Sago palm ( Metroxylon sagu Rottb.) is one of the most productive carbohydrate-producing crops. Unfortunately, only limited information regarding sago palm genetics is available. This study aimed to develop simple sequence repeat (SSR) markers using sago palm NGS genomic data and use these markers to evaluate the genetic diversity of sago palm from Indonesia. De novo assembly of partial sago palm genomic data and subsequent SSR mining identified 29,953 contigs containing 31,659 perfect SSR loci and 31,578 contigs with 33,576 imperfect SSR loci. The perfect SSR loci density was 132.57/Mb, and AG, AAG and AAAT were the most frequent SSR motifs. Five hundred perfect SSR loci were randomly selected and used for designing SSR primers; 93 SSR primer pairs were identified. After synteny analysis using rice genome sequences, 20 primer pairs were validated using 11 sago palm accessions, and seven primers generated polymorphic alleles. Genetic diversity analysis of 41 sago palm accessions from across Indonesia using polymorphic SSR loci indicated the presence of three clusters. These results demonstrated the success of SSR identification and marker development for sago palm based on NGS genome data, which can be further used for assisting sago palm breeding in the future.

<p>ABSTRACT</p><p><br />This research was about in vitro propagation of Pitcher Plant Nepenthes mirabilis. The aims of this research were to determine: 1) the influence of kind and concentration of in vitro medium and also plant growth regulator on germination of Nepenthes mirabilis, 2)the effect of BAP and NAA on shoot <br />multiplication of N. mirabilis. This research consisted of three experiments and all experiments used Completely Randomized Design. On the first experiment MS (Murashige and Skoog) and KC (Knudson C) were used, i.e. full (1), three-fourth (3/4), one-half (1/2) and one-fourth (1/4) Salt Concentration. On the second experiment 10 composition media were used, i.e. ½ MS, ½ MS+TDZ 0.01 ppm, ½ MS+IAA 0.1 ppm, ½ MS+GA3 10 ppm, ½ MS+150 ml coconut water, 1/4KC, 1/4 KC+TDZ 0.01 ppm, ¼KC+IAA 0.1 ppm, 1/4KC+GA3 10 ppm and 1/4KC+ 150 ml coconut water. On the third experiment BAP with 0, 0.5, 1, 2 ppm and NAA 0, 0.1, 0.2, 0.5 ppm were used as factor for shoot multiplication.The result showed that KC medium was the best medium for germination percentage of N. mirabilis (64%). MS or KC medium with ½ or ¼ salt concentration was the suitable for germinating time of N. mirabilis (average 39 days after showing). Adding of TDZ, IAA, and GA3 significantly <br />increased germination percentage (70 – 90%) and decreased germinating time (27 – 38 days after showing). Culture growth on medium with BAP 0 - 1 ppm was the best medium for shoot and leave induction. The best medium for root growth of N. mirabilis was MS or KC medium without NAA.</p><p><br />Key words: Nepenthes mirabilis, MS, KC, TDZ, IAA, GA3, BAP, NAA, in vitro propagation, medium</p>

Abstract. Pesik A, Efendi D, Novarianto H, Dinarti D, Sudarsono S. 2017. Development of SNAP markers based on nucleotide variability of WRKY genes in coconut and their validation using multiplex . Development of molecular markers benefits coconut breeding program. The availability of DNA sequences for coconuts opens the new possibility of developing molecular markers such as single nucleotide amplified polymorphism (SNAP). The study aimed to evaluate nucleotide sequence diversities of WRKY gene in the GenBank database, design gene specific primers for generating WRKY gene specific SNAP markers, optimize multiplex PCR technique and validate SNAP marker effectiveness for evaluating Kopyor coconut germplasm. Based on 35 sequences data of coconut WRKY genes that are available in the GenBank database, we have identified eight informative SNPs and used them to generate SNP-specific primers. We have designed sixteen primer pairs and validated them using singleplex PCR. Subsequently, we optimized the Ta and primer concentrations either for duplex or triplex PCR. Duplex PCR using two sets of primer pairs was more reliable for genotyping Kopyor coconut germplasm than triplex PCR. We have successfully demonstrated the duplex PCR for genotyping Banten Tall, Jember Tall, Kalianda Tall, Pati Dwarf and Sumenep Tall Kopyor coconuts. Therefore, one may use the developed SNAP markers as a simple alternative of co-dominant markers for genetic analysis of coconuts. One may use the developed SNAP markers to investigate the possible association between markers and Kopyor endosperm and other relevant phenotypes in coconuts.

Corynespora cassiicola is an important pathogen causing Corynespora leaf fall disease on the rubber tree. Analysis of virulence, rDNA-ITS sequence and identification of cas gene were undertaken to investigate the effect of agro-climatic conditions and host rubber clones to virulence of 23 C. cassiicola isolates on six clones (RRIC 100, BPM 24, BPM 1, PB 260, GT 1 and RRIM 600) and to observed the evolution pattern of C. cassiicola isolates. Virulence analysis showed that there is an interaction between isolates and clones, indicating the differences of each isolates virulence to six clones. Agro-climatic conditions and host clones influenced the virulence of isolates and rDNA-ITS sequence variation. Analysis of rDNA-ITS showed that there were three of Single Nucleotide Polymorphism (SNP) that separated of isolates into 5 haplotypes. Most of the isolates belonging to the haplotype 1. Phylogenetic analysis indicated that C. cassiicola have a high diversity, however the clustering did not indicate country and host species of isolates. This information will be very useful on developing strategies of disease management and rubber plant breeding towards resistance to CLF disease.

Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi.