Pub Date : 2016-10-25DOI: 10.21082/IJAS.V5N2.2004.P4562
L. Pouyaud, R. Gustiano, G. Teugels
Catfishes are generally one of the economically important groups of fresh and brackish water fishes in the world. In many countries, they form a significant part of inland fisheries, and several species have been introduced in fish culture. Judging from literature, the main constraint to cultivate wild species and to optimise the production of pangasiid catfishes is due to the poorly documented systematics of this family. In the present contribution, the phylogenetic relationships within Pangasiidae are studied to contribute to a better insight in their taxonomy and evolution. The genetic relatedness is inferred using mitochondrial 12S rDNA gene sequences. To resolve the phylogenetic position of Laides in this group of catfish, five genera of Asian and African Schilbeidae are also considered. The results showed that a species group (complex) could be clearly seen in the genetic tree. Pangasius is more derive than the other genera. By using approximate molecular clock/evolutionary calibration from mitochondrial gene, a new episode of speciation for the family marked explosive radiation about 5- 8 million years ago (mya). This adaptive radiation extended until the Late Pleistocene. Regarding the relationships between the Pangasiidae and Schilbeidae, two families show an allopatric distribution with slight overlap. The Pangasiidae occur mainly in Southeast Asia, while the Schilbeidae are seen mainly on the Indian subcontinent (including Myanmar) and Africa. It confirms the separation between Schilbeidae and Pangasiidae occurred in the Early Miocene.
{"title":"CONTRIBUTION TO THE PHYLOGENY OF THE PANGASIIDAE BASED ON MITOCHONDRIAL 12S RDNA","authors":"L. Pouyaud, R. Gustiano, G. Teugels","doi":"10.21082/IJAS.V5N2.2004.P4562","DOIUrl":"https://doi.org/10.21082/IJAS.V5N2.2004.P4562","url":null,"abstract":"Catfishes are generally one of the economically important groups of fresh and brackish water fishes in the world. In many countries, they form a significant part of inland fisheries, and several species have been introduced in fish culture. Judging from literature, the main constraint to cultivate wild species and to optimise the production of pangasiid catfishes is due to the poorly documented systematics of this family. In the present contribution, the phylogenetic relationships within Pangasiidae are studied to contribute to a better insight in their taxonomy and evolution. The genetic relatedness is inferred using mitochondrial 12S rDNA gene sequences. To resolve the phylogenetic position of Laides in this group of catfish, five genera of Asian and African Schilbeidae are also considered. The results showed that a species group (complex) could be clearly seen in the genetic tree. Pangasius is more derive than the other genera. By using approximate molecular clock/evolutionary calibration from mitochondrial gene, a new episode of speciation for the family marked explosive radiation about 5- 8 million years ago (mya). This adaptive radiation extended until the Late Pleistocene. Regarding the relationships between the Pangasiidae and Schilbeidae, two families show an allopatric distribution with slight overlap. The Pangasiidae occur mainly in Southeast Asia, while the Schilbeidae are seen mainly on the Indian subcontinent (including Myanmar) and Africa. It confirms the separation between Schilbeidae and Pangasiidae occurred in the Early Miocene.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67801895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-10-25DOI: 10.21082/IJAS.V4N1.2003.P12-17
E. Ginting, J. Arcot, Julian M. Chox
Megaloblastic anaemia, neural tube defects, coronary heart disease, and some forms of cancer have been linked to an inadequate dietary intake of folate. Legumes are good sources of folate, however, processing may affect folate availability in legume foods. This study investigated the folate content and retention during the preparation of tofu through the trienzyme treatment (protease, α-amylase, and human plasma) and microbiological assay using Lactobacillus casei. The results showed that the total folate content was considerably reduced during tofu preparation, from 273.4 µg 100 g-1 dwb in soybean seed to 108.4 µg 100 g-1 dwb in tofu, yielding a folate retention of 40%. Folate losses were mainly due to leaching into the water during soaking and pressing as well as heat destruction during milling and boiling. High folate loss (51%) was particularly found in the whey. A shorter soaking time (8 hours), optimum extraction, and pressing methods were suggested with respect to minimizing folate losses during tofu preparation. This study suggests that the consumption of 100 g of deep-fried tofu may satisfy 21% of the recommended dietary intake (RDI).
