanfaatan plasma nutfah untuk perbaikan genetik populasi seleksi, dan (7) pembentukan populasi dasar yang mengandung keragaman genetik luas melalui persilangan banyak tetua. Fungsi pengelolaan plasma nutfah lainnya adalah melestarikan sumber daya genetik untuk kebutuhan gen di masa depan, agar dapat menyediakan gen-gen untuk mengantisipasi perubahan ras patogen dan tipe baru serangga hama yang bersifat dinamis, serta penyediaan gen guna mengatasi cekaman abiotik alamiah. Pengelolaan plasma nutfah dinilai berhasil apabila telah mampu menyediakan aksesi plasma nutfah sebagai sumber gen donor dalam program pemuliaan. Pemuliaan tanaman berhasil secara optimal apabila telah memanfaatkan keragaman genetik sifat yang diinginkan, yang tersedia dalam koleksi plasma nutfah. Keterpisahan kelembagaan antara unit kerja pengelolaan plasma nutfah dengan program pemuliaan tidak boleh membatasi keterpaduan program penelitian antara kedua cabang disiplin keilmuan tersebut.</p>

scholarly journals Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

mBio ◽  
2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Eran Bacharach ◽  
Nischay Mishra ◽  
Thomas Briese ◽  
Michael C. Zody ◽  
Japhette Esther Kembou Tsofack ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Infectious Agent ◽  
Farmed Fish ◽  
Reading Frame ◽  
Complementary Sequences ◽  
Influenza C Virus ◽  
Negative Sense ◽  
Global Food

ABSTRACTTilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses.In situhybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease.IMPORTANCEThe economic impact of worldwide trade in tilapia is estimated at $7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development.

scholarly journals Progress of Rubber Breeding Program to Support Agroforestry System in Indonesia

2021 ◽  
Vol 305 ◽  
pp. 03006
Author(s):  
Fetrina Oktavia ◽  
Sahuri ◽  
Dwi Shinta Agustina
Keyword(s):  
Natural Rubber ◽  
Plant Breeding ◽  
Agroforestry System ◽  
Climatic Conditions ◽  
Breeding Program ◽  
Agronomic Characters ◽  
Rubber Plant ◽  
Genetic Components ◽  
Plant Breeding Program ◽  
Planting Materials

The use of superior rubber planting materials is one of the most important components of technology to support the cultivation and sustainability of the natural rubber industry. The effect of the genetic components of planting materials to the rubber productivity can reach 60%, and the rest is the influence of agro-climatic conditions. The aim of the rubber plant breeding program is to obtain the new superior rubber clones that have a high latex yielding potential and good agronomic characters. The fluctuations of natural rubber price and climate changes also influence the direction and objectives of the rubber plant breeding program. To deal with the conditions, it is important to provide the rubber agroforestry technology by through intercropping of rubber with various other crops. The article will provide the information about progress of rubber breeding program in Indonesia and it is role in supporting agroforestry system. Several of new superior rubber clones have been released by IRRI, and some of these clones such as IRR 112 and IRR 118 had been planting with rice, corn, and other crops by through rubber agroforestry system. The system was estimated be able to maintain latex yielding potential of clones as well as farmers’ income can be improved.

scholarly journals Field Phenomics: Will It Enable Crop Improvement?

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
David M. Deery ◽  
Hamlyn G. Jones
Keyword(s):  
Plant Breeding ◽  
Recent Progress ◽  
Crop Improvement ◽  
Breeding Program ◽  
Enabling Technology ◽  
Plant Breeding Program ◽  
Improved Cultivars

Field phenomics has been identified as a promising enabling technology to assist plant breeders with the development of improved cultivars for farmers. Yet, despite much investment, there are few examples demonstrating the application of phenomics within a plant breeding program. We review recent progress in field phenomics and highlight the importance of targeting breeders’ needs, rather than perceived technology needs, through developing and enhancing partnerships between phenomics researchers and plant breeders.

scholarly journals Screening Gogo Rice Local Aceh Cultivars Drought Tolerant Under Polyetilene Glycol 6000

2019 ◽  
Vol 6 (2) ◽  
pp. 200-210
Author(s):  
Muhammad Syahril ◽  
Syamsul Bahri ◽  
Rhido Suhada
Keyword(s):  
Drought Tolerance ◽  
Plant Breeding ◽  
Genetic Material ◽  
Rice Production ◽  
Breeding Program ◽  
Vegetative Stage ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Plant Breeding Program ◽  
Germination Stage

Efforts for increasing rice production nationally, it is necessary to increase the productivity of a land. Utilization of marginal lands like drought land potential to increase rice production nationally. One effort to utilize marginal land like dry land is the use of high-yielding drought tolerant varieties. Until now high-yielding drought tolerant varieties still relatively rare. For this reason, it is necessary to create high-yielding drought tolerant varieties from plant breeding program. One of the standard programs in plant breeding to create high-yielding drought tolerant varieties is provision of genetic material as parental. Local varieties gogo rice Drought-tolerant potential to be used as parental in the plant breeding program to create of high-yielding drought tolerant rice varieties. For this reason, it is necessary to test drought tolerance of local rice cultivars. The study used 10 cultivars exploration results in East Aceh Regency namely Gameso, Sibengkok, Ramos Gunung, Sidol, Sigedul, Rias Kuning, Rias putih, Sibontok, Serumu, and Sileso. Drought tolerance testing using PEG solution (Polyethylene Glycol) 6000 156. 75 g / liter of H2O which is equivalent to the osmotic potential of -3 BAR and aquades as control (0 BAR) an germination stage and early vegetative stage. The results of the study show that 10 cultivars tested in the germination stage, 6 cultivars were selected as drought tolerant cultivars. Furthermore, 6 cultivars tested in the early vegetative stage showed the ability to recover at day 35 and then at day 42 showed no symptoms of drought. 6 drought tolerant cultivars are Gameso, Ramos Gunung, Sigedul, Rias Kuning, Sibontok, and Sileso.

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