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INDONESIA
Indonesian Journal of Agricultural Science
Published by Kementerian Pertanian
ISSN : 1411982X     EISSN : 23548509     DOI : -
Core Subject : Agriculture,
Agriculture, Biological Sciences & Forestry
The journal publishes primary research articles from any source if they make a significant original contribution to the experimental or theoretical understanding of some aspect of agricultural science in Indonesia. The definition of agricultural science is kept as wide as possible to allow the broadest coverage in the journal. Accredited base on Director Decree of Indonesian Institute of Science No. 816/D/2009 with acreditation No. 172/AU1/P2MBI/08/2009. IJAS is newly accredited by the Indonesian Institute of Science in 2012 (No. 473/AU2/P2MI-LIPI/08/2012) for period of 2012-2015.
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Articles 5 Documents
 1 
Search results for , issue "Vol 17, No 2 (2016): October 2016" : 5 Documents clear
GENOMIC VARIATION OF FIVE INDONESIAN CACAO (Theobroma cacao L.) VARIETIES BASED ON ANALYSIS USING NEXT GENERATION SEQUENCING I Made Tasma; Dani Satyawan; Habib Rijzaani; Ida Rosdianti; Puji Lestari; Rubiyo Rubiyo
Indonesian Journal of Agricultural Science Vol 17, No 2 (2016): October 2016
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v17n2.2016.p57-64

Abstract

Indonesian cacao productivity is still low mainly due to the lack availability of superior cacao planting materials. A new breeding method is necessary to expedite cacao yield improvement programs. To date, no study has yet been done to characterize Indonesian cacao varieties at the whole genome level. The objective of this study was to characterize genomic variation of five superior Indonesian cacao varieties using next-generation sequencing. Genetic materials used were five Indonesian cacao varieties, i.e. ICCRI2, ICCRI3, ICCRI4, SUL2 and ICS13. Genome sequences were mapped to the cacao reference genome sequence of Criollo variety. Sequence alignment and genomic variation discovery were done using Bowtie2 and mpileup software of Samtools, respectively. A total of 2,326,088 single nucleotide polymorphisms (SNPs) and 362,081 insertions and deletions (Indels) were obtained from this study. In average, a DNA variant was identified in every 121 nucleotides of the genome sequence. Most of the DNA variants were located outside the genes. Only 347,907 SNPs and Indels (13.18%) were located within protein coding region (exon).  Among the DNA variations within exon, 188,949 SNPs caused missense mutation and 1,535 SNPs induced nonsense mutation.  Unique gene-based SNPs were also discovered from this study that can be used as fingerprints for the particular cacao variety. The DNA variants obtained were excellent DNA marker resources to support cacao breeding programs. The SNPs discovered are useful as materials for genome-wide SNP chip development to be used for gene and QTL tagging of important traits for expediting national cacao breeding program.
Agrobacterium tumefaciens-MEDIATED IN-PLANTA TRANSFORMATION OF INDONESIAN MAIZE USING pIG121Hm-Cs PLASMID CONTAINING nptII AND hpt GENES Edy Listanto; Eny Ida Riyanti; Sustiprijatno Sustiprijatno
Indonesian Journal of Agricultural Science Vol 17, No 2 (2016): October 2016
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v17n2.2016.p49-56

Abstract

Maize (Zea mays L.) productivity in Indonesia is challenged to be increased using genetic engineering. Recent advances in Agrobacterium tumefaciens-mediated in-planta transforma-tion makes it possible to transform maize with low cost, and simple method. This study aimed to confirm pIG121Hm-Cs plasmid in A. tumefaciens, and to estimate the efficiency level of  A. tumefaciens-mediated in-planta transformation of Indonesian maize by using pIG121Hm-Cs plasmid containing nptII and hpt genes. A series of studies were conducted including confirmation of gene construct of pIG121Hm-Cs plasmid in A. tumefaciens, transformation of four maize lines through A. tumefaciens-mediated in-planta technique, acclimatization of transformant plants and molecular analysis of selected plants using polymerase chain reaction (PCR). The pIG121Hm-Cs plasmid was confirmed via PCR analysis using specific primers of nptII and hpt genes and resulted 700 bp and 500 bp for fragments of nptII and hpt, respectively. After selection, acclimatization and molecular analysis steps, the efficiency levels of transformation of four maize lines were low, ranging from 3.8% to 12.8%. The level of transformation efficiency of ST-27 line was the highest accounting for 12.8% of 45 planted embryos on selection medium based on PCR analysis using specific primer for nptII gene. Overall, A. tumefaciens-mediated in planta transformation on maize floral pistil in this study proved to be successful and rapid. Therefore, this enhanced transformation method will be beneficial for Indonesian maize genetic engineering.
PRODUCTION AND QUALITY ENHANCEMENT OF MANGO USING FAN JET SPRAYER IRRIGATION TECHNIQUE Nani Heryani; Budi Kartiwa; Yayan Apriyana; Haris Syahbuddin
Indonesian Journal of Agricultural Science Vol 17, No 2 (2016): October 2016
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v17n2.2016.p41-48

