Studies on the Mechanism of Biological Control of Bacterial Wilt Disease of Tomato by Pseudomonas fluorescens PfG32

博士論文 (Doctoral dissertation)doctoral thesi

Keragaman Genotipik dan Fenotipik 48 Aksesi Kedelai Introduksi Asal Cina

Sebagai salah satu komoditas tanaman pangan penting di Indonesia setelah padi dan jagung, kedelai memerlukan upaya peningkatan keragaman genetik dengan cara introduksi aksesi dari negara lain terutama Cina sebagai salah satu negara asal kedelai di dunia. Marka simple sequence repeat (SSR) dapat digunakan untuk analisis keragaman genetik antaraksesi kedelai introduksi. Tujuan penelitian ini adalah mempelajari keragaman genotipik dan fenotipik 48 aksesi kedelai introduksi asal Cina menggunakan 15 marka SSR. Analisis DNA dilakukan menggunakan PCR dan data hasil PCR menggunakan marka SSR dianalisis menggunakan perangkat lunak XLSTAT, NTSYS, dan PowerMarker. Data karakter morfologis diperoleh dari basis data Germplasm Resources Information Network (GRIN), United States Department of Agriculture (USDA) (www.ars-grin.gov). Data ini digunakan sebagai data keragaman fenotipik yang diperlukan untuk menunjang hasil karakterisasi molekuler. Hasil penelitian menunjukkan bahwa terdapat keragaman karakter morfologis dan molekuler antaraksesi kedelai yang dipelajari. Berdasarkan hasil analisis komponen utama, karakter tinggi tanaman, bobot 100 biji, hasil biji, warna pusar biji, warna trikoma, warna bunga, dan warna polong berkontribusi besar terhadap keragaman total. Analisis molekuler menggunakan marka SSR menunjukkan bahwa terdapat variasi alel yang cukup tinggi (9–25 alel) di antara aksesi kedelai dengan rerata jumlah alel 15,6, sedangkan rerata nilai Polymorphism Information Content (PIC) sebesar 0,89 (0,84–0,94). Seluruh marka SSR memiliki nilai PIC>0,5 yang menunjukkan bahwa marka tersebut informatif untuk studi keragaman genetik kedelai dengan rerata nilai diversitas gen sebesar 0,90. Hasil analisis filogenetik dan analisis koordinat utama menunjukkan bahwa 48 aksesi tersebut mengelompok menjadi tiga dengan koefisien kemiripan 0,84. Pada penelitian ini dilakukan pula uji asosiasi antara marka SSR dan karakter morfologis. Asosiasi yang signifikan ditemukan pada tujuh lokus marka SSR. Persentase keragaman total yang dapat dijelaskan oleh marka SSR tersebut, yaitu 17,25–78,45%. Marka GMES2225 dan Sat_286 berasosiasi dengan warna kulit biji, sedangkan marka GmF35H berasosiasi dengan tinggi tanaman. Informasi keragaman genetik akan sangat bermanfaat sebagai langkah awal untuk kegiatan seleksi tetua persilangan dengan sifat yang diinginkan dalam membantu program pemuliaan kedelai di Indonesia

GROWTH IMPROVEMENT OF TOMATO WITH THE APPLICATION OF BACTERIAL ISOLATES PRODUCING INDOLE ACETIC ACID (IAA) AND PHOSPHATE SOLUBILIZER

Soil bacteria have important roles in biogeochemical cycle for soil fertility and have been manipulated for ecologically-friendly crop production.  The search for beneficial association between microbes and plants for promoting growth and health should be studied for tomato growth improvement. The study aimed to  evaluate 19 microbial isolates which produced indole acetic acid (IAA) affecting growth and development of tomato (Palupi variety), and  molecularly identify the most effective isolates in improving tomato growth based on 16s rDNA sequences. The experiment was conducted in pots using a complete randomized design with three replications. The parameters observed included plant height, plant dry weight, root length, root dry weight, and fruit fresh weight.  The isolates that significantly improved tomato growth were molecularly identified using 16s rRNA sequence. The phenotypic properties such as IAA content and phosphate solubilizing index (PI) of the superior isolates were determined. Results showed that the application of bacterial isolates on tomato significantly increased plant dry weight and fruit yield. From 19 isolates tested, Aj 3.7.1.14 significantly increased plant dry weight, root length, and fruit yield. This isolate produced IAA of about 14.77 ppm and PI of 1.86.  Molecular analysis on Aj 3.7.1.14 demonstrated that the isolate had 89% similarity to Pseudomonas fragi. The identified P. fragi was found to be the most effective isolate for improving tomato growth and fruit yield. Another isolate, Bacillus amyloliquefaciens was found to promote root length, root dry weight, and fruit yield. These isolates are potential to be further investigated for field trial

Genetic Diversity of Jatropha spp. Germplasm Based on Morphological and Molecular Markers

