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Windarsih G, Riastiwi I, Dewi AP. Yuriyah S. 2022. Stomatal and epidermal characteristics of Zingiberaceae in Serang District, Banten, Indonesia. Biodiversitas 23: 5373-5386. The stomatal and epidermal characteristics can be used as additional evidence in plant taxonomy activity. The aim of the study was to identify the stomatal and epidermal characteristics of Zingiberaceae in Serang District, Banten, Indonesia. The samples used were 11 species of Zingiberaceae in Serang District region. The stomatal and epidermal collection was carried out using the replica technique. Based on the results, all species has brachyparatetracytic type of stomata, on both adaxial and abaxial surfaces of the leaf. The densities of stomata of all species observed on abaxial were higher than adaxial surface of the leaf. The stomatal density on adaxial surface of leaf between 1.71-4.43 stomata per unit leaf area of 171,602 µm2, while on abaxial 10.46-42.22 stomata per unit leaf area. The stomatal index on adaxial surface is between 1.34-6.97%, while on abaxial 7.54-30.25%. The length of guard cells on adaxial surface is between 30.30-47.85 µm, while on abaxial 29.86-50.68 µm. The width of guard cells on adaxial surface between 18.67-31.73 µm, while on abaxial 19.97-31.95 µm. The adaxial epidermal cells have a column, polygonal, or rectangular shapes, while the abaxial has poligonal or rectangular-shaped epidermal cells. The epidermal cells that are over leaf veins have polygonal or rectangular-shaped cells.

Windarsih G, Utami DW, Yuriyah S. 2021. Morphological characteristics of Zingiberaceae in Serang District, Banten, Indonesia. Biodiversitas 22: 5507-5529. Zingiberaceae, known as ginger family, is a family of monocotyledon belonging to the Zingiberales order. This family is widely used its rhizome for various purposes, especially as medicinal plant. The morphological characters can be used to help the identification of species in the field of plant taxonomy. The aim of study was to characterize the morphological traits, both vegetative and generative organs, of Zingiberaceae from Serang District, Banten. Plant specimens were collected from Serang District, Banten, including in Pabuaran, Gunungsari, and Ciomas sub-district using purposive sampling. The examination of morphological characters data was conducted through observation and documentation. There were 13 species/varieties of Zingiberaceae collected from the studied area, i.e. Amomum compactum, Alpinia purpurata, Curcuma xanthorrhiza, C. longa, C. heyneana, C. mangga, C. aeruginosa, Kaempferia rotunda, Etlingera elatior, Zingiber zerumbet, Z. officinale, Zingiber officinale var. rubrum, and Z. cassumunar, in which the generative organs were found only in eight species/cultivars of them. Based on the morphological characters of vegetative organs, thirteen species/cultivars had a similarity distance coefficient from 37% to 94%; while based on the morphological characters of both vegetative and generative organs, the eight species/cultivars had a similarity distance coefficient from 31% to 94%. The results showed that using the characters of vegetative organs data were still able to provide consistent grouping results with the generative organs.

Yuriyah S, Darnaedi D, Setia TM, Windarsih G, Utami DW. 2021. Phenotype and genotype variability of interspecific rice lines related to bacterial leaf blight resistance (Xanthomonas oryzae pv. oryzae) character. Biodiversitas 22: 4123-4130. Wild rice species are the source of the gene pool for rice genetic diversity. The cross-species crosses (interspecific crosses) play an important role in breeding, namely in terms of expanding the diversity of desirable characters, such as disease resistance and improvement in yield potential. Currently, the genes from wild rice species have been successfully introgressed into cultivated rice so that they can overcome the rice production constraints, including the introgression of genes for the bacterial leaf blight (BLB) resistance. The purpose of this study was to analyze the variability of phenotype and genotype performance of lines derived from wild rice species for the character of resistance to BLB disease. A total of 33 selected backcross lines derived from wild rice species of O. rufipogon and O. glaberrima as the donor parents and 2 control varieties (resistant and susceptible to BLB disease), were used in this study. The evaluation of phenotype and genotype of resistance characters to BLB disease was carried out during a vegetative phase of the plant. The resistance evaluation was carried out in a greenhouse, while the genotype performance was analyzed using 4 STS markers linked to Xa4, Xa7, and Xa13 genes. The result of the phenotype evaluation showed that there were variations among the resistance of the tested lines. Three lines derived from a Situ Bagendit/Oryza rufipogon cross were resistant to all BLB races used in the testing. Those three lines indicated to have the allele of the Xa7 resistance gene based on the genotype performance which grouped with the Code variety that had the Xa7 resistance gene.

