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"Genes related to starch synthesis and the metabolism contribute to a variety of physicochemical properties thatdetermine the eating/cooking qualities of rice. Our previous study suggested that a set of molecular markers was able toestimate the eating quality of japonica rice. The present study reports the genetic diversity of 22 japonica rice varietiesbased on markers corresponding to starch synthesizing genes. The mean of the polymorphic information content (PIC:0.135) value and the diversity index (0.171) indicated a low genetic diversity in these varieties. The phylogenetic treeclearly demonstrated three main clusters: 1) cluster I contained seven varieties with similar physicochemical properties;2) cluster II only showed a Japanese variety, Koshihikari, and 3) cluster III included the most Korean varieties (14varieties). This phylogenetic analysis did not completely represent the physicochemical properties differentiation of thejaponica varieties, although it did reveal an initial clue to the close relationship between Korean rice and the Japaneseand Chinese varieties. Notably, these markers were also able to identify a premium japonica rice. The molecularmarkers and information concerning the genetic relationship would be useful in improving the japonica rice along withits starch quality of in breeding program.Keragaman Genetik Padi Japonica berdasarkan Marka terkait Gen Sintesis Pati. Gen terkait sintesis danmetabolism pati berkontribusi pada berbagai sifat fisiko-kimia yang menentukan mutu rasa dan hasil masak (cooking)beras. Penelitian sebelumnya menunjukkan bahwa satu set marka molekuler mampu memprediksi mutu rasa berasjaponica. Pada studi ini dilaporka keragaman genetik 22 varietas padi japonica berdasarkan marka untuk gen-genpensintesis pati. Rata-rata nilai polymorphic information content (PIC:0,135) dan indeks keragaman (0,171)menunjukkan keragaman genetik yang rendah dalam varietas padi ini. Pohon filogenetik menunjukkan tiga kelompokutama yang dibentuk: 1) klaster I terdiri dari tujuh varietas dengan sifat fisikokimia yang mirip; 2) klaster II hanyaterdiri dari verietas premium Jepang, Koshihikari, dan 3) klaster III mengelompokkan sebagian besar varietas Korea (14varietas). Analisis filogenetik ini belum sepenuhnya menggambarkan diferensiasi varietas japonica berdasarkan sifatfisiko-kimia, namun hasil ini mengungkapkan petunjuk awal korelasi yang erat antara padi Korea dengan varietasJepang dan Cina. Marka-marka tersebut juga mampu mengidentifikasi beras premium japonica. Marka molekuler daninformasi kekerabatan genetik ini akan berguna dalam membantu mengembangkan padi japonica terkait dengan mutupati dalam program pemuliaan"

"Keragaman Genetik Core Collection Isolat Bacterial Leaf Blight (Xanthomonas oryzae pv. oryzae) Indonesia berdasarkan Marka Molekular VNTR dan avrXa7. Bacterial leaf blight (BLB) adalah salah satu penyakit utama padi yang disebabkan oleh bakteri pathogen Xanthomonas oryzae pv. oryzae. Penelitian ini bertujuan untuk mengidentifikasi dan menganalisis keragaman genetik 18 isolat isolates yang terdiri dari 7 ras dan 11 haplotipe yang berasal dari beberapa lokasi koleksi di Indonesia. Analisis keragaman genetik dilakukan menggunakan marka VNTR (Variable Number of Tandem Repeat) dan marka gen avrxa7. Pola pita DNA hasil amplifikasi digunakan sebagai data input biner untuk membuat dendogram keragaman. Berdasarkan dendogram tersebut, terdapat tiga kelompok genotipe X. oryzae pv. oryzae dengan tingkat virulensi yang berbeda. Ras VII (IXO80_021) yang termasuk dalam kelompok I dan Ras VIII-A (IXO 80_024) yang termasuk dalam kelompok II merupakan ras BLB yang tidak virulen. Sedangkan kelompok III merupakan kelompok ras dan haplotipe yang bersifat virulen.

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Bacterial leaf blight (BLB) is one of the major diseases in rice caused by Xanthomonas oryzae pv. oryzae. This study aimed to identify and analyze the genetic diversity of 18 BLB isolates that consist of 7 races and 11 haplotypes from various locations in Indonesia. The genetic diversity analysis was conducted on the basis of the VNTR (Variable Number of Tandem Repeat) markers and the avrxa7 gene marker. The banding pattern of the amplification product was made into binary data as input for the construction of a dendogram. Based on the dendogram, three X. oryzae pv. oryzae genotype groups with different virulence levels were formed. The VII (IXO80_021) race of X. oryzae pv. oryzae genotype group I and the VIII-A (IXO 80_024) race of genotype group II were avirulent, whereas the races and haplotypes of genotype group III were virulent."

