Judul: Isolation and characterization of an aluminum tolerance gene in Rice
Abstrak: Aluminum (Al) toxicity is the major limiting factor of crop production in acid soil. Aluminum tolerance in rice is considered as a quantitative trait controlled by many genes. The objectives of this research were to isolate, clone, characterize the aluminum tolerance gene, and to develope codominant marker for rice B11 gene. Plant materials used in this research were four rice genotypes namely Grogol, Hawara Bunar, IR64, and Krowal, and the F2 segregating rice population derived from a cross between Al-sensitive rice genotype IR64 and Altolerant rice genotype Hawara Bunar. A rice Al tolerance gene was isolated based on a combination between rye-rice syntenic relationship and RT-PCR (Reverse Transcription-Polymerase Chain Reaction) approaches. The cDNA of rice Al tolerance gene was synthesized from mRNA isolated from Hawara Bunar after being stressed under 15 ppm Al at pH 4.0 for 24 hours. The Al tolerance gene was characterized by sequencing, bioinformatically analyzing, and introducing it to tobacco plant. The inheritance pattern of rice Al tolerance gene was analyzed by developing the CAPS (Cleaved Amplified Polymorphism Sequence) codominant marker of rice Al tolerance gene through a series of PCR, sequencing, and restriction enzyme analysis of the PCR fragment from IR64 and Hawara Bunar, followed by testing the marker in F2 rice population. This research has succesfully cloned an Al tolerance gene from Indonesian local rice genotype Hawara Bunar, called B11 gene. The B11 gene expression was induced by Al with higher expression level in Hawara Bunar than that of IR64. Transgenic tobacco plants carrying the gene were more tolerant to Al stress than that of nontransgenic tobacco plants. The B11 protein was similar to bacterial ribosomal L32 proteins and was predicted as a transcription factor with bZIP domain and C2H2-zinc finger like motif. Comparison between the B11 gene sequences of the IR64 and Hawara Bunar showed 8 SNPs (Single Nucleotide Polymorphisms). One of the SNPs located at nucleotide 668 causing AluI restriction site based polymorphism between IR64 and Hawara Bunar, which was then used as a basis of B11-CAPS codominant marker development. The marker segregation followed a single gene inheritance pattern. The marker might be used for MAS (Masrker Assisted Selection) in rice breeding programs to obtain Al-tolerant lines.
Keyword: Oryza sativa, Rice breeding, Al tolerance gene, Root re-growth, Transgenic plant, CAPS marker

Judul: Molecular Marker Application on Selection of A Rice Backcross Population derived from a Cross between IR64/Hawara Bunar to Obtain Aluminum-Tolerant Rice Lines.
Abstrak: Since 1971 the increase of food demand in Indonesia, especially rice is much greater (181.6%) than the increase of population (108%), therefore an effort to increase rice production is unavoidable. Currently, the ability of agricultural land to provide area for rice cultivation tends to decline from year to year due to massive conversion of productive lands into industrial and residential uses. The situation leads to expand rice cultivation into the utilization of marginal lands, such as acid soils for rice cultivation. However, rice cultivation in acid soils will face many constraints, which mainly due to the aluminum (Al) toxicity. The use of Al-tolerant rice varieties with high productivity will be an alternative solution to overcome the Al toxicity problem in acid soils. There is an Indonesian local rice genotype named Hawara Bunar that tolerant to Al stress and can be used as a Al-tolerant donor parent in rice breeding program. However, the potential productivity of the genotype is not as high as rice cv IR64. The use of a backcross population derived from a cross between both genotypes with cv IR64 as a recurrent parent is an approach to develop Altolerant rice cultivar with high productivity. It has been identified that a Quantitative Trait Loci (QTL) for Al-tolerance trait is located on the short arm of rice chromosome 3 flanked by markers RM489 and RM517 (Miftahudin et al. 2008; Akhmad 2009). The objectives of the study were to (1) increase molecular markers density in the area of QTL for Al-tolerance trait on rice chromosome 3 flanked by two SSR markers RM489 and RM517, (2) re-identify QTLs for Al tolerance trait in the previous Al-tolerance QTL area on rice chromosome 3, (3) and carry out marker assisted backcross selection (MABS) ob a rice backcross population derived from a cross between IR64/Hawara Bunar to obtain Al-tolerant rice lines with superior agronomic traits. The research was conducted from September 2009 to May 2012 at the Laboratory of Plant Physiology and Molecular Biology, Department of Biology, Bogor Agricultural University and at the Research Institute for Agricultural Biotechnology and Genetic Resources (Biogen) Bogor. An F2 population derived from a cross between rice cv IR64 and Hawara Bunar were used to increase marker density and re-identify Al-tolerance QTL, while BC2F1 plants and BC2F2 populations that have been developed from the previous and this studies, respectively, were selected through MABS combined with physiological and agronomic characters based selection. An amount of 17 SSR markers were screened for polymorphism between the two parents to obtain markers that being used to increase marker density. Five markers, which were RM2790, RM545, RM14535, RM14543, and RM14552, were polymorphic and could be mapped in between markers RM489 and RM517 with the average distance of 3 cM between adjacent markers. Al-tolerance QTL were identified in the previous QTL location between markers RM2790 and RM14552 (LOD 3.4) based on the Main Root Elongation characters. Foreground and background selections were successfully carried out on BC2F1, BC2F2 and BC2F3 populations using five foreground and 50 background SSR markers. The MABS obtained two BC2F3 rice lines (number 175-63-34 and
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Judul: Hamiltonian formulation for linear waves motion in two layers fluid
Abstrak: The surface wave could be considered as a wave that separates two fluids, namely water and air. Based on this assumption, it is introduced the interfacial wave, a wave between two layers of fluid with different density. The formulation of interfacial waves motion begins with deriving the base equation of irrotational ideal fluid. Furthermore, according to irrotational fluid assumption, the base equation can be stated in velocity potential. In this derivation, the fluids domain is assumed to be restricted by rigid lid boundary conditions, both at the upper and lower limit. Therefore, the interfacial waves motion can be explained in a hamiltonian formulation. In the hamiltonian formulation, total energy is defined as the sum of kinetic and potential energy. The hamiltonian system is obtained from reduction of kinetic energy by using the Dirichlet Neumann Operator. The resulted kinetic energy equation is nonlinear. Therefore, this form is linearized by first part of the Taylor expansion. This linearization gives a dispersion relation of linear wave. Based on this dispersion relation, the phase speed of the linear wave depends on the density ratio of the two layers fluid.
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