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EVALUASI KEMUDAHAN TRANSFER MARKA SSR PADI UNTUK MENGANALISIS KERAGAMAN GENETIK FAMILI POACEAE TOLERAN KEKERINGAN Fatimah, Fatimah; Masumah, Masumah; Prasetiyono, Joko; Sustiprijatno, Sustiprijatno
JURNAL BIOLOGI INDONESIA Vol 15, No 1 (2019): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v15i1.3764

Abstract

ABSTRACTAnticipating climate change and its impacts on crop production, it requires the development of adaptive rice varieties that respond to drought stress and minimize the damage while keeps growing and maintaining yield. The aim of this study was to evaluate the transferability of rice simple sequence repeat (SSR) markers to Poaceae family and analyze the genetic diversity among 16 accessions of Poaceae family (12 genera and 14 species) using 41 rice SSR markers. The result revealed that the transferability of rice SSR markers was varied. High amplification produced in rice group (>70%) and low amplification in grass group (<30%) with an average of 35.2%. A total of 128 cross-species alleles were identified with an average of 3 alleles/locus. The value of gene diversity ranged from 0.15 to 0.83 with an average of 0.53 and the value of Polymorphic Information Content (PIC) ranged from 0.14 to 0.80 with an average of 0.46. The results of phylogenetic analysis determined two clusters at similarity coefficient of 0.72. The first cluster consisted of 14 accessions from Poaceae family (12 genera and 14 species) while the second cluster consisted of two cultivated rice varieties (Inpari 30 and Situ Bagendit). The genetic relatedness data revealed from this study could be used as basic information for parental selection. The 14 accessions of Poaceae family have a potential for drought tolerant donor and separated clearly from cultivated rice varieties (Inpari 30 and Situ Bagendit) for recipient parents in spike-stalk injection method (SIM) to develop drought tolerant rice varieties.  Keywords: Cross amplification, Drought tolerant, Inpari 30, Situ Bagendit   
IMPROVEMENT OF EARLY MATURITY IN RICE VARIETY BY MARKER ASSISTED BACKCROSS BREEDING OF Hd2 GENE Fatimah, Fatimah; Prasetiyono, Joko; Dadang, Ahmad; Tasliah, Tasliah
Indonesian Journal of Agricultural Science Vol 15, No 2 (2014): October 2014
Publisher : Indonesian Agency for Agricultural Research and Development - MOA

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Abstract

Early-maturing and high-yielding rice variety is very useful for increasing rice production in Indonesia. The aim of this research was to develop new lines of Indonesian rice containing Hd2 gene using Code variety as a recipient parent and Nipponbare variety as a donor parent through targetted MAB approach using RM1362 and RM7601 in chromosom 7 for foreground selection. After two generations of backcrossing, the positive alleles of Hd2 gene from Nipponbare had successfully trans-ferred into Code. The plant number CdNp_29 in BC2F2 popula-tion had the highest genome recovery of 82.7%. The twelve BC2F3 plants were selected for self-pollination to generate BC2F4. These selected lines that carried the Hd2 gene were screened in the greenhouse for the evaluation of heading date and agronomic traits. All improved lines had Hd2 gene similar to the donor parent Nipponbare. The heading date of the breeding lines ranged from 73 to 89 days (Code 85 days) or fill the third criterion of rice maturity that is 103-104 days compared to Code of 116-119 days, whereas their agronomic performances were similar with that of Code. Application of MABc for im-proving rice early maturity has accelerated the development and selection in early generation of superior lines having genetic background of Code. It is expected that the newly developed lines of Code will be utilized to increase rice production in Indonesia.
IMPROVEMENT OF EARLY MATURITY IN RICE VARIETY BY MARKER ASSISTED BACKCROSS BREEDING OF Hd2 GENE Fatimah, Fatimah; Prasetiyono, Joko; Dadang, Ahmad; Tasliah, Tasliah
Indonesian Journal of Agricultural Science Vol 15, No 2 (2014): October 2014
Publisher : Indonesian Center for Agricultural Library Technology Dissemination - IAARD

