Judul: Development of Single Nucleotide Polymorphisms (SNPs) Marker based on SAD Gene in Oil Palm (Elaeis guineensis Jacq.)
Abstrak: Oil palm (Elaeis guineensis Jacq.) is an important economic crop species due to the versatile applications of its crude and kernel oils. The necessity to improve oil palm, which is the world’s most productive oil producing plant under cultivation currently for high yield and oil quality to meet the growing global demand especially in term of its healthy component, oleochemical industrial needs and biodiesel utilization has become a major area of focus for oil palm breeders. Marker assisted selection have played a crucial role in oil palm breeding programs and single nucleotide polymorphism (SNP) maker is one of those technology that has recently attracted breeders. High content of oleic acid (18:1) has proven to be that needed component of oil palm and other vegetable oils that can greatly contribute to oil quality improvement. Stearoyl Acyl-carrier-protein Desaturase (SAD) is a key enzyme for oleic acid biosynthesis which plays an important role in determining the composition of unsaturated fatty acids in oil palm. In oil palm, SAD gene is located in chromosome 7, 8, and 9. This research focused on chromosome 7 and 9. There are 3 exon region in each of these two chromosomes. Specific primers were designed base on the 6 exon and neighboring intron region. Genomic DNA from three oil palm sources were amplified using these specific primers. We identified 9 SNP loci (4 in the exon and 5 in the intron) in SAD gene fragment and developed 9 allele-specific single nucleotide amplified polymorphism (SNAP) marker for oleic acid prediction. Four out of the nine SNAP marker developed and tested on 25 oil palm accessions were polymorphic and reasonably informative. The average expected and observed heterozygosities were 0.391 and 0.404, respectively. The mean polymorphism information content (PIC) was 0.312. Our results showed that these SNAP markers will be useful if validated in larger oil palm population in predicting oleic acid composition and genetic variation in oil palm breeding programs based on SAD gene fragment. This research account for the first specific study of SNAP marker development based on SNPs loci in both intron and exon region of SAD gene sequence in chromosomes 7 and 9 of oil palm. The result of our research will allow direct MAS specifically for oleic acid content and generally for unsaturated fatty acid prediction in oil palm at an early growth stage with less resources and time and also carried on genetic diversity analysis based on SAD gene. In addition, this research result will have set the pitch for further genetic diversity studies on the progeny of cross between the species of oil palm (E.guineensis and E.oleifera). Initial evaluation of the SNAP markers developed in this study is significantly beneficiary for oil palm breeders.
Keyword: Allele-specific, expected heterozygosities, observed heterozygosities, oil quality, SAD, SNP

Judul: Genetic Diversity and Identification of Specific Production Character Markers of Oil Palm Progeny and Parent with SSR Marker
Abstrak: This thesis studies the relationship between microsatellite markers with the character of the production of oil palm (Elaeis guineensis Jacq.) in an attempt to get specific markers that can be useful in the parental selection. The first experiment was carried out by observing the genetic diversity of 80 progeny palm oil that has been classified by the character of high and and low production. Each of these 20 individuals were observed for the characters of oil to bunch (OB), bunch number (BN), oil yield (OY) and fresh fruit bunches (FFB). The results showed a fairly high genetic diversity of the four characters, which is shown by the quite high average percentage of polymorphic and PIC, ie 52.78% and 0.51. Construction of dendogram based on UPGMA can distinguish the characters from one to another by the percentage of genetic similarity 56-100% or ~44% of genetic diversity. The separation of the characters into the four groups was also confirmed using PCoA (Principle Coordinate Analysis). It also found the specific markers for the characters observed, ie one marker specific to the character of OB, four markers specific to the character of BN, one marker specific to the character of OY and two marker specific to the character of FFB. The second experiment was conducted to identify specific markers of the four characters. Correlation and stepwise regression approach used in this experiment. The results showed that there are 11 specific markers were obtained using the correlation approach, as well as 16 specific markers obtained using stepwise regression approach. From the results it is known that one marker positively correlated and regressed to the OB, two markers positively correlated and regressed to the BN, one marker positively regressed to OY, but only one marker that positively correlated to OY, and no one is positively correlated or regressed to FFB. The third experiment was conducted to determine the genetic diversity of Dura parents which is used as female parent in experiments 1 and 2, and its role in the diversity of the four characters tested. Two populations of Dura selfing with 30 samples per population used for analysis. The analysis showed parental separation into two groups based on the selfing. Group A, with ~20% genetic diversity, is the result of D1 selfing. While Group B, with ~28% genetic diversity is the result of D2 selfing. Both genetic material has a low genetic diversity within groups, but higher genetic diversity between group (~ 68%), as well as confirmed by PCoA and Structure. The results of t-test analysis showed that the pair D1 and D2 with a fourth character, has a significant effect on the character of the OB, OY and FFB, while the character of BN, Dura influence is not significant.
Keyword: Elaeis guineensis Jacq, half-sibs, Dura Deli, specific markers, correlation, stepwise regression

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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