Germplasm of Jatropha spp. with high genetic diversity is needed to develop a new superior variety of Jatropha spp. Morphological and molecular characterizations are important to support development of their superior hybrid varieties. The aims of this study were to identify Jatropha spp. accesion potential for genetic improvement using morphological characters and analyze their genetic diversity using SSR markers. A total of eight genotypes of Jatropha spp. originated from several localities in Indonesia and Thailand was observed. Results showed that accessions of Jatropha spp. were varied in morphological and molecular characters. Based on principle component analysis, characters of stem color, leaf veins, leaf shapes, flower position, total branch number, productive branch number, petiole color, and petal color contributed most to the total diversity. Based on oil seed content, potential accessions identified for further genetic improvement were J. podagrica (34.63%) and J. curcas (29.64%). The results of molecular analysis showed that high allele variation (3–7 alleles) was observed among Jatropha spp. accessions with an average allele number of 4.12 and the average Polymorphism Information Content (PIC) value was 0.57 (0.46–0.77). Three SSR markers showed PIC value >0.5 indicating that these markers were informative for genetic diversity detection of Jatropha spp. The phylogenetic analysis showed that seven accessions of Jatropha spp. could be divided in two groups at similarity coefficent of 0.53. Results of genetic diversity analysis in this study should be useful for proper identification and selection for appropriate parents to assist in breeding of Jatropha spp. in Indonesia

Keragaman Genotipik dan Fenotipik 48 Aksesi Kedelai Introduksi Asal Cina

Sebagai salah satu komoditas tanaman pangan penting di Indonesia setelah padi dan jagung, kedelai memerlukan upaya peningkatan keragaman genetik dengan cara introduksi aksesi dari negara lain terutama Cina sebagai salah satu negara asal kedelai di dunia. Marka simple sequence repeat (SSR) dapat digunakan untuk analisis keragaman genetik antaraksesi kedelai introduksi. Tujuan penelitian ini adalah mempelajari keragaman genotipik dan fenotipik 48 aksesi kedelai introduksi asal Cina menggunakan 15 marka SSR. Analisis DNA dilakukan menggunakan PCR dan data hasil PCR menggunakan marka SSR dianalisis menggunakan perangkat lunak XLSTAT, NTSYS, dan PowerMarker. Data karakter morfologis diperoleh dari basis data Germplasm Resources Information Network (GRIN), United States Department of Agriculture (USDA) (www.ars-grin.gov). Data ini digunakan sebagai data keragaman fenotipik yang diperlukan untuk menunjang hasil karakterisasi molekuler. Hasil penelitian menunjukkan bahwa terdapat keragaman karakter morfologis dan molekuler antaraksesi kedelai yang dipelajari. Berdasarkan hasil analisis komponen utama, karakter tinggi tanaman, bobot 100 biji, hasil biji, warna pusar biji, warna trikoma, warna bunga, dan warna polong berkontribusi besar terhadap keragaman total. Analisis molekuler menggunakan marka SSR menunjukkan bahwa terdapat variasi alel yang cukup tinggi (9–25 alel) di antara aksesi kedelai dengan rerata jumlah alel 15,6, sedangkan rerata nilai Polymorphism Information Content (PIC) sebesar 0,89 (0,84–0,94). Seluruh marka SSR memiliki nilai PIC>0,5 yang menunjukkan bahwa marka tersebut informatif untuk studi keragaman genetik kedelai dengan rerata nilai diversitas gen sebesar 0,90. Hasil analisis filogenetik dan analisis koordinat utama menunjukkan bahwa 48 aksesi tersebut mengelompok menjadi tiga dengan koefisien kemiripan 0,84. Pada penelitian ini dilakukan pula uji asosiasi antara marka SSR dan karakter morfologis. Asosiasi yang signifikan ditemukan pada tujuh lokus marka SSR. Persentase keragaman total yang dapat dijelaskan oleh marka SSR tersebut, yaitu 17,25–78,45%. Marka GMES2225 dan Sat_286 berasosiasi dengan warna kulit biji, sedangkan marka GmF35H berasosiasi dengan tinggi tanaman. Informasi keragaman genetik akan sangat bermanfaat sebagai langkah awal untuk kegiatan seleksi tetua persilangan dengan sifat yang diinginkan dalam membantu program pemuliaan kedelai di Indonesia

Diversity and Population Structure of Local Rice Varieties from Indonesia Revealed by SSR Markers

Indonesia's local rice varieties (Oryza sativa L.) have a wide range of diversity that can be valuable sources for crop improvement with molecular markers. This study investigated local rice varieties' genetic diversity and population structure using simple sequence repeat (SSR) markers. The SSR markers demonstrated their informativeness for genotypic characterization as represented by the gene diversity indices and polymorphic information content. The UPGMA dendrogram divided 63 varieties into two distinct clusters with different levels of sub-grouping and the tendency according to their origins, as supported by PCoA. In contrast, PCA of these varieties according to agro-morphological traits was scattered in all quadrants. Thus, DNA level variation analyzed by SSR seems to complement the phenotypic traits, which were not well structured and revealed significant genetic diversity among varieties, within, and among populations (P<0.01). The pattern of grouping structure analysis of total varieties into two subpopulations is similar to the dendrogram according to SSR markers but better resembles the pedigree information of the set local varieties. These findings have implied their importance in rice breeding for genetic improvement, maintenance, and management of local genetic resources in Indonesia

