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Introduksi Konstruk Gen CsNitr1-L dengan Promotor Ubiquitin melalui Agrobacterium tumefaciens dan Deteksi Molekulernya pada Padi Kultivar Nipponbare Enngarini, Wening; Polosoro, Aqwin; Sustiprijatno, Sustiprijatno; Trijatmiko, Kurniawan Rudi
JURNAL BIOLOGI INDONESIA Vol 13, No 2 (2017): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v13i2.3400

ABSTRACTNitrogen based fertilizers such as urea and NPK are primary needs for rice farmers. To get significant improvement of crop yield, the more quantity of fertilizers are applied. It make negative impact for surrounding environment. Based on that, the efforts should be done to suppress the demand of fertilizers such as by developing Nitrogen Use Efficiency crops. CsNitr1-L is one of gene that related to Nitrogen Use Efficiency trait in plant. The objectives of this research are to develop the construction of CsNitr1-L gene candidate in pCAMBIA1300-Ubi1 promoter and to obtain the transformants of rice cultivar Nipponbare which contain the construction of CsNitr1-L gene candidate. The construction of pCAMBIA1300::Ubi1::CsNitr1-L has successfully assembled and was transformed to immature embryo of rice cultivar Nipponbare using Agrobacterium tumefaciens strain LBA4404. It was obtained 146 lines of T0 Nipponbare. PCR analysis of T0 Nipponbare lines showed that 66 of them was identified as positive T0 lines contained hptII and CsNitr1-L genes. Transformation efficiency obtained was 11,9%. The result of analysis copy number using Southern Hybridization in positive PCR of T0 lines randomly indicated that 4 lines have a single copy of transgene. Based on these results, it can be concluded that CsNitr1-L gene construct was successfully introduced into the genome of the rice plant cultivar Nipponbare and the positive PCR of T0 lines containing the gene of hptII and CsNitr1-L, also a single copy of the transgene was obtained.Keywords: Nitrogen use efficiency trait, gene construction, rice kultivar Nipponbare

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)

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.

INTRODUKSI KONSTRUK GEN CSNITR1-L DENGAN PROMOTOR UBIQUITIN MELALUI AGROBACTERIUM TUMEFACIENS DAN DETEKSI MOLEKULERNYA PADA PADI KULTIVAR NIPPONBARE Enngarini, Wening; Polosoro, Aqwin; Sustiprijatno, Sustiprijatno; Trijatmiko, Kurniawan Rudi
JURNAL BIOLOGI INDONESIA Vol 13, No 2 (2017): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v13i2.3400

ABSTRACTNitrogen based fertilizers such as urea and NPK are primary needs for rice farmers. To get significant improvement of crop yield, the more quantity of fertilizers are applied. It make negative impact for surrounding environment. Based on that, the efforts should be done to suppress the demand of fertilizers such as by developing Nitrogen Use Efficiency crops. CsNitr1-L is one of gene that related to Nitrogen Use Efficiency trait in plant. The objectives of this research are to develop the construction of CsNitr1-L gene candidate in pCAMBIA1300-Ubi1 promoter and to obtain the transformants of rice cultivar Nipponbare which contain the construction of CsNitr1-L gene candidate. The construction of pCAMBIA1300::Ubi1::CsNitr1-L has successfully assembled and was transformed to immature embryo of rice cultivar Nipponbare using Agrobacterium tumefaciens strain LBA4404. It was obtained 146 lines of T0 Nipponbare. PCR analysis of T0 Nipponbare lines showed that 66 of them was identified as positive T0 lines contained hptII and CsNitr1-L genes. Transformation efficiency obtained was 11,9%. The result of analysis copy number using Southern Hybridization in positive PCR of T0 lines randomly indicated that 4 lines have a single copy of transgene. Based on these results, it can be concluded that CsNitr1-L gene construct was successfully introduced into the genome of the rice plant cultivar Nipponbare and the positive PCR of T0 lines containing the gene of hptII and CsNitr1-L, also a single copy of the transgene was obtained.Keywords: Nitrogen use efficiency trait, gene construction, rice kultivar Nipponbare