Resistance screening of promising rice lines in Indonesia requires the use of brown planthopper (BPH) biotypes 1, 2, and 3. Three BPH populations have been raised as biotypes 1, 2, and 3 on differential rice host of improved varieties Pelita I-1 (no Bph gene), IR26 (Bph1), and IR42 (bph2), respectively. Three alternative populations have also been developed on the respective traditional varieties TN1 (no Bph gene), Mudgo (Bph1), and ASD7 (bph2). Although these populations displayed two virulent patterns other than biotype 1 to 3 phenotypes, they were expected to be discriminated into two virulence groups by SSR analysis. The study aimed to investigate the level of genetic variation among the six BPH populations using SSR markers and to relate it with the observed virulence patterns. Genotyping of 30 females with 29 polymorphic SSR markers revealed higher genetic parameter values in populations reared on improved varieties than those on traditional varieties. This difference was marked as two population clusters in PCoA plots corresponding to the host variety type, in contrast to the previous assumption that clustering would be based on virulence patterns. The presence of individuals with unwanted virulence allele, either resulting from contamination during the long period of rearing or lack of host adaptation period, is suspected. The result of this study indicates that the six populations are not suitable for resistance screening. Virulence selection must be performed until they attain biotype 1 to 3 phenotypes which can be genetically separated by DNA markers.

Windarsih G, Utami DW, Yuriyah S. 2019. Genetic diversity and productivity of Gracilaria coronopifolia as alternative for food resource based on RAPD marker. Biodiversitas 20: 3758-3765. Gracilaria coronopifolia is one of potential seaweed as an alternative for food resources, especially for agar source. The information about the genetic profile of G. coronopifolia will be useful for assisting in conservation and breeding efforts. RAPD marker is expected to be utilized for characterization of the species with high productivity based on genetic profile. This research aims to determine the genetic diversity and productivity of G. coronopifolia based on RAPD marker. The samples were collected from Anyer Beach, Banten, Indonesia i.e. Tanjung Tum Beach, Mambruk Hotel Beach, and Patra Comfort Anyer Beach, as well as the cultivation ponds of seaweed in Lontar Village, Banten, Indonesia. Five RAPD primers (OPA-01, OPA-16, OPT-05, OPR-02, and UBC-594) were screened to characterize the genetic profile of samples. The results showed that all primers produced polymorphic bands. Based on the genetic profile, the samples of G. coronopifolia were separated into two main clusters, consisted of group A (Tanjung Tum Beach, Patra Beach, and Mambruk Beach) with a coefficient of similarity of 0.44 and group B (Lontar Village) with a similarity coefficient of 0.43. The sample from Lontar Village was separated outside from the other three samples at the waters of Anyer Beach. The sample from Lontar Village had the highest talus height (18.0 cm) and dry weight (1.250 g/clump). The UBC-594 primer was the most associated with the talus height and dry weight on the band size of 50 bp, thus this primer was assumed can be used as a selection marker for the talus height and dry weight of G. coronopifolia.

The utilization of molecular marker technology for Blast (Pyricularia grisea) resistance in rice breeding could accelerate and improve the precision of selection. This study aimed to identify and to select the BC3F2 progenies from Situ Patenggang and the opted Blast Monogenic Lines based on their resistance to blast disease in green house and field using molecular characterization. A total of 200-300 BC3F2 population strains resulted in 4 crosses between Situ Patenggang varieties and Monogenic Varieties IRBLta2-Re, IRBLkp-k60, IRBLi-F5 and IRBLa-A were used as total genetic material in the study. Blast resistance assay was initially carried out in a greenhouse and further selection was conducted in the endemic blast area, Sukabumi. The selected Molecular marker was STS (Sequence Taq Sites) marker for foreground selection and 384-SNPs (Single Nucleotide Polymorphism) chip for background selection. The number of lines from each cross was selected by greenhouse assay i.e: 25 lines derived from Situ Patenggang/IRBLta and Situ Patenggang/IRBLkp, 21 plants for crossing Situ Patenggang/IRBLi, and 22 plants for Situ Patenggang/IRBLa-A. The results of field experiment revealed that blast resistance response of the selected lines was varied from 0 to 5. Lines of foreground were successfully selected using STS markers specified for Pii, Pita, Pikp and Pia genes. As for the background selection by SNPs markers, some lines carried the recurrent parent genetic background, Situ Patenggang. Overall, 20 resistance lines that harbored the target genes and Situ Patenggang background were obtained. Further observation was entailed to these twenty selected lines in order to attain promising lines candidate for blast resistance.

Situ Patenggang is an elite upland rice variety well-accepted by farmers, but recently this variety started to be attacked by blast disease (Pyricularia grisea) that causes yield loss up to 50%. To overcome this problem, Bio Patenggang variety has been developed through molecular breeding using blast-resistant monogenic lines as donor parents. The aim of this research was to present molecular breeding approach of Bio Patenggang development, including steps from the phenotypic selection on candidate lines to the genotypic analysis assisted by molecular markers. The phenotypic performances were assessed using Distinctness, Uniformity, and Stability (DUS) testing by following the standard method stated in the rice test guidelines. The genotypic analyses were performed using foreground and background markers. Four BC3F7 lines were selected as the candidates of the Situ Patenggang-derived variety. Based on ANOVA and Principal Component Analysis (PCA), phenotypic performances of the four lines demonstrated no significant differences with that of Situ Patenggang. The selected lines have also passed the foreground analysis confirming that the lines contained Pita, Pii, Pik-p, and Pia last resistance genes. Background analysis showed that the selected lines demonstrated agronomic perfomances very similar to that of Situ Patenggang. Association analyses showed that 14 markers were associated with the target traits and 10 out of the 14 markers were identified as co-segregation markers. The four selected lines, therefore, were proposed to be released as Situ Patenggang-derived variety. One of the lines (Sta-8-S15-TB16) has been approved to be released as a new variety, namely ‘Bio Patenggang Agritan’.

