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All Journal Jurnal Planta Tropika BERITA BIOLOGI JURNAL BIOLOGI INDONESIA
Nurul Hidayatun
Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian, Jl. Ragunan 29, Pasar Minggu, Jakarta Selatan 12540, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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Pengembangan Identitas Spesifik Berbasis Marka SSR pada 29 Varietas Kedelai Lokal Indonesia Lestari, Puji; Risliawati, Andari; Utami, Dwinita Wikan; Hidayatun, Nurul; Santoso, Tri Joko; Chaerani, Chaerani
JURNAL BIOLOGI INDONESIA Vol 12, No 2 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (765.015 KB) | DOI: 10.14203/jbi.v12i2.2888

Abstract

ABSTRACTSoybean is an important legume crop in Indonesia and local varieties from different regions are diversed. Accurate identification of local varieties is needed to determine the genetic identity in order to protect them to indicate the geographical origin and registration purpose. This study aimed to analyze DNA fingerprints of local varieties of soybean in Indonesia to develop a specific identity using SSR markers along with the marker set. A total of 29 local varieties/accessions was analyzed using 9 selected SSR markers with semi automated genetic analyzer on the basis of capillary electrophoresis. Total markers successfully detected 50 alleles in all varieties, with the average polymorphism information content (PIC) of each locus (0.579) and the genetic diversity index (0.629) were quite high as a reflection of diversity of the local varieties. Based on the analysis of the genetic diversity index, PIC, rare alleles, dominant allele frequency, analysis of genetic distance, 6 SSRs (Satt009, Satt038, Satt177, Satt242, Satt308 and Satt114) were selected as a set of markers for variety identification. Although three varieties can not be distinguished because of their close genetic relationship, but the digital coding indicates that local varieties of soybeans have possessed specific identities (ID) representing variation of SSR alleles. The selected SSR loci with additional identifier can be used to develop ID of Indonesian local soybean in the germplasm collection. Overall, the marker set is a powerful tool to complement morphological markers for the protection of local soybean varieties that contribute in accelerating local varieties improvement in the future agriculture.Keywords: specific identity, SSR, Indonesian local soybean variety, DNA fingerprint.
KERAGAMAN BAKTERI ENDOFITIK DnSOLASI DARI EMPAT VARIETAS PADI DENGAN METODA ARDRA Susilowati, Dwi N; Hidayatun, Nurul; Tasliah, Tasliah; Mulya, K
BERITA BIOLOGI Vol 10, No 2 (2010)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/beritabiologi.v10i2.1978

Abstract

Sixty eight endophytic bacteria were isolated from four different rice varieties (IR64, Cirata, Code and Limboto) obtained from agroecosystem in Cikembar, Sukabumi, West Java. Those isolates were subjected for analysis the diversity based on genetic fingerprinting through Amplified Ribosomal DNA Restriction Analysis (ARDRA) method. The objective of this research is to characterize the predominant endophyte bacteria are present within various rice varieties grown on agroecosystem in Cikembar, Sukabumi by using ARDRA method. The results shows that restriction analysis with both Rsal and HaelH was sufficient to allocate the endophyte bacteria from four different rice varieties into the 29 types. Moreover, Rsal alone was capable of resolving the 11 types, followed by HaelH 14 types. In general, the result may explain that there is no collinierity between the cluster and their host plant. Staphylococcus, Bacillus, Agrobacterium, Serratia, Klebsiella, Acidovorax and Pseudomonas were identified as endophytic bacteria from rice varieties in this agroecosystem based on their 16S rRNA sequences. Seven types were placed in close proximity to these genera, but other types were still unknown. Among these isolates, genera Staphylococcus and Bacillus are common to rice endophytes.
IDENTIFIKASI 26 ISOLAT BAKTERI ENDOFITIK DAN FILOSFER PADI DENGAN ANALISIS SEKUEN16S RDNA Hidayatun, Nurul; Susilowati, Dwi N; K Mulya, K Mulya
BERITA BIOLOGI Vol 10, No 4 (2011)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (408.127 KB) | DOI: 10.14203/beritabiologi.v10i4.763