Resistance Analysis of CRISPR/Cas9 Genome-Edited Chili M2 Mutant Lines against Pepper Yellow Leaf Curl Viral Disease Prasetya, Wandy Murti; Hadiarto, Toto; Enggarini, Wening; Polosoro, Aqwin; Suharsono, Suharsono
Jurnal AgroBiogen Vol 17, No 1 (2021): 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.v17n1.2020.p1-10

Pepper yellow leaf curl virus (PepYLCV) infection transmitted by silverleaf whitefly (Bemisia tabaci [Gennadius]) can decrease chili pepper yield up to 100%. At this moment, there is no chili pepper variety resistant to PepYLCV available. Genome editing approach through CRISPR/Cas9 is an effort to develop variety resistance to the viral infection. The purpose of this study was to obtain M2 lines developed by CRISPR/Cas9 system on proliferating cell nuclear antigen (PCNA) gene for resistance to PepYLCV. A total of four M2 lines (C47-7, L84-2, L84-23, and L120-19) consisting of 60 chili plants were tested for their resistance to PepYLCV. PCR analysis was performed to detect the presence (infection) of the virus. The results showed that a total of 35 plants derived from the four lines were resistant to PepYLCV. They consisted of 7 plants from C47-7 line, 11 plants from L84-2 line, 9 plants from L84-23 line, and 8 plants from L120-19 line. PCR analysis confirmed that the resistant plants obtained from this study were negatively infected by the virus. Since not all tested plants were resistant to virus infection, the PCNA gene allele in these resistant lines were most likely heterozigotes. Sequencing of PCNA gene of the resistant lines is needed to confirm that the resistance phenotypes obtained was due to mutation of the gene. Therefore, further selection needs to be performed to obtain stable and PepYLCV-resistant lines.

Optimasi Ekstraksi RNA dan Teknik Kloning: Studi Kasus Kloning Gen Heading Date 3a pada Kelapa Sawit Polosoro, Aqwin; Enggarini, Wening; Kusumanegara, Kusumawaty; Hadiarto, Toto; Miftahudin, Miftahudin; Supena, Ence Darmo Jaya
Vegetalika Vol 13, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/veg.92085

Pembungaan memegang peranan penting bagi tumbuhan karena memfasilitasi rekombinasi genetik, sehingga mendukung perkembangan keragaman genetik yang penting. Keluarga protein phosphatidylethanolamine binding proteins (PEBP) memainkan peran penting dalam mengatur waktu pembungaan dan dormansi benih di beragam spesies tanaman. Penelitian ini bertujuan untuk merancang vektor biner dengan membangun pCAMBIA1300 yang menggabungkan rangkaian gen EgHd3a dari kelapa sawit. Proses konstruksi gen meliputi ekstraksi RNA, sintesis cDNA, amplifikasi gen EgHd3a, kloning gen menjadi vektor kloning, subkloning ke dalam vektor biner pCAMBIA1300, dan diakhiri dengan validasi gen melalui analisis sekuens. Pada ekstraksi RNA, metode PCL-Chisam telah terbukti efektif melalui ekstraksi berulang, meningkatkan kualitas dan kuantitas total RNA. Dalam proses kloaning, metode konvensional menghadapi tantangan dalam memilih lokasi pembelahan yang tepat. Untuk mengatasi kendala ini, penggunaan enzim dengan overhang yang kompatibel diusulkan sebagai solusi potensial. Secara khusus, penggantian BamHI dari BglII telah secara efektif mengatasi tantangan ini. Konfirmasi integrasi fragmen gen ke dalam plasmid pCAMBIA1300 dicapai melalui pengurutan. Meskipun perbedaan diidentifikasi dalam rangkaian EgHd3a-2, perubahan ini tidak berdampak pada asam amino yang dikodekan, sehingga menjaga integritas rangkaian protein