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

Resistance Test of Promising Rice Lines Against Bacterial Leaf Blight (Xanthomonas oryzae pv. oryzae) Race III, IV, and VIII. Siti Yuriyah, Dwinita W. Utami, and Ida Hanarida. Development of new superior rice varieties resistant to bacterial leaf blight (BLB) has been conducted through utilizing of a wide rice germplasm, from crossing between IR64 and Oryza rufipogon. The aim of this study is to get promising rice lines that resistant to BLB race III, IV, and VIII. The experiments were conducted at greenhouse and Laboratory of Molecular Biology, ICABIOGRAD Bogor, using of 13 promising rice lines that have different levels of resistance to inoculum from pure cultures of BLB race III, IV and VIII. Of these 13 rice lines, six lines showed resistance to race III (Bio5-AC-Blas/BLB-03, Bio62-AC-Blas/BLB-03, Bio111-BC-PIR7, Bio129-BC-WBC, Bio148-Mamol, and Bio154-Mamol-Dro), one line showed resistance to race IV (Bio154-Mamol-Dro), and one line showed resistance to race VIII (Bio5-AC-Blas/BLB-03), with severity rate 1.8 to 8.1%. Of these improve lines Bio5-AC-Blas/BLB-3 and Bio 111-BCPir- 7, were released as new rice varieties, namely Inpari HDB and Inpari Blas, respectively. AbstrakPerakitan varietas padi unggul baru tahan terhadap hawar daun bakteri (HDB) terus dilakukan melalui pemanfaatan sumber daya genetik yang luas. Saat ini telah dirakit galur-galur unggul yang berasal dari persilangan IR64 dan padi liar Rupifogon. Penelitian ini bertujuan untuk mengevaluasi ketahanan galur harapan padi terhadap penyakit HDB dari Ras III, IV, dan VIII. Percobaan dilakukan di rumah kaca dan Laboratorium Kelti Biologi Molekuler, BB Biogen, Bogor. Materi genetik yang digunakan adalah 13 galur harapan padi dan biakan murni dari Ras III, IV, dan VIII. Metode inokulasi dengan pengguntingan dan skoring ketahanan dilakukan sesuai dengan sistem penilaian dari Yashitola et al. (1997). Dari 13 galur padi harapan yang diuji, diperoleh enam galur tahan terhadap Ras III (Bio5-AC-Blas/BLB-03, Bio62-AC-Blas/BLB-03, Bio111- BC-PIR7, Bio129-BC-WBC, Bio148-Mamol-Dro, dan Bio154-Mamol-Dro), satu galur tahan terhadap Ras IV (Bio154-Mamol-Dro) dan satu galur tahan terhadap Ras VIII (Bio5-AC-Blas/BLB-03), dengan tingkat keparahan sebesar 1,8-8,1%. Dalam perkembangannya, dua dari galur harapan, yaitu galur Bio5-AC-Blas/BLB-03 dan Bio111-BC-Pir-7 disetujui untuk dilepas sebagai varietas Inpari HDB dan Inpari Blas.

Brown planthopper is the most important rice pest in Indonesia. Its high adaptability to feed and reproduce on previously introduced resistant varieties to form more virulent population often causes BPH outbreak and hopperburn that lead to total crop yield loss. Rice breeding for resistant to BPH requires information on the current status of BPH virulences in the fields to anticipate the virulence adaptation on new varieties. The objectives of this study were to investigate the degree of virulence of BPH populations and to cluster the BPH virulence to form BPH core collection. Thirteen BPH populations collected from paddy fields in six provinces (Banten, West Java, Central Java, East Java, South Kalimantan, and South Sulawesi) in 2011 and 2013 were tested on 10 differential rice varieties and seven host varieties of BPH populations, using the standard seedbox screening technique. Based on resistance reaction of four differential varieties (TN1, Mudgo, ASD7, and Rathu Heenathi), most BPH populations were identified as more virulent than biotype 4 (T1, Banten, PG, West Java; BY, East Java; B2 and B3, South Kalimantan; X1 and X3, South Sulawesi), four populations were biotype 4 (JWDL, Central Java; SD, East Java; X2 and X4, South Sulawesi), and one population each was biotype 3 (T2, Banten) and biotype 2 (S1, West Java). Populations X1 and B3 showed broad virulences to all varieties, whereas T2 was the least virulent. BPH field’s population had evolved into more virulence than biotype 4. Genotype resistance screening should use the BPH of this virulence population. Five BPH clusters which were further divided into 10 subclusters representing differential virulence toward 10 differential varieties were present in the tested BPH. Each virulence cluster was characterized by its ability to overcome four to eight single or double resistant genes. This BPH virulence core collection can be used in the characterization studies of candidate for resistant varieties or to form near-isogenic lines, or to study the insect and rice plant interaction.

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.

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.

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.