Judul: Molecular Characterization of Resistance Banana Cultivars to Panama Wilt Disease Caused by Fusarium oxysporum f.sp. cubense
Abstrak: Sustainability of banana and plantain in Indonesia encounters the development of banana pests and diseases that dramatically decreased national banana production. Panama wilt disease caused by Fusarium oxysporum f.sp. cubense (FOC) is one of major banana diseases that infected almost all of banana plantation in Indonesia. A series of experiments were carried out to isolate, characterize resistance gene analogues (RGAs) and defense gene analogues (DGAs), and to develop molecular markers for disease resistance against fusarium wilt. The experiment was started by the assessment of resistance banana cultivars against FOC tropical race-4 (TR4), and selected two cultivars showed resistant to FOC i.e. Calcuta-4 and Klutuk Wulung. From those selected cultivars and one resistant cultivar, Rejang, 17 RGAs were isolated and characterized and showed high sequence identity to NBS-LRR. The RGA sequences were designated as MNBS1-MNBS17. Based on phylogenetic analysis, the RGAs were classified into four groups. First group contained 14 RGA sequences (MNBS1-MNBS14), and the other three groups contained one sequence MNBS15, MNBS16, and MNBS17, respectively. The isolation and characterization of DGA (chitinase and β-1,3-glucanase genes) were carried out using local banana cultivars. Eight putative chitinase sequences (586 bp in length) were isolated from Rejang, Klutuk Wulung, Kepok, Ambon Hijau and Barangan. The sequences were showed high identity (90 %) to banana class II chitinase gene and coded by MaChi. Four putative β-1,3- glucanase sequences (788 bp in length) were isolated and characterized from Rejang, Klutuk Wulung, Ambon Hijau and Barangan. The sequences shared 99 % identity to banana β-1,3-glucanase, and designated as MaGlu. Based on SNP identification, it was revealed that RGA sequences from Rejang (MNBS2-MNBS5) and Calcuta-4 (MNBS6-MNBS14) contained 16 and 9 putative SNPs, respectively. Based on SNP analysis, RGA sequences of Rejang and Calcuta-4 generated 4 and 8 haplotypes, respectively. Twenty two SNPs were identified from 8 chitinase fragments and generated 8 haplotypes, while 8 putative SNPs were identified from 4 β-1,3-glucanase fragments and generated 4 haplotypes. SNAP markers were developed based on non synonymous SNPs identified from RGA (MNBS) and DGA (chitinase and β-1,3-glucanase) sequences. Using PCR technique and allel specific primers approaches, 7 loci based on RGA and DGA sequences were selected as SNAP markers for FOC resistance banana cultivars, there were SNP4_MNBS, SNP2_MChi, SNP6_MChi, SNP8_MChi, SNP10_MChi, SNP11_MChi, and SNP1_MGlu. However, the use of SNP1_MGlu locus can be omitted, because without SNP1_MGlu primers, the grouping of banana cultivar base on FOC resistance will be better.
Keyword: DGA, haplotype, RGA, SNP, SNAP marker

Judul: Density of Fusarium oxysporum and Phytonematodes of Banana Plantation at PTPN VIII Parakansalak
Abstrak: Banana is the most consumed of horticulture commodity plants. The government and society also cultivate some banana varieties such as Cavendish, Raja Buluh, and Barangan. Considering the production demand is also increased, the government also implemented the fruit self-sufficiency program in the Minister of Plantation Regulation Number 86/Permentan/OT.140/8/2013. Therefore, BUMN began to cultivate banana plants in several plantation sectors owned by the company. During the banana plants’ cultivation process, many problems are faced, one of which is the banana plant attacked by a pathogen. The primary pathogen that attacks the banana plant is Fusarium oxysporum causing the fusarium wilt. F. oxysporum is categorized as the soil-borne pathogen that infected banana plant through the wound of plant tissue. The wound found in the plants’ root could be identified as the natural wound result of plant growth process or caused by several vectors such as nematode. Many researchers reported that nematode has a significant role in the process of fusarium wilt disease, which is caused by F. oxysporum. This research aims to observe the abundance of F. oxysporum and phytonematode founded in the banana plant and the relation of both pathogens in causing fusarium wilt. The hypothesis of this research that phytonematode founded a positive correlation toward the severity of fusarium wilt disease. The method used in this research was observing the severity of fusarium wilt of banana plant Emas Kirana varieties that’s most know as Mas Kirana. Based on the predetermined score rating. Soil and root samples was collected which was conducted by purposive method. From every block, samples were taken from 5 different clumps with different disease severities. Samples were collected from 5 different blocks as replication. Sample from 5 different blocks with the same disease severity were then mix for future research. The abundance of F. oxysporum and phytonematodes were calculated by applying conventional and molecular methods. Isolation of phytonematodes from soil were conducted by extracting the phytonematodes from soil samples by using a floatation centrifugation method. Identification of phytonematodes to the genus level were carried out by observing the morphology of their anterior to posterior. The abundance of phytonematodes then calculated under microscope by placed 1 ml of phytonematode suspension on cyrus dish, and repeated 3 times. Furthermore, the number of phytonematodes was calculated using the formula of absolute population calculation. Calculation of F. oxysporum was conducted by two ways, conventional (growing on synthetic media) and molecular methods. The conventional method was performed by serial dilution of soil samples, followed by cultured on Martin Agar, and incubated for 3-4 days before counting the number of F. oxysporum colonies grow on medium. To prove that F. oxysporum growing on Martin Agar is Foc, molecular identification was carried out using specific primer Foc1/F (5’-CAGGGGATGTATGAGGAGGCT-3’) and Foc2/R (3’-GTGACAGCGTCGTCTAGTTCC-5’). PCR result then visualized on agarose gels. Real-time PCR technique was also conducted to count the abundance of F. oxysporum from soil samples. The standard curve construction is started by isolating the competent bacteria cell of DH5 alpha that has been added the synthesis gene of F. oxysporum. The cell transformation is becoming plasmid that
Keyword: Panama disease, real-time PCR, tropical race 4

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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