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v15n2.2014.55-64

Abstract

Early-maturing and high-yielding rice variety is very useful for increasing rice production in Indonesia. The aim of this research was to develop new lines of Indonesian rice containing Hd2 gene using Code variety as a recipient parent and Nipponbare variety as a donor parent through targetted MAB approach using RM1362 and RM7601 in chromosom 7 for foreground selection. After two generations of backcrossing, the positive alleles of Hd2 gene from Nipponbare had successfully trans-ferred into Code. The plant number CdNp_29 in BC2F2 popula-tion had the highest genome recovery of 82.7%. The twelve BC2F3 plants were selected for self-pollination to generate BC2F4. These selected lines that carried the Hd2 gene were screened in the greenhouse for the evaluation of heading date and agronomic traits. All improved lines had Hd2 gene similar to the donor parent Nipponbare. The heading date of the breeding lines ranged from 73 to 89 days (Code 85 days) or fill the third criterion of rice maturity that is 103-104 days compared to Code of 116-119 days, whereas their agronomic performances were similar with that of Code. Application of MABc for im-proving rice early maturity has accelerated the development and selection in early generation of superior lines having genetic background of Code. It is expected that the newly developed lines of Code will be utilized to increase rice production in Indonesia.
Identifikasi Marka Polimorfik untuk Pemuliaan Padi Toleran Defisiensi Fosfor Prasetiyono, Joko; Aswidinoor, Hajrial; Moeljopawiro, Sugiono; Sopandie, Didy; Bustamam, Masdiar
Jurnal AgroBiogen Vol 4, No 2 (2008): Oktober
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

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Abstract

Information on polymorphismsamong rice parents are very important in ricebreeding for tolerance to phosphorus defficiency. A studywas conducted at the Molecular Biology Laboratory,Indonesian Center Agricultural Biotechnology and GeneticResources (ICABIOGRAD) from October 2006 to July 2007 toidentify polymorphism markers from 6 rice genotypes. Therice genotypes, i.e., Dodokan, Situ Bagendit, Batur, Kasalath,NIL-C443, dan K36-5-1-1 were analyzed for polymorphismsusing 496 SSR markers, which cover the rice genomes.Seven of the 496 markers were used as foreground andrecombinant selection markers, and the rests (489 markers)were used as background selection markers. PCR amplificationswere separated on a 5% polyacrylamide gel andcolored by the silver staining method. Three different markersamong the seven foreground and recombinant selectionmarkers were selected from each crossing, which aretightly linked with Pup1 gene and have a distance less than 5cM. These markers are Dodokan vs Kasalath (RM277, SSR3,RM519), Dodokan vs NIL-C443 (RM277, SSR3, RM519),Dodokan vs K36-5-1-1 (RM277, SSR3, RM519), Situ Bagenditvs Kasalath (RM28102, SSR3, RM519), Situ Bagendit vs NILC443(RM28102, SSR3, RM519), Situ Bagendit vs K36-5-1-1(RM511, SSR3, RM519), Batur vs Kasalath (RM277, RM1261,RM519), Batur vs NIL-C443 (RM277, RM1261, RM519), andBatur vs K36-5-1-1 (RM28102, SSR3). Variations in backgroundselection primers were found in each chromosomeand in each parent combinations. Primers on chromosome4, 5, and 12 showed the lowest polymorphisms; moreprimers are needed for these chromosomes.
EVALUATION OF SEVERAL PUP1-LINES OF RICE (ORYZA SATIVA L.) ON NUTRIENT SOLUTION AND AT THE FIELD Prasetiyono, Joko; Suhartini, Tintin; Soemantri, Ida Hanarida; Tasliah, ,; Moeljopawiro, Sugiono; Aswidinnoor, Hajrial; Sopandie, Didy; Bustamam, Masdiar
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 40 No. 2 (2012): Jurnal Agronomi Indonesia
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (385.883 KB) | DOI: 10.24831/jai.v40i2.13200

