Evaluasi Dan Identifikasi Marka Penanda Gen Ketahanan Penyakit Hawar Daun Bakteri Pada Padi Lokal Sulawesi Selatan

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)

Faktor Virulensi AvrBs3/PthA Pada Ras III, Ras IV, Ras VIII, Dan IXO93-068 Patogen Hawar Daun Bakteri (Xanthomonas Oryzae Pv. Oryzae)

AvrBs3/PthA Virulence Factor of Bacterial Leaf BlightRace III, Race IV, Race VIII, and IXO93-068. Dwinita W.Utami, Triny S. Kadir, and Siti Yuriyah. Bacterial leafblight (BLB) is an important disease of rice and presentthroughout many of the rice-growing regions in the world,also in Indonesia. Xanthomonas oryzae pv. oryzae (Xoo) isthe causal agent and a member of the Protebacteria and likemany other this phyllum have a type III secretion system forprotein virulence effector (PVE) released on their pathogenicitysystem. Commonly, PVE in Xanthomonas sp., iscoded by AvrBs3/PthA family gene. This research wascoducted to identify the virulence factor of AvrBs3/PthA ondominant Indonesian BLB isolates (Race III, Race IV, RasVIII, and IXO93-068). This objective was obtained bysequence analysis through designed markers for membersof the virulence factor AvrBs3/PthA gene family (PthXo4,avrXa7#38, PthXoS and avrXa7sacB50). Results gave informationthat RaceIII is a dependent elicitor race due to noPVE transcript formed and intraceluler protein target withRLL type on NLS (nuclear localization signal). RaceIV andRaceVIII are the virulent race which PVE active formed withintraceluler protein target and have the RLL and RLLP typefor the NLS signal. While isolate IXO93-068 is a virulenisolate that active formed a PVE but the extraceluler proteintarget is due to no type of NLS. Based on cluster analysis,Race VIII has a genetic distance closely to PthXoS andavrXa7sacB50

Pencarian Alel Untuk Identifikasi Gen Ketahanan Penyakit Hawar Daun Bakteri, Xa7 Pada Plasma Nutfah Padi Lokal Indonesia

Allele Mining of Bacterial Blight Resistance Gene, Xa7 onIndonesian Local Rice Germplasm. Dwinita W. Utami,Endang M. Septiningsih, Trini S. Kadir, Fatimah, and SitiYuriyah. The abundance of novel genetic variation existingin germplasm collections is the foundation for varietyimprovement in plant breeding program. Nevertheless,studies on Indonesian genetic diversity rice germplasmusing molecular markers are still poorly. Recent advances inutilizing of simple sequence repeat (SSR) in QTL mappingand whole rice genome sequences were positive support ongenetic diversity of rice germplasm research. Based on theseadvance technology, we developed the research to discovernew alleles at important gene loci that can be used for riceimprovement. This approach is recognized as allele miningtechnology. On this study the target genes for allele miningresearch is the resistance gene for bacterial leaf blightpathogen, Xa7. This point was introduced by identify thegenetic diversity of 96 accessions Indonesian local ricegermplasm. The Xa7 allele mining was done by SNP (singlenucleotide polymorphism) designing primers based on DNAsequence around the gene target. The significant LD mapwas detected by association mapping between phenotypeand SNP genotyping data of the selected germplasm whichhaving superior performance on BLB resistance andrepresenting on genetic diversity clustering. The resultsshown that Xa7 allele variation were found in Parekaligolara(Indica, 15141), and Gajah Mada (Indica, 5856), whichresistant to BLB races IV and VIII on generative stage andfield condition. The significant Xa7-SNP8 and Xa7-SNP11markers were associating with the LD map position of Xa7gene on 28, 05-28,1Mb of chromosome 6 in rice genome

Analisis Keragaman Genetik 161 Aksesi Mangga Indonesia Menggunakan Marka Mikrosatelit

Mango is one of the fiveimportant fruit crops in the world. Microsatellite markers canbe used to analyze genetic diversity among mangoaccessions. The purpose of this research was to determinethe relationship among mango germplasm collection usingmicrosatellite markers. A total of 161 mango accessionsoriginated from Indonesian Tropical Fruit Research Institute(Cukurgondang Field Station), Pasuruan, East Java, wereused in this research. Twenty-six microsatellite markerswere used to genotype each accession. Genotyping wasconducted using Beckman Coulter® CEQ™ 8000 machine.Genetic relationship among accecions was analyzed usingthe Unweighted Pair Group Method with Arithmetic Mean(UPGMA) method, followed by bootstrap analysis. The resultshowed that high allele variation (15-75 alleles) wasobserved among mango accesions tested, with an averageallele number of 38.69. The average of PolymophismInformation Content (PIC) value was 0.548 (0.021-0.949).Fifteen microsatellite markers showed PIC value >0.5indicated that these markers were suitable for mangodiversity studies. Cluster analysis divided the mangocollections into two groups. Group I consisted of 95accessions, and group II consisted of 66 accessions. NinetyIndonesian indigenous mangos (84.11% of Indonesianmango accessions) could be separated from the introducedaccessions

