Judul: Comparative Genomics and Phylogenetic Analysis of Indonesian Coconuts with Other Important Palms Species Based on Chloroplast Genome
Abstrak: Kelapa adalah salah satu spesies terpenting secara ekonomi dari famili Arecaceae. Kelapa unik yang memiliki endosperm remah, lembut, dan terlepas dari batok kelapa akibat dari mutasi alami yang dikenal secara lokal di Indonesia sebagai kelapa kopyor. Penelitian ini mencakup karakterisasi genom kloroplas kelapa kopyor varietas (var.) Genjah Hijau dan analisis komparatif genomik antar spesies palma lainnya. Berdasarkan analisis sekuens, genom kloroplas kelapa var. Genjah Hijau Kopyor memiliki panjang 158 462 bp dan memiliki struktur kuadripartit yang terdiri dari satu daerah large single-copy (LSC; 86 198 bp), satu daerah small single-copy (SSC; 17 712 bp) dan dua daerah inverted repeat yang identik (IR; 27 276 bp). Genom terdiri dari 116 gen. Analisis komparatif menunjukkan bahwa daerah pengkode protein lebih terkonservasi dibandingkan dengan daerah non-pengkode protein. Analisis filogenetik menunjukkan bahwa kelapa memiliki hubungan yang erat dengan Phoenix dactylifera. Karakterisasi genom ini ddapat memberikan informasi untuk mengembangkan penanda spesifik gen, pemetaan genom kloroplas, program pemuliaan tanaman, studi evolusi, dan konservasi kelapa kopyor., Coconut is one of the most economically important trees of family Arecaceae. This unique coconut has curd, fluffy, and crumbly endosperm because of natural mutation that is locally known in Indonesia as kopyor coconut. This research encompasses the characteristics of kopyor coconut var. Green Dwarf chloroplast genome and comparative genomics between other palm species. Based on sequence analyses, the chloroplast genome of kopyor coconut var. Green Dwarf was 158 462 bp in length and it had a typical quadripartite structure composed of a large single-copy (LSC; 86 198 bp), a small single-copy (SSC;17 712 bp) and two identical inverted repeat (IR; 27 276 bp). The genome consisted of 116 genes. Comparative analysis showed that the coding regions are more conserved than non-coding regions. The phylogenetic analysis showed that the coconut had a closed relationship with the Phoenix dactylifera. These genome characterizations could provide information to develop gene-specific markers, chloroplast genome mapping, plant breeding program, evolutionary study, and conservation of kopyor coconut.
Keyword: anotasi, genom kloroplas, kopyor, komparatif genomik

Judul: Genetic Similarity and Pollen Dispersal Analysis on Pati Kopyor Coconut Population Based on SSR and SNAP Marker Analysis
Abstrak: Pollination of female flower of kopyor coconut by male pollen of normal coconut could result in reduced kopyor fruit yield. Therefore, investigating pattern of pollen dispersal in a mix population of kopyor and normal coconut provenances would be beneficial. Moreover, evaluating genetic similarity among the studied population and their progenies would also beneficial for predicting the quality of produced seed nuts. The objectives of this experiment were : (1) to evaluated genetic similarity of the kopyor coconut parents population and their progenies, (2) to evaluate pattern of pollen dispersal among mix population of kopyor and normal fruit producing coconut in Pati, Central Java, (3) evaluated relevancy of pollen dispersal among mix population with their kopyor fruit yield. There were 95 adult palms evaluated as male parent candidate and 84 seeds harvested from 15 selected female parents as progeny population. The female parents were selected based on their high productivity from field evaluation. All population was used for genetic structure and similarity analysis and also pollen dispersal. Every adult palms were numbered using a marker and noted for the coordinate position using GPS. This research consisted of two stages, the first analyzed of genetic similarity among individual of adult plants and their progenies, and the second analyzed the pollen dispersal using molecular markers SSR and SNAP. The analyses of the genetic similarities were initiated with primer screening. Among 36 SSR loci tested, 32 loci resulted in a (+) product when they were used to amplify coconut DNA and only CnCir_B12, CnCir_86, CnCir_87 and CnCir_56 resulted in polymorphic SSR markers. Moreover, SNAP locus corresponding to position 14 of SNP of coconut sucrose synthase gene were also used. These loci were used to genotype candidate parents and progenies population. Results of the experiment indicated the average of allele per locus and average of PIC were 4.5 and 0.46, respectively. Cluster analysis using DICE coefficient based on molecular data resulted in an estimate of intra population of adult palms similarity and intra population of progenies were at least 18% and 43%, respectively. Intra population of progenies were more closely related than intra population of adult palms. Results of STRUCTURE analysis grouped most of the individuals into either Tall, Dwarf or Hybrid types, as they were suspected based on the morphology of the palms. However, a number of individuals grouped as Tall, and some as Dwarf based on their morphology, were actually identified as Hybrids based on alleles constitutions of the evaluated markers. The objectives of the second experiment were to evaluate pollen dispersal among coconut provenances using SSR and SNAP markers and its effects on kopyor fruit yield. Four SSR markers and one SNAP marker were used to genotype 95 provenances and 84 progenies harvested from 15 female parents. Parent-offspring relationships were determined based on genotype data using CERVUS software. The distances between male and female parents trees were calculated based on the GPS data after male parents identification. Results of the experiment indicated self-pollinations occurred in a number o sampled female parents since the distance of pollen dispersal was 0 m. Meanwhile, the furthest distance
Keyword: dwarf coconut, genetic similarity, genetic structure, pollination, tall coconut

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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