Abstract

The research was subjected to identify 26 endophytic and phyllosphere bacteria isolated from 4 rice varieties using sequencing method of 16S rDNA.The sequences were then aligned with reference sequence from Gen-Bank data library by BLAST program from NCBI to find the most related identity of the isolates analysed.The sequencing analysis revealed that some isolates have a high identity to Staphylococcus and Serratia (5 isolates each), Bacillus (4 isolates), Microbacteria (3 isolates), Pseudomonas (2isolates) and Klebsiella, Acidovorak, Bulkholderiaceae, Agrobacterium and Shewanella (1 isolate each). No specific isolate dominated in both endophytic and phyllosphere group, nor host-specific isolate found in the four rice varieties.
PENGEMBANGAN IDENTITAS SPESIFIK BERBASIS MARKA SSR PADA 29 VARIETAS KEDELAI LOKAL INDONESIA Lestari, Puji; Risliawati, Andari; Utami, Dwinita Wikan; Hidayatun, Nurul; Santoso, Tri Joko; Chaerani, Chaerani
JURNAL BIOLOGI INDONESIA Vol 12, No 2 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v12i2.2888

Abstract

ABSTRACTSoybean is an important legume crop in Indonesia and local varieties from different regions are diversed. Accurate identification of local varieties is needed to determine the genetic identity in order to protect them to indicate the geographical origin and registration purpose. This study aimed to analyze DNA fingerprints of local varieties of soybean in Indonesia to develop a specific identity using SSR markers along with the marker set. A total of 29 local varieties/accessions was analyzed using 9 selected SSR markers with semi automated genetic analyzer on the basis of capillary electrophoresis. Total markers successfully detected 50 alleles in all varieties, with the average polymorphism information content (PIC) of each locus (0.579) and the genetic diversity index (0.629) were quite high as a reflection of diversity of the local varieties. Based on the analysis of the genetic diversity index, PIC, rare alleles, dominant allele frequency, analysis of genetic distance, 6 SSRs (Satt009, Satt038, Satt177, Satt242, Satt308 and Satt114) were selected as a set of markers for variety identification. Although three varieties can not be distinguished because of their close genetic relationship, but the digital coding indicates that local varieties of soybeans have possessed specific identities (ID) representing variation of SSR alleles. The selected SSR loci with additional identifier can be used to develop ID of Indonesian local soybean in the germplasm collection. Overall, the marker set is a powerful tool to complement morphological markers for the protection of local soybean varieties that contribute in accelerating local varieties improvement in the future agriculture.Keywords: specific identity, SSR, Indonesian local soybean variety, DNA fingerprint.
Evaluasi Karakter Morfo-fisiologis Sumber Daya Genetik Padi Berumur Genjah Setyowati, Mamik; Hidayatun, Nurul; Sutoro, Sutoro; Kurniawan, Hakim
PLANTA TROPIKA: Jurnal Agrosains (Journal of Agro Science) Vol 2, No 2 (2014)
Publisher : Universitas Muhammadiyah Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18196/pt.2014.025.66-73

Abstract

Rice varieties with short maturity and high productivity can be achieved when there is available genetic resources in a sufficient level of variability. Morphological characters, such as leaf thickness and crop growth rate, could affect in crop productivity. Evaluation of seed germination rate, crop growth rate,  and their efficiency used for nitrogen have been done on 25 accessions of rice. Seed germination rate of B11283-6C-PN-5-MR-34-1-1-3, Lariang, B11742-RS-2-3-MR-34-1-2-3 reached 1,0-1,3 g/hill/day during seed initiation, while Dodokan and Silugonggo reached 0.7-0.8 g/hill/day. Danau Atas, B.11283-6C-PN-5-MR-2-3-Sl-1-2-1-1, B11742-RS-2-3-MR-34-1-2-3 and B11742-RS-2-3-MR-34-1-4-1 lines show good perfomance, moreover B11742-RS-2-3-MR-34-1-1-3, B11742-RS-2-3-MR-34-1-1-4 and B11742-RS-2-3-MR-34-1-1-4 lines produced grain yield higher than Silugonggo and Dodokan varieties. Those lines could be harvested at about 96 days after planting.
Co-Authors A.A. Ketut Agung Cahyawan W Andari Risliawati, Andari Chaerani Chaerani Dwi N Susilowati DWINITA WIKAN UTAMI Hakim Kurniawan, Hakim K Mulya, K Mulya Mamik Setyowati, Mamik Mulya, K PUJI LESTARI Sutoro Sutoro Tasliah Tasliah TRI JOKO SANTOSO