{"title":"DETERMINATION OF FOLATE RETENTION DURING TOFU PREPARATION USING TRIENZYME TREATMENT AND MICROBIOLOGICAL ASSAY","authors":"E. Ginting, J. Arcot, Julian M. Chox","doi":"10.21082/IJAS.V4N1.2003.P12-17","DOIUrl":"https://doi.org/10.21082/IJAS.V4N1.2003.P12-17","url":null,"abstract":"Megaloblastic anaemia, neural tube defects, coronary heart disease, and some forms of cancer have been linked to an inadequate dietary intake of folate. Legumes are good sources of folate, however, processing may affect folate availability in legume foods. This study investigated the folate content and retention during the preparation of tofu through the trienzyme treatment (protease, α-amylase, and human plasma) and microbiological assay using Lactobacillus casei. The results showed that the total folate content was considerably reduced during tofu preparation, from 273.4 µg 100 g-1 dwb in soybean seed to 108.4 µg 100 g-1 dwb in tofu, yielding a folate retention of 40%. Folate losses were mainly due to leaching into the water during soaking and pressing as well as heat destruction during milling and boiling. High folate loss (51%) was particularly found in the whey. A shorter soaking time (8 hours), optimum extraction, and pressing methods were suggested with respect to minimizing folate losses during tofu preparation. This study suggests that the consumption of 100 g of deep-fried tofu may satisfy 21% of the recommended dietary intake (RDI).","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67801493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-10-01DOI: 10.21082/ijas.v17n2.2016.p65-74
R. Reflinur, P. Lestari, Suk-ha Lee
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.
{"title":"THE POTENTIAL USE OF SSR MARKERS TO SUPPORT THE MORPHOLOGICAL IDENTIFICATION OF INDONESIAN MUNGBEAN VARIETIES","authors":"R. Reflinur, P. Lestari, Suk-ha Lee","doi":"10.21082/ijas.v17n2.2016.p65-74","DOIUrl":"https://doi.org/10.21082/ijas.v17n2.2016.p65-74","url":null,"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.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-10-01DOI: 10.21082/ijas.v17n2.2016.p49-56
E. Listanto, E. I. Riyanti, Sustiprijatno Sustiprijatno
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 npt II 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 npt II and hpt genes and resulted 700 bp and 500 bp for fragments of npt II 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 npt II 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.
{"title":"Agrobacterium tumefaciens-MEDIATED IN-PLANTA TRANSFORMATION OF INDONESIAN MAIZE USING pIG121Hm-Cs PLASMID CONTAINING nptII AND hpt GENES","authors":"E. Listanto, E. I. Riyanti, Sustiprijatno Sustiprijatno","doi":"10.21082/ijas.v17n2.2016.p49-56","DOIUrl":"https://doi.org/10.21082/ijas.v17n2.2016.p49-56","url":null,"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 npt II 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 npt II and hpt genes and resulted 700 bp and 500 bp for fragments of npt II 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 npt II 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.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-10-01DOI: 10.21082/ijas.v17n2.2016.p75-83
Muhammad Imam Nugraha, W. Annisa, L. Syaufina, S. Anwar
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.
泥炭地毛管水对植物根区供水具有重要作用。在一些水位较浅的地区，根系区当前的含水量主要取决于地下水位。通过观察泥炭土颜色、水分分布、含水量和疏水性的变化，研究了不同土壤密度和地下水位下泥炭土的毛细水动力学。这项研究是在南加里曼丹Banjarbaru的印度尼西亚沼泽农业研究所的温室中进行的。试验采用2因素、3个重复的随机区组设计。第一个因素是泥炭的容重(BD)，即BD-1(实际为0.1 g cm-3)和BD-2(压缩为0.2 g cm-3)。第二个因子是模拟地下水位(GWL)，由GWL-1 (-100 cm)、GWL-2 (-70 cm)和GWL-3 (-40 cm)组成。结果表明:泥炭土毛管水分的上升高度最大可达50 cm，其特征是表层含水量的上升幅度分别为105 ~ 127%和141 ~ 181%;用BD-2处理GWL-3的水含量最高(308%)，用BD-1处理GWL-1的水含量最低(37%)。由于BD-2的微孔数量较多，因此随着BD值的增加，毛细水量逐渐增加。
{"title":"CAPILLARY WATER RISE IN PEAT SOIL AS AFFECTED BY VARIOUS GROUNDWATER LEVELS","authors":"Muhammad Imam Nugraha, W. Annisa, L. Syaufina, S. Anwar","doi":"10.21082/ijas.v17n2.2016.p75-83","DOIUrl":"https://doi.org/10.21082/ijas.v17n2.2016.p75-83","url":null,"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.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-10-01DOI: 10.21082/ijas.v17n2.2016.p41-48
N. Heryani, B. Kartiwa, Y. Apriyana, H. Syahbuddin
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.