Perbandingan Metode Ekstraksi DNA pada Tanaman Ulin (Eusideroxylon zwageri) Ridzqya, Salsabila Al Alya; Polosoro, Aqwin; Enggarini, Wening; Kusumanegara, Kusumawaty; Helmanto, Hendra; Magandhi, Mahat; Satyawan, Dani; Hadiarto, Toto; Yuniaty, Alice
Buitenzorg: Journal of Tropical Science Vol 1 No 1 (2024): Buitenzorg: Journal of Tropical Science
Publisher : Innovation Centre for Tropical Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.70158/buitenzorg.v1i1.7

DNA isolation is a routine procedure in molecular analysis. The method of plant genome DNA extraction has been widely available throughout global laboratories. Several labs made some modifications to obtain optimal results. This research was aimed to analyse two types of DNA extraction methods for ironwood plant (Eusideroxylon zwageri), one tropical rain forest woody plant known for its high strength and durability. The results indicate that isolation DNA kit produced high DNA purity with lower concentrations while CTAB methods generated lower DNA purity with higher concentrations. This may be used as consideration of DNA isolation for downstream molecular analyses. Keywords: DNA extraction, ironwood, CTAB, genomic DNA

Studi perbandingan DNA barcoding untuk Bambu Awaliah, Seli Rizqi; Polosoro, Aqwin
Buitenzorg: Journal of Tropical Science Vol 1 No 2 (2024): Buitenzorg: Journal of Tropical Science
Publisher : Innovation Centre for Tropical Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.70158/buitenzorg.v1i2.9

The Bambusoideae subfamily, a significant group within the Poaceae family, contains diverse genera with complex taxonomic relationships. This study aimed to elucidate the phylogenetic relationships and genetic diversity within the bamboo, focusing on the utility of DNA barcoding markers, i.e., ITS2, matK, and rbcL, in bamboo species identification. By analyzing sequence data from these markers, phylogenetic trees were constructed using the maximum likelihood method to infer evolutionary relationships among species. The results showed that ITS provides the highest resolution for species-level identification, distinguishing closely related species more effectively than matK and rbcL. While matK demonstrated robust genus-level classification, rbcL was limited by its high conservation, making it more suitable for broader taxonomic groupings. These findings contribute to a better understanding of bamboo taxonomy and highlight the importance of marker selection based on the taxonomic resolution required. The study also emphasizes the complementary use of these markers to provide a comprehensive view of bamboo phylogenetics. Keywords: bamboo taxonomy, DNA barcoding, ITS2, matK, rbcL

Modulasi pembungaan untuk efisiensi pemuliaan dan optimalisasi biomassa: Tinjauan molekuler dan bioteknologi Polosoro, Aqwin
Buitenzorg: Journal of Tropical Science Vol 2 No 1 (2025): Vol. 2 No. 1 (2025): Buitenzorg: Journal of Tropical Science
Publisher : Innovation Centre for Tropical Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.70158/buitenzorg.v2i1.18

Regulation of flowering time is a critical determinant of plant reproductive success and a key trait for optimizing crop adaptation, yield stability, and breeding efficiency. This review highlights recent advances in the molecular pathways controlling flowering, including photoperiod sensing, vernalization and temperature response, autonomous and hormonal regulation, and floral integrator networks. Key genes such as FT, SOC1, FLC, TFL1, and Ghd7 serve as central nodes within these interconnected pathways. The application of genetic engineering tools—including gene overexpression, CRISPR/Cas-mediated knockouts, promoter editing, and transient expression systems—has enabled precise manipulation of flowering phenology across a wide range of crops. These strategies have accelerated fast-track breeding in temperate and tropical perennials and facilitated the enhancement of vegetative biomass in forage and industrial crops through delayed flowering. However, the deployment of flowering-modified genotypes presents challenges, including environmental interactions, phenological trade-offs, biosafety regulation, and potential ecological impacts. Future directions should emphasize the integration of flowering time control with speed breeding platforms, genomic selection, and climate-adaptive trait design, tailored to species—and region—specific requirements. Such multidisciplinary approaches will be vital to advancing crop resilience, productivity, and sustainability under changing environmental conditions. Keywords: flowering time regulation, genetic engineering, FT gene, fast-track breeding, biomass optimization

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 : BRIN

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

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.

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