DEGRADASI DINDING SEL Phytophthora capsici OLEH ENZIM KARBOSI METIL SELULASE ASAL Trichoderma harzianum

&lt;p&gt;Phytophthora capsici Leonian adalah patogen penyebab penyakit busuk pangkal batang lada (Piper nigrum L). Trichoderma harzianum Rifai merupakan agen hayati yang cfektif dan menyebabkan lisis miselia P. capsici. Penelitian ini bertujuan unluk mcngc(ahui peran enzim karboksimetilselulase (CMC-ase) yang diproduksi oleh T. harzianum dalam mendegradasi dinding sel P capsici. Penelitian terdiri atas tiga aktivitas yaitu (a) deteksi produksi enzim CMC-ase, (b) hidrolisis dinding sel P. capsici. dan (c) penggunaan siapan kasar dinding sel (SKDS) P. capsici oleh T. harzianum sebagai satu-satunya sumber karbon dalam media tumbuhnya Aktivitas enzim dideleksi secara kualitatif dengan membandingkan zona bening yang terbentuk pada medium karboksi metil selulosa (CMC) yang diperlakukan dengan satu tetcs iltrat kultur 7 harzianum dan diwarnai dengan larulan congo red, sedangkan aktivitas CMC-ase secara kuantitatif diukur sebagai nilai setara glukosa yang terlepas dari substrat setelah diinkubasi dengan ekstrak kasar CMC-ase. Enzim CMC-ase dickstrak dari kultur filtrat T. harzianum F.51 melalui pengendapan protein dengan 85% ammonium sulfat pada suhu 4°C diikuti dengan sentrifusi dan dialisis. Aktivitas spcsifik enzim tersebut dalam mendegradasi CMC (30,29 unif//g protein) lebih rendah dari aktivitas enzim selulase komersial (97.18 unit/^g protein). Enzim selulase komcrsial dan ekstrak enzim dari kultur 7 harzianum juga dapat menghidrolisis SKDS P. capsici N2 dengan aktivitas masing-masing 31.18 unit dan 19.26 unit. Isolat F-51 tumbuh dan menghasilkan aktivitas enzim serupa manakala karboksimclil selulosa pada media tumbuh diganti dengan SKDS sebagai sumber karbon tunggal Hasil ini menunjukkan bahwa CMC-ase berperan penting dalam mckanisme antagonis T. harzianum terhadap /' capsici. Penelitian lebih lanjut dalam mckanisme produksi enzim ini berpeluang untuk meningkatkan potensi agen hayati.&lt;/p&gt;&lt;p&gt;Kata kunci : Piper nigrum L., Trichoderma harzianum Rifai, Phytophthora capsici. karbosimctilsclulasc, agen hayati&lt;/p&gt;&lt;p&gt; &lt;/p&gt;&lt;p&gt;&lt;strong&gt;ABSTRACT&lt;/strong&gt;&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Degradation of cell wall of Phytophthora capsici N2 by carboxy methyl cellulose &amp;lt;;/ Trichoderma harzianum ES1&lt;/strong&gt;&lt;/p&gt;&lt;p&gt;Phytophthora capsici l-eonian is a causal agent of foot rot disease on black pepper (Piper nigrum L ). Trichoderma harzianum Rifai is an effective biocontrol agent and causes lyscs on P. capsici mycelium This experiment was aimed to study the role of carboxymethylccllulose (CMC- ase) produced by T. harzianum in degrading P. capsici cell wall. The experiment was composed in three activities (a) detection of the CMC-ase enzyme production, (b) degradation of P. capsici cell wall by crude extract of the enzyme, and (c) utilization of crude cell wall preparation (cwp) of P. capsici by T. harzianum as single carbon source in its growth medium CMC-ase activity was detected qualitatively on carboxymethylccllulose (CMC) medium, and quantitatively it was measured as glucose equivalent released from substrate after treated with crude extract of CMC-ase. CMC-ase was extracted from culture iltrate of T. harzianum F-51 by precipitation of protein with 85% ammonium sulphate at 4°C followed by dialysis with distilled water and liophyllizcd. Activity of the extracted enzyme on degradation of CMC (30.29 unil-'/jg protein) was lower than activity of commercial cellulose (97.18 united g protein) Commercial cclullosc and the extracted enzyme also degraded crude cell wall prepared (CWP) from P. capsici N2 as indicated with the presence of glucose equivalent released from CWP after incubation with the enzyme; with specific activity of 31.18 unit and 19.26 unit respectively. Trichoderma harzianum grown in medium suplemented with the crude cell wall of P. capsici as a single carbon source produced CMC-ase. Those results indicated that CMC-ase has important role on parasitism of T. harzianum on P. capsici Further investigation is required to elucidate mechanism of production of CMC-ase in T. harzianum for improvement of biocontrol activity of the fungus.&lt;/p&gt;&lt;p&gt;Key words: Piper nigrum L., Trichoderma harzianum Rifai, Phytophthora capsici, carboxymethylcellulosc, biocontrol&lt;/p&gt;</jats:p