{"title":"PRODUCTION AND QUALITY ENHANCEMENT OF MANGO USING FAN JET SPRAYER IRRIGATION TECHNIQUE","authors":"N. Heryani, B. Kartiwa, Y. Apriyana, H. Syahbuddin","doi":"10.21082/ijas.v17n2.2016.p41-48","DOIUrl":"https://doi.org/10.21082/ijas.v17n2.2016.p41-48","url":null,"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.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-10-01DOI: 10.21082/ijas.v17n2.2016.p57-64
I. M. Tasma, D. Satyawan, H. Rijzaani, I. Rosdianti, P. Lestari, Rubiyo Rubiyo
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.
{"title":"GENOMIC VARIATION OF FIVE INDONESIAN CACAO (Theobroma cacao L.) VARIETIES BASED ON ANALYSIS USING NEXT GENERATION SEQUENCING","authors":"I. M. Tasma, D. Satyawan, H. Rijzaani, I. Rosdianti, P. Lestari, Rubiyo Rubiyo","doi":"10.21082/ijas.v17n2.2016.p57-64","DOIUrl":"https://doi.org/10.21082/ijas.v17n2.2016.p57-64","url":null,"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.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-01DOI: 10.21082/ijas.v17n1.2016.p9-16
Yosi Zendra Joni, R. Prihatini, D. Efendi, I. Roostika
Somatic embryogenesis is a technique for regenerating embryos derived from somatic cells of various plant species. This technique along with the utilization of plant growth regulator (PGR) might benefit for mass propagation and improvement of plant species through biotechnological tools. The study aimed to determine the effect of different plant growth regu-lators, namely 6-benzyladenine (BA) and thidiazuron (TDZ) on the embryogenic callus induction as well as casein hydrolysate and malt extract on the somatic embryo development of mangosteen. The explants used were in vitro young stems of mangosteen clone Leuwiliang. This study consisted of two experiments, namely induction of embryogenic callus and formation of somatic embryo. The first experiment was arranged as factorial in a completely randomized design with BA (0 and 0.7 mg l-1) as the first factor and TDZ (0, 0.1, 0.5 and 1.0 mg l-1) as the second factor. The second experiment consisted of four treatments, i.e. casein hydrolysate and malt extract at the rate of 500 and 1,000 mg l-1. The results showed that the best medium for embryogenic callus induction was MS supplemented with 0.1 mg l-1 TDZ, which resulted semifriable calli. Casein hydrolysate and malt extract could not induce the formation of somatic embryos. After two times subcultures on the same MS medium supplemented with 0.5 mg l-1 TDZ and 0.7 mg l-1 BA, a total of 33.8 somatic embryos per explant was induced. The successful somatic embryogenesis would support mangosteen breeding and in vitro mass propagation program.
