Dwinita Wikan Utami

A relative expression of Xa7 gene controlling bacterial leaf blight resistance in indonesian local rice population (Oryza sativa L.)

Discovery of new alleles at important gene loci through allele mining could support the rice improvement program to sustain national food security. Evaluation of the existing Indonesian local rice landraces is an important point to detect the potential of functional alleles. One of the bacterial leaf blight (BLB) resistance alleles, Xa7 was detected in Indonesian rice landrace germplasm, Parekaligolara. To validate this potential allele, field evaluation on the segregating population, expression analysis using real time RT-PCR, and sequencing were carried out. Two selected Parekaligolara progenies lines (F4 and F6) from double crosses with other selected landraces were clearly more resistant to a dominant Indonesian BLB, Race IV. Specific primers of Xa7-LD40 successfully amplified the alleles of F4 and F6 lines approximately 300 bp in length. The amplicon sequenced using vector-targeted primers, resulting 264 bp which were flanked between 602 and 866 bp sites. The translated sequence which produced 60 amino acids (open reading frame) ORF, showed homology with the encoding gene associated with the defense system to biotic stress, BTB/POZ. As integrated researches for many potential biotic and abiotic stresses alleles on Indonesian landraces germplasm, this outcome expectedly supports rice landraces utilization for developing of elite cultivars which survive on global changed conditions and benefiting to national food security.

Evaluasi dan Identifikasi Marka Penanda Gen Ketahanan Penyakit Hawar Daun Bakteri pada Padi Lokal Sulawesi Selatan

Abstract One of the limiting factors on rice production, especially in South Sulawesi, is the bacterial leaf blight (BLB) disease infection caused by Xanthomonas oryzae pv. oryzae (Xoo). The use of resistant variety is considered as the most effective method to control Xoo. Local cultivar could serve as resistance source for Xoo resistance. The objectives of this research were to evaluate and identify markers for Xoo resistance in rice local cultivars from South Sulawesi based on comparison with the resistance response of the differential varieties and association analysis between resistance phenotype and genotype of molecular markers. Three Xoo races (race III, IV, and VIII) were tested on IRBB differential lines and local cultivars. The genotype analysis was done by using the molecular marker linked to Xoo resistance. Meanwhile, the association analysis was done by combination analysis (U-joint) using generalized linear model (GLM). The resistance test result showed that single gene isogenic lines (IRBB 5, IRBB 7, and IRBB 21), multiple genes isogenic lines (IRBB 50, IRBB 52, IRBB 53, IRBB 54, IRBB 56, IRBB 58, IRBB 64, and IRBB 66), and Ase Andele accession were resistant to the three Xoo races. Association test obtained one significant marker that associated with the resistance to race III (marker Xa26-STS2), four markers significantly associated with the resistance to race IV (Xa1-STS15, Xa4-STS44, xa13-STS51, and Xa21-STS6), and two markers significantly associated with the resistance to race VIII (Xa7-STS57 and RM 20589). Abstrak Salah satu faktor pembatas produksi padi, di Sulawesi Selatan khususnya, adalah serangan penyakit hawar daun bakteri (HDB) yang disebabkan oleh Xanthomonas oryzae pv. oryzae (Xoo). Upaya yang dipandang efektif untuk mengendalikan penyakit HDB adalah penanaman varietas tahan. Perakitan varietas padi dengan menggunakan gen-gen tahan dari berbagai kultivar berpeluang menghasilkan varietas tahan HDB. Kultivar lokal berperan sebagai salah satu sumber keragaman genetik untuk beberapa sifat ketahanan penyakit. Penelitian ini bertujuan mengevaluasi dan mengidentifikasi marka penanda gen ketahanan penyakit hawar daun bakteri pada padi lokal Sulawesi Selatan berdasarkan sistem standar diferensial dan analisis molekuler. Analisis uji ketahanan fenotipe dilakukan menggunakan tiga ras HDB (ras III, IV, dan VIII) dan galur diferensial (galur IRBB). Analisis genotipe dilakukan menggunakan marka molekuler terkait ketahanan terhadap HDB yang ditampilkan sebagai dendrogram keragaman. Analisis asosiasi dilakukan dengan analisis gabungan (U-joint) menggunakan generalized linear model (GLM). Hasil pengujian ketahanan menunjukkan galur isogenik dengan gen tunggal (IRBB 5, IRBB 7, dan IRBB 21), galur isogenik dengan multipel gen (IRBB 50, IRBB 52, IRBB 53, IRBB 54, IRBB 56, IRBB 58, IRBB 64, dan IRBB 66), dan aksesi Ase Andele bersifat tahan terhadap ketiga ras uji. Dari uji asosiasi, diperoleh satu marka signifikan yang berasosiasi dengan ketahanan terhadap ras III (Xa26-STS2), empat marka signifikan berasosiasi dengan ketahanan terhadap ras IV (Xa1- STS15, Xa4-STS44, xa13-STS51, dan Xa21-STS6), dan dua marka signifikan berasosiasi dengan ketahanan terhadap ras VIII (Xa7-STS57 dan RM 20589). Kata kunci: Gen ketahanan, hawar