Abstract

Phosphorus (P) deficiency is one of major problems in rice cultivation. Development of a tolerant variety to P deficient soil is expected to reduce the needs of P fertilizer. The aim of this research was to evaluate the agronomic performance of Pup1-introgression rice lines. This research consisted of two separate experiments, an evaluation on rice grown in nutrient solution in the greenhouse of ICABIOGRAD, Bogor; and field evaluation at upland rice screening site Taman Bogo, Lampung. The rice lines used were BC2 F3 derived from crossing of Situ Bagendit with Kasalath and NIL-C443, and from crossing of Batur with Kasalath and NIL-C443. Molecular analysis was conducted to verifiy the Pup1 introgression in the lines used and successfully confirmed the occurance of homozygote Pup1 segment in those lines. Evaluation of rice lines grown in nutrient solution was performed in a split plot factorial design, using the dose of Al (0 and 45 ppm Al3+) as main plots and dose of P (0.5 and 10 ppm P) as subplots. Field evaluation was performed in split plot design, with P fertilization (0 and 500 kg SP-18 ha-1) as main plots and BC2 F3 lines as the subplots. Evaluation using Yoshida nutrient solution showed that the BC2 F3 lines had greater total dry weight under low-P condition (37.5-112.5%), especially under Al-toxicity, compared to the respective parental varieties (Situ Bagendit and Batur). Field evaluation showed that the Pup1-introgression lines had greater shoot dry weight than the respective parental lines (10.5-74.82%). However there was no significnant effect of Pup1 introgression in terms of weight of filled grain.
Molecular Evaluation for Drought Tolerant Using Marker Assisted Breeding Method Fatimah, Fatimah; Prasetiyono, Joko; Trijatmiko, Kurniawan Rudi; Sustiprijatno, Sustiprijatno
ANNALES BOGORIENSES Vol 22, No 2 (2018): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2018.v22.n2.94-100

Abstract

   The sustainability and increasing the national rice production require the readiness of food and agriculture sector cope with the impacts of climate change, land degradation, drought area, sloping production and the raising of population growth. Adaptation plays an important role in ensuring the sustainability of food security. This research aimed to develop drought-tolerant variety of Inpari 30 (submergence tolerance variety) and Situ Bagendit through marker-assisted backcrossing-through pyramiding gene of identified QTLs for foreground selection and to explore SSRs and 6K SNPs for background selection distributed in 12 rice chromosome of drought tolerant donor (Cabacu) and recipient rice (Inpari 30 and Situ Bagendit). The foreground selection revealed that flanking SSRs of each QTLs (qRPF2.1, qGPP2.1, qSPP4.1 and Sub1) was less than 2 cM. The background selection through polymorphic survey of Rice 6K SNP primers revealed 2457 (53,3%) polymorphic SNPs on Inpari 30 vs Cabacu and 2563 (55,6%) polymorphic SNPs on Situ Bagendit vs Cabacu with the average distance about 0.74 cM/chromosome. The genotypic selection of F1 Inpari 30/Cabacu and F1 Situ Bagendit/Cabacu have already in heterozygote condition for these 4 QTLs target. These lines was continued for backcross breeding to develop BC1F1 Inpari 30/Cabacu and BC1F1 Situ Bagendit/Cabacu generation.
Analisis Molekuler Piramida Gen Xa pada Progeni Padi Varietas Ciherang dan Inpari 13 ., Fatimah; Prasetiyono, Joko; Priyatno, Tri Puji; Yunus, Muhammad; Suhartini, Tintin; Ridwan, Iman; Baroya, Mushlihatun
JURNAL BIOLOGI INDONESIA Vol 11, No 1 (2015): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v11i1.2161