"ABSTRACTTanaman obat dipercaya oleh masyarakat Indonesia memiliki berbagai khasiat untuk menyembuhkan penyakit. Senyawa aktif yangada pada tanaman dapat berasal dari metabolit sekunder ataudari bakteri endofit dan filosfer yang hidup berasosiasidengan tanaman obat. Sebanyak 18 isolat bakteri endofit dan 32 isolat bakteri filosfer telah dimurnikan dari tanaman Citrus sp.,Pluchea indica, Curcuma longa, Nothopanax scuttelarium,Piper crocatum, dan Andrographis paniculata.Sebanyak 72% isolat bakteri endofit memiliki aktivitasproteolitik dan sebanyak 11% memiliki aktivitas lipolitik.Bakteri filosfer yang memiliki aktivitas proteolitik sebanyak 59% dan sebanyak 19% memiliki aktivitas lipolitik. Analisis keragaman bakteri tersebut dilakukan dengan teknik amplified ribosomal DNArestriction analysis (ARDRA) dan digesti gen penyandi 16S rRNA dengan menggunakan enzim restriksi endonuklease MspI, RsaI, danSau961. Keragaman bakteri endofit dan filosfer pada beberapa sampel tanaman obat cukup tinggi. Bakteri yang diisolasi daritanaman obat yang sama tidak selalu memiliki kekerabatangenetik yang dekat. Sementara itu, bakteri asal tanaman P.indicamemiliki kekerabatan yang cukup dekat satu sama lain.

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AbstractHerbal plants have been believed by Indonesians to be an alternative medicine to treat illnesses. The bioactivecompounds in the plant can be derived from secondary metabolites or from endophytic and phyllosphere bacteria which coexist within medicinal plants. A total of 18 endophytic bacteria and 32 phyllosphere bacteria were isolated from the herbal plants ofCitrus sp., Pluchea indica, Curcuma longa, Nothopanax scuttelarium, Piper rocatum, and Andrographis paniculata. About 72% of endophytic bacteria isolates have proteolytic activity and about 11% havelipolytic activity. On the other hand, about 59% of phyllosphere bacteria isolates have proteolytic activity and about 19% have lipolytic activity. Phylogenetic diversity analysis was conducted by using the amplified ribosomal DNA restriction analysis (ARDRA) method and the sequence of 16S rDNA was digested with endonuclease restrictionenzymes: MspI, RsaI, and Sau961. The diversity of endophytic and phyllosphere bacterium from the samples of herbal plants was high. Bacteria isolated from the same herbal plant does not always have a close genetic relationship except for the bacteria isolated from the P. indica plant which showed a close genetic relationship with each other."

"Bacterial leaf blight (BLB) is one of the major diseases in rice caused by Xanthomonas oryzae pv. oryzae. This studyaimed to identify and analyze the genetic diversity of 18 BLB isolates that consist of 7 races and 11 haplotypes fromvarious locations in Indonesia. The genetic diversity analysis was conducted on the basis of the VNTR (VariableNumber of Tandem Repeat) markers and the avrxa7 gene marker. The banding pattern of the amplification product wasmade into binary data as input for the construction of a dendogram. Based on the dendogram, three X. oryzae pv. oryzaegenotype groups with different virulence levels were formed. The VII (IXO80_021) race of X. oryzae pv. oryzaegenotype group I and the VIII-A (IXO 80_024) race of genotype group II were avirulent, whereas the races andhaplotypes of genotype group III were virulent.Keragaman Genetik Core Collection Isolat Bacterial Leaf Blight (Xanthomonas oryzae pv. oryzae) Indonesiaberdasarkan Marka Molekular VNTR dan avrXa7. Bacterial leaf blight (BLB) adalah salah satu penyakit utama padiyang disebabkan oleh bakteri pathogen Xanthomonas oryzae pv. oryzae. Penelitian ini bertujuan untuk mengidentifikasidan menganalisis keragaman genetik 18 isolat isolates yang terdiri dari 7 ras dan 11 haplotipe yang berasal daribeberapa lokasi koleksi di Indonesia. Analisis keragaman genetik dilakukan menggunakan marka VNTR (VariableNumber of Tandem Repeat) dan marka gen avrxa7. Pola pita DNA hasil amplifikasi digunakan sebagai data input bineruntuk membuat dendogram keragaman. Berdasarkan dendogram tersebut, terdapat tiga kelompok genotipe X. oryzaepv. oryzae dengan tingkat virulensi yang berbeda. Ras VII (IXO80_021) yang termasuk dalam kelompok I dan RasVIII-A (IXO 80_024) yang termasuk dalam kelompok II merupakan ras BLB yang tidak virulen. Sedangkan kelompokIII merupakan kelompok ras dan haplotipe yang bersifat virulen."

"Alstonia scholaris (L.) R.Br. is a popular timber and medicinal tree species in Indonesia.The species is valued for its quality light wood timber and for its medicinal properties. Information on its existing genetic potential is currently lacking. The present study was carried out to optimize PCR and to screen primers among accessions collected from different part of region in Indonesia using random amplified polymorphic DNA (RAPD) markers in order to suggest appropriate primer and PCR conditions used in A.scholaris. Results showed that 26 primers generated 575 scorable bands of which 524 (92 %) were polymorphic. Fourteen highly polymorphic primers (100% polymorphic) are recorded from 48 primer used, i.e.OPA-2, OPA-03, OPA-05, OPA-06, OPA-10,OPA-12, OPA-15, OPA-18, OPA-19, OPC-03, OPC-10, OPC-12, OPC-17, and OPN-14. Based on the RAPD markers, a dendrogram was constructed using the UPGMA method.The range of genetic distance was from 0.18-0.45.The molecular dara grouped the genotypes into three main clusters."