Abstract

Lack of water in reproductive phases (flowering, fruit formation and maturation) of mango can reduce fruit production and quality. In these phases the plant must be protected from water stress. The aim of the research was to assess the effect of irrigation on the productivity and quality of mango fruits. The study was conducted at the Cukurgondang Experimental Station, Pasuruan, East Java, from April to December 2013, using 40 mango trees of 21 year-old Arumanis variety. Mangoes were planted on five rows with eight plants for each row and 6 m x 6 m spacing within the row. Fan jet sprayer irrigation was installed using hose according to plant diameter. The irrigation technique of fan jet sprayer with four nozzles per plant was applied at 125, 100, 75, 50 and 0% of crop water requirements or equal to 828, 663, 497, 331 and 0 liters of water per tree, every seven days. The parameters observed were the number and weight of fallen fruits and the number, weight and quality of mangoes harvested. The results showed that irrigation of 50% and 75% of crop water requirement had the highest and lowest number of fallen fruits (26% and 14% of total production), respectively. The highest and lowest total number of mangoes were 3.108 and 1904 fruits, respectively, which were achieved at irrigation of 50% and 75% of crop water requirement. Further, the highest and lowest total weight of mango fruits were 1036.2 and 677.9 kg respectively which were achieved at irrigation of 50% and 125% of crop water requirement. Mango fruits produced were dominated by grades 2 and 3 with A quality.
CAPILLARY WATER RISE IN PEAT SOIL AS AFFECTED BY VARIOUS GROUNDWATER LEVELS Muhammad Imam Nugraha; Wahida Annisa; Lailan Syaufina; Syaiful Anwar
Indonesian Journal of Agricultural Science Vol 17, No 2 (2016): October 2016
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v17n2.2016.p75-83

Abstract

Capillary water in peatlands has a very important role in supplying water to the root zone of plants. The current water content in the root zone depends mainly on groundwater levels in some areas with shallow water levels. The study aimed to measure the capillary water dynamics in peat soils at various soil densities and groundwater levels which were observed from the changes in peat color, moisture distribution, water content and hydrophobicity of peat soil. The study was conducted in the greenhouse of Indonesian Swampland Agricultural Research Institute, Banjarbaru, South Kalimantan. The experiment was arranged in a randomized block design with two factors and three replications. The first factor was the bulk density (BD) of peat, namely BD-1 (on actual condition, 0.1 g cm-3) and BD-2 (compressed into 0.2 g cm-3). The second factor was simulated groundwater levels (GWL) consisting of GWL-1 (-100 cm), GWL-2 (-70 cm) and GWL-3 (-40 cm) from soil surfaces. The results showed that the rise of capillary water in peat soil reached a maximum height of 50 cm which was characterized by the increase in water content at the top layer in the range of 105–127% for BD-1 and 141–181% for BD-2. The highest value of water content (308%) was achieved in the treatment of GWL-3 with BD-2 and the lowest (37%) was in the treatment of GWL-1 with BD-1. The rate of capillary water rose progressively corresponded to the increase in BD value because the number of micropores of BD-2 was greater.
THE POTENTIAL USE OF SSR MARKERS TO SUPPORT THE MORPHOLOGICAL IDENTIFICATION OF INDONESIAN MUNGBEAN VARIETIES Reflinur Reflinur; Puji Lestari; Suk-Ha Lee
Indonesian Journal of Agricultural Science Vol 17, No 2 (2016): October 2016
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v17n2.2016.p65-74

Abstract

Mungbean varieties were mainly characterized based on morphological traits. Molecular genetic approach is expected to help the breeder in identification of mungbean varieties in more detail and to protect intellectual property right. This study aimed to identify Indonesian mungbean varieties based on DNA fingerprint profile using a marker set to support morphological characters. A total of 22 Indonesian mungbean accessions were characterized based on 21 morphological traits and 55 simple sequence repeats (SSRs) primers. Of the total 22 mungbean varieties used in the present study, 16 varieties were improved varieties and remaining six varieties were local varieties originated from Java, Nusa Tenggara and Sulawesi collected in GeneBank of ICABIOGRAD. The results showed that the 21 morphological characters were not sufficient to differentiate 22 mungbean varieties, while SSR analysis revealed that eight multi-alleles markers and high polymorphic information content (PIC) values have been successfully selected for varietal identification. The selected markers enabled to differentiate each mungbean variety according to their genetic marker with the lowest distance of 0.125, demonstrating the robustness of the selected marker set as a tool to identify a specific DNA fingerprint profile as a varietal identity (ID). The genetic identity of a variety was shown by digital barcoding which represented a series of alleles produced by corresponding markers. The DNA fingerprint profile of each variety would be beneficial as reference identities of a mungbean variety. 

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