Abstract

Bacterial leaf blight (BLB) is a major disease in Indonesian lowland rice.This research was undertaken to pyramid three BLB resistant genes xa5, Xa7 and Xa21 and one background BLB resistant gene Xa4 into Ciherang and Inpari 13 varieties. The donor parent Code (Xa4+Xa7) was crossed with Angke (Xa4+xa5) while Ciherang and Inpari 13 were crossed with IRBB21 (Xa21). Progenies were selected using marker assisted selection and yield component observation. Foreground selection was conducted using SSR and STS markers linked with the targeted genes in the F1 and DCF1 population. Individuals with triple positives Xa genes were screened for the presence of Xa4 gene as the background. Selected heterozygote plants in F1 Code x Angke, F1 Ciherang x IRBB21 and F1 Inpari 13 x IRBB21 were used to develop DCF1 population. Molecular analysis on DCF1 population through alleles of three BLB resistant genes xa5, Xa7 and Xa21 and one background BLB resistant gene Xa4 resulted 8 (2,6%) in DCF1 Ciherang and 13 (3,5%) in DCF1 Inpari 13. Yield component characters on F1 Code x Angke resulted significant in number of panicle. F1 Ciherang x IRBB21, F1 Inpari 13 x IRBB21 and DCF1 Ciherang resulted significant in weight of empty grain while DCF1 Inpari 13 resulted no significance in all of observed characters. Keywords: Rice, F1 Population, DCF1 Population, molecular marker, Xa gene 
Molecular Detection of Resistance To Bacterial Leaf Blight on Conde Indonesian Rice Variety Fatimah, Fatimah; Prasetiyono, Joko; Polosoro, Aqwin; Baroya, Mushlihatun
ANNALES BOGORIENSES Vol 22, No 1 (2018): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (667.986 KB) | DOI: 10.14203/ab.v22i1.337

Abstract

Rice bacterial leaf blight (BLB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) affected grain yield and decreasing rice production in rice growing countries. Conde, Indonesian rice variety, exhibits high resistance to most of the Indonesian races of (BLB) and has been used in Indonesia for cultivated rice. This study was aimed to conduct the molecular detection between proximal markers in chromosome 6 and relative expression of Conde rice variety compare to IRBB7 in Xa7 region. The population screening, BLB evaluation and molecular detection around the Xa7 region were conducted. The results showed from the collection of individual recombinants between resistant and susceptible parents narrow the region containing the BTBPOZ domain. The sequence alignment of Xa7LD37 in two resistant and three susceptible cultivars demonstrated a perfect association. The sequence alignment in exon region of Loc_Os06g46240 in Nipponbare, IRBB7, and IR64 identified indel/SNPs in this region leading to nucleotide substitution and frameshift resulting in amino acid change between resistant and susceptible cultivars. It was predicted that Conde revealed the similar gene action with Xa7 gene for BLB that encodes a BTB POZ domain.
Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers Prasetiyono, Joko; Hidayatun, Nurul; Tasliah, Tasliah
Jurnal AgroBiogen Vol 14, No 1 (2018): June
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/jbio.v14n1.2018.p1-10

Abstract

Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.
Effect of Introgression of Pup1 Locus on Rice Seedling under Phosphorus Deficiency Hidayatun, Nurul; Prasetiyono, Joko
Jurnal AgroBiogen Vol 14, No 2 (2018): December
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/jbio.v14n2.2018.p97-104

Abstract

The lack of soil-phosphorus (P) element will result in plant growth retardation. Plants could survive in P deficiency stress by increasing the ability of P uptake or by increasing the efficiency in the P utilization. The aims of this study were to understand genetic composition of rice genotypes possessing Pup1 locus and to know root and leaf growth responses at different P availability condition. The three rice genotypes (IR74, IR74-Pup1, and Kasalath) were analyzed for their genetic composition using SNP markers. The phenotypic experiment was arranged using a Completely Randomized Design with four replications and performed hydroponically in nutrient solution with different availability of P. The result showed that IR74-Pup1 had 84.4% similarities to its parent (IR74) with 13.6% of donor segments, where the Pup1 locus located. The influence of Pup1 locusintrogression on total length, surface area, diameter, and volume of the root varied at each growth stage. IR74 and IR74-Pup1 had root and leaf growth restriction on low P, but Pup1 locus introgression showed better growth performance, both in normal P and in low P conditions. The introgression of Pup1 locus increases plant ability to reduce the impact of growth inhibitioncaused by P deficiency.