IDENTIFIKASI MARKA RGA (RESISTANCE GENE ANALOG) UNTUK SIFAT KETAHANAN BUSUK PANGKAL BATANG PADA PLASMA NUTFAH LADA (Piper nigrum)

Limbah hasil penyulingan tanaman atsiri berpotensi sebagai mulsa dan repelen (penolak) hama serangga, sehingga perlu dilakukan penelitian. Penelitian ini bertujuan untuk memanfaatkan mulsa dari limbah tanaman atsiri yang dikombinasikan dengan aplikasi pestisida nabati untuk mengendalikan Crocidolomia binotalis pada tanaman brokoli. Penelitian dilaksanakan di Kebun Percobaan Manoko, Balai Penelitian Tanaman Rempah dan Obat (Balittro) sejak Maret sampai Agustus 2011. Penelitian dirancang dalam acak kelompok, dengan sembilan perlakuan dan diulang tiga kali. Perlakuan terdiri dari limbah nilam dan serai wangi yang dikombinasikan dengan aplikasi insektisida nabati BP1 (formula minyak cengkeh, serai wangi dan temulawak) dan BP2 (formula minyak cengkeh, serai wangi dan jarak pagar) serta insektisida kimia sebagai pembanding, dan tanpa aplikasi (kontrol). Pengamatan dilakukan terhadap tingkat kerusakan tanaman akibat serangan hama C. binotalis, produksi tanaman, kadar N tanah dan populasi mikroba di dalam tanah sebelum tanam dan sesudah panen. Hasil penelitian menunjukkan bahwa kombinasi aplikasi limbah tanaman atsiri dengan insektisida nabati berbahan aktif eugenol, sitronellal dan xanthorizol (BP1) berbeda nyata positif dengan perlakuan kontrol tetapi berbeda nyata negatif dibandingkan dengan kombinasi aplikasi insektisida sintetis terhadap kerusakan akibat serangan C. binotalis. Perlakuan insektisida mampu memberikan kenaikan hasil 14% lebih tinggi dibanding kontrol. Kenaikan produksi yang tertinggi dihasilkan oleh perlakuan kombinasi aplikasi limbah nilam dengan insektisida sintetis yaitu sebesar 40%. Aplikasi limbah tanaman atsiri tidak menaikkan secara nyata unsur N, tetapi memberikan kontribusi yang nyata unsur K terutama aplikasi limbah nilam. Aplikasi limbah nilam berpengaruh terhadap pertumbuhan dan produksi brokoli.Upaya peningkatan produktivitas lada dapat dilakukan dengan penggunaan bahan tanaman unggul lokal. Tujuan dari penelitian ini adalah untuk mengetahui potensi hasil, komponen hasil dan mutu lada lokal asal Sukabumi dan varietas pembanding Petaling-1, di dua agroekologi berbeda, di kabupaten Sukabumi dan kabupaten Purwakarta. Pengamatan dilakukan pada 10% tanaman contoh dari tiap populasi, pada sifat hasil per pohon, komponen hasil dan mutu. Data dianalisis dengan uji t. Pertumbuhan, hasil, komponen hasil dan mutu lada kedua varietas secara umum lebih baik di Purwakarta dari pada di Sukabumi. Hasil uji t memperlihatkan bahwa hasil per pohon, karakter jumlah malai per tanaman, panjang malai, jumlah biji per malai, bobot malai dan panjang tangkai malai berbeda antara varietas lokal dengan varietas Petaling-1, dan lada lokal lebih baik dari Petaling-1. Hasil lada lokal per pohon di Purwakarta 2,79 kg, dan varietas Petaling-1, yaitu1,67 kg per pohon. Di Sukabumi hasil buah segar lada lokal juga lebih tinggi dari varietas Petaling-1 berturut-turut 2,13 kg dan 1,30 kg per pohon. Malai lada lokal 9-13,5 cm, dengan jumlah buah per malai 70-140 butir, lebih panjang dan lebih banyak dari malai Petaling-1 berturut-turut 5-9 cm, dan 20-60 butir. Mutu lada putih maupun lada hitam berbeda antar lokasi, dan mutu di Purwakarta lebih baik dari pada di Sukabumi. Di kedua lokasi, mutu lada lokal baik kadar minyak atsiri, oleoresin maupun piperin lebih baik dari Petaling-1. Bobot buah segar lada lokal sama dengan Petaling-1 sehingga cocok untuk diproses menjadi lada putih.Pemanfaatan limbah nilam hasil penyulingan masih sangat terbatas dan pada umumnya limbah tersebut digunakan sebagai tambahan bahan bakar penyulingan nilam. Untuk mengoptimalkan pemanfaatan limbah nilam tersebut sekaligus membantu mengatasi kebutuhan dan mahalnya pupuk buatan saat ini maka dilakukan sebuah percobaan pot di Balai Penelitian Tanaman Rempah dan Obat (Balittro) Bogor pada tahun 2008. Rancangan penelitian yang digunakan adalah Rancangan Acak Kelompok faktorial dengan tiga ulangan. Faktor pertama adalah tiga dosis pemupukan kompos limbah nilam masing-masing 0, 1,5 dan 3,0 kg pot-1 dan faktor kedua adalah tiga dosis pemupukan NPK masing-masing 0, 8, dan 16 g pot-1. Hasil penelitian menunjukkan bahwa aplikasi pupuk kompos maupun pupuk NPK mampu meningkatkan jumlah cabang primer. Aplikasi tiga kilogram kompos limbah nilam pot-1 meningkatkan bobot terna nilam secara nyata pada ketiga dosis NPK yang diberikan. Tingginya kadar N pada kompos limbah nilam (3,59%) menyebabkan kompos limbah nilam sangat efektif meningkatkan kesuburan pada tanah percobaan dan memperbaiki pertumbuhan tanaman nilam. Aplikasi pupuk kompos pada perlakuan tanpa pupuk NPK (K2P0) lebih baik dibanding perlakuan pupuk NPK tanpa kompos (K0P2). Kombinasi perlakuan pemupukan kompos dan NPK tertinggi (K2P2) mampu menghasilkan terna nilam segar tertinggi sebesar 335 g tanaman-1. Proses penyulingan dan pengomposan mampu menurunkan senyawa fenolik yang bersifat alelopatik dan toksik seperti asam koumarat, asam adipat, asam sinapat, dan asam hidroksi benzoat pada daun nilam. Kadar minyak nilam varietas Sidikalang beragam dengan kisaran antara 2,39 sampai dengan 4,34% bahan kering.

Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties

Profile of molecular marker can be used for variety identification, genetic purity monitoring of germplasm and additionalrequirement in proposing intellectual property protection. DNA fingerprinting of soybean had been applied at the ICABIOGRADIAARDsince 2004 using simple sequence repeat (SSR) markers which were run automatically by CEQ 8000 Genetic Analyzerplatform based on capillary electrophoresis system. This method had produced unique DNA fingerprints of the varieties tested,but the marker set to efficiently identify the varieties had not yet been developed. This study aimed to develop a set of SSRmarkers as a tool to identify the Indonesian soybean varieties. Fourty two soybean varieties were analyzed using 14 random SSRmarkersA total of 168 alleles that were obtained from the polymorphism analysis. The average of polymorphic informationcontent (PIC) value observed was 0.7337 per SSR locus. Based on marker reproducibility rate, PIC value, number of rare alleles,frequency of dominant alleles, and percentage of SSR fragment detected by genetic analyzer, we identified five SSR markers i.e.Satt414, Satt147, Satt308, Satt009, and Satt516 as a SSR marker set to be used for soybean variety identification purposes. Thismarker set was used to develop the identity (ID) of the 42 Indonesian soybean varieties.

Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes)

Genetic Diversity of 96 Accession of Rice Germplasm Using 30 SSR Markers Linked to Heading Date Genes (HD Genes). Dwinita W. Utami, Sutoro, Nurul Hidayatun, Andari Risliawati, and Ida Hanarida. Rice with early maturity is one of an important genetic resources in rice germplasm collection. Characterization and identification of genetic diversity is an important issue for plant variety protection. Molecular identification by microsatellite markers using Genetic Analyzer enables resolve of this issue. The objective of this research is to identify the genetic diversity of 96 rice accessions based on their specific DNA fingerprint using microsatellite markers. A total of 96 accessions consisting of a diverse variety of maturity classification were genotyped with 30 SSR markers linked to HD genes which spread out in 12 chromosomes of rice geneome. The total 297 alleles were detected indicated the level of marker informativeness. RM5607 generated 7 allele with the size range from 103 to 197 and the highest PIC at 0.90. RM3571 (linked to HD12 gene) has a significant value associated with varieties which have early maturity trait. Clustering analysis showed the cluster based on Sub Species genome background and on early maturity trait.