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

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 mengendalikanpenyakit HDB adalah penanaman varietas tahan. Perakitan varietas padi dengan menggunakan gen-gen tahan dari berbagaikultivar berpeluang menghasilkan varietas tahan HDB. Kultivar lokal berperan sebagai salah satu sumber keragaman genetikuntuk beberapa sifat ketahanan penyakit. Penelitian ini bertujuan mengevaluasi dan mengidentifikasi marka penanda genketahanan penyakit hawar daun bakteri pada padi lokal Sulawesi Selatan berdasarkan sistem standar diferensial dan analisismolekuler. 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 ditampilkansebagai dendrogram keragaman. Analisis asosiasi dilakukan dengan analisis gabungan (U-joint) menggunakan generalizedlinear model (GLM). Hasil pengujian ketahanan menunjukkan galur isogenik dengan gen tunggal (IRBB 5, IRBB 7, dan IRBB21), galur isogenik dengan multipel gen (IRBB 50, IRBB 52, IRBB 53, IRBB 54, IRBB 56, IRBB 58, IRBB 64, dan IRBB 66), danaksesi Ase Andele bersifat tahan terhadap ketiga ras uji. Dari uji asosiasi, diperoleh satu marka signifikan yang berasosiasidengan 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)

Evaluasi Mutu Fisikokimia Beras Hasil Persilangan antara Empat Padi Varietas Unggul dan Padi Liar (Oryza glaberrima dan O. rufipogon)

The physicochemical quality of rice is evaluated to ensure that it is fit for consumption and meets established quality standards. This study aims to analyze the physicochemical properties of rice strains resulting from crosses between four high-yielding varieties of rice and two wild rices so that the appropriate genotype is obtained for the development of quality rice. The research was conducted from November 2019 to March 2020 at the Quality Laboratory, Muara Experimental Garden, Rice Research Center, Bogor. The rice genotypes used were 22 strains resulting from crosses between high-yielding varieties of rice (Ciherang, Inpari 13, Inpari 10, and Situ Bagendit), and wild rice (Oryza glaberrima and O. rufipogon), 4 comparison varieties of crossbred elders, and two comparison varieties of organoleptic tests (Memberamo and IR42). Physical and chemical qualities were observed in terms of grain moisture content, grain density, broken skin rice yield, milled rice yield, head rice yield, rice length, rice shape, and rice liming, amylose content, gelatinization temperature, and organoleptic. The results showed that the strains 44-F-C21, 58-F-C21, and 59-F-C21 provided fairly good rice quality with head rice yields above 80% and higher than their respective elders (Situ Bagendit and Ciherang), and water content below 14%. These strains had characteristic characteristics, namely medium rice form, amylose content of 26.38%, and alkali score of 2-3. Most of these genotypes also exhibited high gelatinization temperatures, medium rice texture, and savory rice flavors. The genotype selected from the results of crosses between high-yielding varieties of rice and wild rice has the potential to be developed because there are genetic improvements from its elders on several physicochemical characteristics of rice.   Keywords: amylose content; gelatinization temperature; physicochemical properties; rice lines; wild ric

Faktor Virulensi AvrBs3/PthA pada Ras III, Ras IV, Ras VIII, dan IXO93-068 Patogen Hawar Daun Bakteri (Xanthomonas oryzae pv. oryzae)

AvrBs3/PthA Virulence Factor of Bacterial Leaf BlightRace III, Race IV, Race VIII, and IXO93-068. Dwinita W.Utami, Triny S. Kadir, and Siti Yuriyah. Bacterial leafblight (BLB) is an important disease of rice and presentthroughout many of the rice-growing regions in the world,also in Indonesia. Xanthomonas oryzae pv. oryzae (Xoo) isthe causal agent and a member of the Protebacteria and likemany other this phyllum have a type III secretion system forprotein virulence effector (PVE) released on their pathogenicitysystem. Commonly, PVE in Xanthomonas sp., iscoded by AvrBs3/PthA family gene. This research wascoducted to identify the virulence factor of AvrBs3/PthA ondominant Indonesian BLB isolates (Race III, Race IV, RasVIII, and IXO93-068). This objective was obtained bysequence analysis through designed markers for membersof the virulence factor AvrBs3/PthA gene family (PthXo4,avrXa7#38, PthXoS and avrXa7sacB50). Results gave informationthat RaceIII is a dependent elicitor race due to noPVE transcript formed and intraceluler protein target withRLL type on NLS (nuclear localization signal). RaceIV andRaceVIII are the virulent race which PVE active formed withintraceluler protein target and have the RLL and RLLP typefor the NLS signal. While isolate IXO93-068 is a virulenisolate that active formed a PVE but the extraceluler proteintarget is due to no type of NLS. Based on cluster analysis,Race VIII has a genetic distance closely to PthXoS andavrXa7sacB50