{"title":"EFFECT OF DIFFERENT SOURCES OF PLANT GROWTH REGULATOR ON THE INDUCTION AND DEVELOPMENT OF MANGOSTEEN SOMATIC EMBRYOS","authors":"Yosi Zendra Joni, R. Prihatini, D. Efendi, I. Roostika","doi":"10.21082/ijas.v17n1.2016.p9-16","DOIUrl":"https://doi.org/10.21082/ijas.v17n1.2016.p9-16","url":null,"abstract":"Somatic embryogenesis is a technique for regenerating embryos derived from somatic cells of various plant species. This technique along with the utilization of plant growth regulator (PGR) might benefit for mass propagation and improvement of plant species through biotechnological tools. The study aimed to determine the effect of different plant growth regu-lators, namely 6-benzyladenine (BA) and thidiazuron (TDZ) on the embryogenic callus induction as well as casein hydrolysate and malt extract on the somatic embryo development of mangosteen. The explants used were in vitro young stems of mangosteen clone Leuwiliang. This study consisted of two experiments, namely induction of embryogenic callus and formation of somatic embryo. The first experiment was arranged as factorial in a completely randomized design with BA (0 and 0.7 mg l-1) as the first factor and TDZ (0, 0.1, 0.5 and 1.0 mg l-1) as the second factor. The second experiment consisted of four treatments, i.e. casein hydrolysate and malt extract at the rate of 500 and 1,000 mg l-1. The results showed that the best medium for embryogenic callus induction was MS supplemented with 0.1 mg l-1 TDZ, which resulted semifriable calli. Casein hydrolysate and malt extract could not induce the formation of somatic embryos. After two times subcultures on the same MS medium supplemented with 0.5 mg l-1 TDZ and 0.7 mg l-1 BA, a total of 33.8 somatic embryos per explant was induced. The successful somatic embryogenesis would support mangosteen breeding and in vitro mass propagation program.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-01DOI: 10.21082/ijas.v17n1.2016.p37-34
R. Prihatini, N. Saleh
Natural exposure of extremely low frequency electromagnetic field (ELF-EMF) occurs in the environment and acts as one of the abiotic factors that affect the growth and development of organisms. This study was conducted to determine the effect of ELF-EMF on the tissue cultured banana and slipper orchid chlorophyll content as one of the indicators in measuring plant photosynthetic capacity. Four days old banana (Musa sp. cv. Berangan) corm and seven days old slipper orchid (Paphiopedilum rothschildianum) cultures were exposed to 6 and 12 mT ELF-EMF generated by controllable ELF-EMF built up machine for 0.5, 1, 2 and 4 hours. After exposure, the banana and orchid cultures were incubated at 25° C for 8 and 16 weeks, respectively. The results showed that the ELF-EMF exposure had different effects on banana and slipper orchid cultures though both plant species belong to monocotyledon. The highest increase in chlorophyll content on banana was resulted by the high intensity and long duration of ELF-EMF exposure (12 mT for 4 hours), whereas on slipper orchid the modest and short duration of ELF-EMF exposure produced the most excessive chlorophyll content. Different ELF-EMF exposures (12 mT for 4 hours and 6 mT for 30 minutes) had potential to be applied on each plant to improve in vitro plant (banana and slipper orchid, respectively) growth. The increased chlorophyll and carotene/xanthophyll content on banana indicated that the banana was more tolerant to ELF-EMF exposure compared to slipper orchid.
{"title":"SENSITIVITY OF PIGMENT CONTENT OF BANANA AND ORCHID TISSUE CULTURE EXPOSED TO EXTREMELY LOW FREQUENCY ELECTROMAGNETIC FIEL","authors":"R. Prihatini, N. Saleh","doi":"10.21082/ijas.v17n1.2016.p37-34","DOIUrl":"https://doi.org/10.21082/ijas.v17n1.2016.p37-34","url":null,"abstract":"Natural exposure of extremely low frequency electromagnetic field (ELF-EMF) occurs in the environment and acts as one of the abiotic factors that affect the growth and development of organisms. This study was conducted to determine the effect of ELF-EMF on the tissue cultured banana and slipper orchid chlorophyll content as one of the indicators in measuring plant photosynthetic capacity. Four days old banana (Musa sp. cv. Berangan) corm and seven days old slipper orchid (Paphiopedilum rothschildianum) cultures were exposed to 6 and 12 mT ELF-EMF generated by controllable ELF-EMF built up machine for 0.5, 1, 2 and 4 hours. After exposure, the banana and orchid cultures were incubated at 25° C for 8 and 16 