Evaluasi Toleransi Plasma Nutfah Padi Lokal pada Lahan Masam Kahat Fosfor

Local variety is the major component in upland rice cultivation as well as breeding material in variety improve-ment. Local upland rice varieties have been adapted to specific location, preferred and adopted by farmers although they are late in maturity. These reasons make it majority of farmers in West Pasaman District (West Sumatra) still cultivate local upland rice varieties. To know the yield potential and agronomic characters of widely cultivated of upland rice in West Pasaman District, a variety trial conducted in 2010. Five local varieties and one improve variety planted a Randomized complete block arrangement with three replications. Observa-tion conducted on agronomic characters and yield and yield components. The results showed that local variteies were tall (153-171 cm) and late maturity (130-157 days). The local varieties also showed higher number of spikelet/panicle (249-454) lighter 1.000 grains weight (<20 g) and higher yield than improved variety (4.27-5.51 compared to 2.85 t/ha). In general all plant characters showed high heritability estimate (except number of productive tiller/hillr). High estimated of genetic variation coefficient and genetic advance were shown on number of grain per panicle. Based on these genetic parameters, selection at early generation for high yield can conducted on number of grain per panicle.Phosporus (P) deficiency is one of limiting factor for rice growth. In Indonesia P deficiency much occurs in acid soils. The use of P deficiency tolerant varieties is the best solution compared to the application of P fertilizer due to more efficient in cost. The purpose of this study was to evaluate the local rice germplasm collected from several regions in Indonesia to P deficiency in acid soil. The study was conducted in Jasinga West Java during wet season of 2006- 2007 with the soil condition lack of P. The experiments were conducted with the two treatments: first, without P fertilizer and second with P fertilizer equivalent of 25 kg P/ha. The total 100 accessions of rice germplasm were screened in this field based on a randomized block design with three replications. Fertilizing were given on experiments I and II with the composition: urea 300 kg/ha and 100 kg KCl. The field design was done by plotting size is 1 x 5 m2, spacing plant of 25 cm x 25 cm, and planting two seeds per hole. The yield components characters which were observed: number of tillers, plant dry weight, plant height and flowering. The results of combined analysis showed that there is a significant interaction between P and genotype on the tiller number, whereas the dry weight of plant, plant height, and flowering were is not significant. The evaluation of 100 local rice genotypes to P deficiency by indicators of the tiller number and dry weight of plants obtained 19 genotypes that are tolerant to P deficiency with the relative value of tillers number and dry weight of plants more than 80%. Local varieties Mandalet, Ganefo, Padi Belanda, Pulut Jangan, Padi Ubek Bala, and Padi Krayan were the most tolerant to conditions without P which showed the tillers number more 1-21% rather than the conditions with P fertilizer. There are three selected genotypes, Pulut Jangan, Padi Ubek Bala, and Padi Krayan which increased the number of tillers and dry weight of plants in without P conditions. The increasing of tillers number were reach 1-17% while the dry weight increased 12-41%.

A Bioinformatics Workflow for Genetic Association Studies of Traits in Indonesian Rice

Asian rice is a staple food in Indonesia and worldwide, and its production is essential to food security. Cataloging and linking genetic variation in Asian rice to important traits, such as quality and yield, is needed in developing superior varieties of rice. We develop a bioinformatics workflow for quality control and data analysis of genetic and trait data for a diversity panel of 467 rice varieties found in Indonesia. The bioinformatics workflow operates using a back-end relational database for data storage and retrieval. Quality control and data analysis procedures are implemented and automated using the whole genome data analysis toolset, PLINK, and the [R] statistical computing language. The 467 rice varieties were genotyped using a custom array (717,312 genotypes total) and phenotyped for 12 traits in four locations in Indonesia across multiple seasons. We applied our bioinformatics workflow to these data and present prototype genome-wide association results for a continuous trait - days to flowering. Two genetic variants, located on chromosome 4 and 12 of the rice genome, showed evidence for association in these data. We conclude by outlining extensions to the workflow and plans for more sophisticated statistical analyses.