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All Journal Indonesian Journal of Agricultural Science BERITA BIOLOGI JURNAL BIOLOGI INDONESIA ANNALES BOGORIENSES
Joko Prasetiyono
Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Immunology & microbiology Medicine & Pharmacology

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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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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.
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.
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.
PERBAIKAN PADI (Oryza sativa L.) VARIETAS CIHERANG UNTUK SIFAT UMUR GENJAH DAN PRODUKSI TINGGI MENGGUNAKAN MARKA MOLEKULER Prasetiyono, Joko; Tasliah, Tasliah; Dadang, Ahmad; Fatimah, Fatimah
BERITA BIOLOGI Vol 12, No 1 (2013)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (365.173 KB) | DOI: 10.14203/beritabiologi.v12i1.518

Abstract

The improvement of rice (Oryza sativa L.) Ciherang variety for early maturity and high production traits was carried out by Marker Assisted Backcrossing (MAB) method using Nipponbare as donor parent. The foreground selection of Hd2 gene was laid on flanking markers of RM1362 and RM7601 in QTL region. The selection process of F1 to BC2F2 plants were based on molecular markers and agronomic characters. The BC2F3 plants were challenged to bacterial leaf blight to know their resistance in this hybridization. The results indicated that the foreground and background selection were not sufficient as selection tools therefore they would be more accurate if assosiated with agronomic characters. Four selected lines derived from Ciherang x Nipponbare crossed (BC2F3 plant # 283, 307, 373, and 462) could be promising lines with early maturity and high productioncompared to Ciherang. Selected BC2F3 lines flowered earlier than original Ciherang up to 7-10 days, while the yield increasing was 3.55 to 9.2% higher based on weight of filled grains/plant, and from 3.58 to 19.39% higher based on the number of filled grain/plant. However, all of BC2F3 lines were not resistant to bacterial leaf blight attack.
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   
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 
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   
Co-Authors Ahmad Dadang Baroya, Mushlihatun Baroya, Mushlihatun Baroya, Mushlihatun Fatimah . fatimah Fatimah Iman Ridwan, Iman Kurniawan Rudi Trijatmiko, Kurniawan Rudi Masumah, Masumah Muhammad Yunus Polosoro, Aqwin Sustiprijatno Sustiprijatno, Sustiprijatno Tasliah Tasliah Tintin Suhartini Tri Puji Priyatno