weeks, respectively. The results showed that the ELF-EMF exposure had different effects on banana and slipper orchid cultures though both plant species belong to monocotyledon. The highest increase in chlorophyll content on banana was resulted by the high intensity and long duration of ELF-EMF exposure (12 mT for 4 hours), whereas on slipper orchid the modest and short duration of ELF-EMF exposure produced the most excessive chlorophyll content. Different ELF-EMF exposures (12 mT for 4 hours and 6 mT for 30 minutes) had potential to be applied on each plant to improve in vitro plant (banana and slipper orchid, respectively) growth. The increased chlorophyll and carotene/xanthophyll content on banana indicated that the banana was more tolerant to ELF-EMF exposure compared to slipper orchid.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-01DOI: 10.21082/ijas.v17n1.2016.p1-8
W. Annisa, D. Nursyamsi
Organic matter has a function to maintain reductive conditions and to chelate toxic elements in acid sulphate soils. The study aimed to assess the dynamics of ferrous iron (Fe2+) in acid sulphate soil and its correlation with soil redox potential (Eh) and plant growth. The experiment was arranged in two factorial randomized block design with three replications. The first factor was two types of organic matter: (1) control (without organic matter), (2) rice straw and (3) rush weed (Eleocharis dulcis). The second factor was time of decomposition of organic matter: I1 = 2 weeks, I2 = 4 weeks, I3 = 8 weeks, and I4 = 12 weeks (farmer practice). The results showed that concentration of ferrous iron in the soil ranged from 782 to 1308 mg kg-1 during the rice growing season. The highest constant rate of iron reduction (k F2+) was observed on application of rice straw and rush weed with decomposition time of 8 weeks with the k Fe2+ value of 0.016 and 0.011 per day, respectively, while the ferrous iron formation without organic matter had the k Fe2+ value of 0.077 per day. The ferric iron (Fe3+) reduction served as a function of soil Eh as indicated by the negative correlation of ferrous iron and Eh (r = -0.856*). Organic matter decreased exchangeable iron due to chelating reaction. Iron concentration in roots was negatively correlated with soil soluble iron (r = -0.62*). Application of rice straw decomposed for 8 weeks increased the height of rice plant up to 105.67 cm. The score of Fe2+ toxicity at 8 weeks after planting ranged from 2 to 3, so rice crop did not show iron toxicity symptoms.
{"title":"IRON DYNAMICS AND ITS RELATION TO SOIL REDOX POTENTIAL AND PLANT GROWTH IN ACID SULPHATE SOIL OF SOUTH KALIMANTAN, INDONESIA","authors":"W. Annisa, D. Nursyamsi","doi":"10.21082/ijas.v17n1.2016.p1-8","DOIUrl":"https://doi.org/10.21082/ijas.v17n1.2016.p1-8","url":null,"abstract":"Organic matter has a function to maintain reductive conditions and to chelate toxic elements in acid sulphate soils. The study aimed to assess the dynamics of ferrous iron (Fe2+) in acid sulphate soil and its correlation with soil redox potential (Eh) and plant growth. The experiment was arranged in two factorial randomized block design with three replications. The first factor was two types of organic matter: (1) control (without organic matter), (2) rice straw and (3) rush weed (Eleocharis dulcis). The second factor was time of decomposition of organic matter: I1 = 2 weeks, I2 = 4 weeks, I3 = 8 weeks, and I4 = 12 weeks (farmer practice). The results showed that concentration of ferrous iron in the soil ranged from 782 to 1308 mg kg-1 during the rice growing season. The highest constant rate of iron reduction (k F2+) was observed on application of rice straw and rush weed with decomposition time of 8 weeks with the k Fe2+ value of 0.016 and 0.011 per day, respectively, while the ferrous iron formation without organic matter had the k Fe2+ value of 0.077 per day. The ferric iron (Fe3+) reduction served as a function of soil Eh as indicated by the negative correlation of ferrous iron and Eh (r = -0.856*). Organic matter decreased exchangeable iron due to chelating reaction. Iron concentration in roots was negatively correlated with soil soluble iron (r = -0.62*). Application of rice straw decomposed for 8 weeks increased the height of rice plant up to 105.67 cm. The score of Fe2+ toxicity at 8 weeks after planting ranged from 2 to 3, so rice crop did not show iron toxicity symptoms.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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