INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE

51-58

Authors: Edy Listanto, Eny Ida Riyanti, Tri Joko Santoso, Toto Hadiarto and A. Dinar Ambarwati

Development of potato cultivars with high levels of broad spectrum resistance is a key long-term management strategy against late blight disease caused by Phytophthora infestans. Six progeny lines of hybridization between transgenic potato Katahdin SP951 with non-transgenic Granola and Atlantic were selected based on agronomical characteristics and resistance to late blight disease. The study aimed to analyze the number of insertions and stability of inserted RB gene in the transgenic potato lines. The research was carried out through plant DNA extraction, southern blot analysis and polymerase chain reaction (PCR). Southern blot analysis was used to detect the number of inserts integrated into potato genome, while PCR analysis was used to detect stability of RB gene from generation to generation. The results showed that the progenies obtained from hybridization between Atlantic and transgenic Katahdin SP951 (lines No. 20 and 27) and between Granola and transgenic Katahdin SP951 (line No. 69) contained one copy number of RB gene, according to the probing of nptII. The result is similar to that of inserted RB gene found in the parental transgenic Katahdin SP951. The presence of RB gene in four different generations (G0, G1, G2 and G3) showed stable integration of the gene into the plant genome. The single copy number of RB gene will repress the occurrence of silencing gene expression. The stability analysis of RB gene can determine that the gene is still present in plant genome after several generations.

71-78

Authors: Rubiyo, Nur Kholilatul Izzah, Indah Sulistiyorini and Cici Tresniawati

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

87-96

Authors: NLP Indi Dharmayanti and Risza Hartawan

Epidemiological studies on H5N1 avian influenza viruses indi-cated that the viruses do not transmit efficiently from human to human. Transmissibility of viruses among human population is very complex and polygenic. Studies on molecular determinants facilitating interspecies transmission of the viruses suggested that two polymerase complex proteins such as PB2 and PB1-F2 are important. PB2 is critical in determining the host specificity, whereas mutations in PB1-F2 increase the viral virulence. The study aimed to characterize the polymerase complex of PB2 and PB1-F2 proteins of H5N1 avian influenza viruses isolated from Indonesia. The DNA samples encoding the PB2 and PB1-F2 complex proteins of several H5N1 isolates were sequenced and analyzed. Pathogenicity of the viruses was studied in both avian and mammal models. The sequencing results showed that there was no mutation in both proteins of PB2 and PB1-F2 of the avian influenza virus isolates. The molecular character for host specificity was consistent with the animal experiment results. The H5N1 virus isolates were only infectious and pathogenic in chickens, but not in BALB/C mice as the mammal model. The study suggests that host range of H5N1 virus isolates of Indonesia is restricted to poultry and not transmisible to mammal model used in this study.

1-10

Authors: Sutoro, Puji Lestari, Reflinur and Hakim Kurniawan

Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.

21-30

Authors: Elza Surmaini, Tri Wahyu Hadi, Kasdi Subagyono and Nanang Tyasbudi Puspito

Indonesia consistently experiences dry climatic conditions and droughts during El Niño, with significant consequences for rice production. To mitigate the impacts of such droughts, robust, simple and timely rainfall forecast is critically important for predicting drought prior to planting time over rice growing areas in Indonesia. The main objective of this study was to predict drought in rice growing areas using ensemble seasonal prediction. The skill of National Oceanic and Atmospheric Administration’s (NOAA’s) seasonal prediction model Climate Forecast System version 2 (CFSv2) for predicting rice drought in West Java was investigated in a series of hindcast experiments in 1989-2010. The Constructed Analogue (CA) method was employed to produce downscaled local rainfall prediction with stream function (y) and velocity potential (c) at 850 hPa as predictors and observed rainfall as predictant. We used forty two rain gauges in northern part of West Java in Indramayu, Cirebon, Sumedang and Majalengka Districts. To be able to quantify the uncertainties, a multi-window scheme for predictors was applied to obtain ensemble rainfall prediction. Drought events in dry season planting were predicted by rainfall thresholds. The skill of downscaled rainfall prediction was assessed using Relative Operating Characteristics (ROC) method. Results of the study showed that the skills of the probabilistic seasonal prediction for early detection of rice area drought were found to range from 62% to 82% with an improved lead time of 2-4 months. The lead time of 2-4 months provided sufficient time for practical policy makers, extension workers and farmers to cope with drought by preparing suitable farming practices and equipments.

39-50

Authors: Dwi N. Susilowati, I M. Sudiana, N.R. Mubarik and A. Suwanto

Rhizobacteria are important components of soil and directly or indirectly influence the soils quality and plant growth for maintaining adequate plant nutrition and reducing the negative environmental effects of fertilizers. Applying high dose of chemical fertilizers in most of rice fields in the coastal areas could reduce the quality of the soil in the long time. There are few studies addressed to verify the species and functional diversity of cultivable rhizobacteria associated with rice plant in the coastal soils. The objective of the study was to verify the species and functional diversity of rhizobacteria isolated from the coastal soils of two rice production areas of Subang and Indramayu, West Java. Special focus was given to verify phosphate solubilization, nitrogen fixation, IAA and cellulase production of the selected 78 strains of rice rhizobacteria isolated from the coastal paddy field, as well as taxonomical analyses based on 16S rRNA. The results showed that among 78 bacterial isolates from the coastal paddy field, mostly were belonging to the Firmicutes, most of them affiliated with genera Bacillus, 75 strains produced IAA, 32 strains fixed nitrogen, 37 strains solubilized phosphate and 33 strains produced cellulase. Several strains of the rhizobacteria were capable of producing plant growth promoting substances (PGPR), alone or in combination, such as IAA, fixing nitrogen, solubilizing phosphate, and producing cellulase. Taking all of these diverse PGPR characteristics into account, it is clear that the 78 identified isolates have great potential for improving saline soils of the coastal paddy fields in Indonesia.

47-54

Authors: Eny Ida Riyanti, Edy Listanto, Alberta Dinar Ambarwati

Late blight caused by Phytophthora infestans is an important disease on potato. Several potato hybrids have been generated by crossing local varieties (Atlantic and Granola) with Katahdin SP951 which contains late blight resistance gene RB. Prior to release, these hybrids need to be evaluated for their environ-mental effects on non-target organisms and natural pests and diseases. The objectives of the study were to investigate the effect of LBR potato hybrids on beneficial soil microbes, pests and diseases. The trial was conducted in the confined field trial (CFT) in Lembang, West Java. The parental non-transgenic (NT) clones (Granola, Atlantic and Katahdin) and LBR hybrids (four clones of Atlantic x Katahdin SP951 hybrids; 10 clones of Granola x Katahdin SP951) were planted at a plant spacing of 30 cm x 70 cm. Fungicide applications were used as treat-ments (no spray, five and twenty times sprays). The experi-ment was arranged in a randomized completely block design with three replications. The parameters determined were popula-tions of N2 fixing and P solubilizing bacteria, soil C/N ratio as well as natural pests and diseases. The results showed that the transgenic LBR potato hybrids did not have negative effect on N fixing bacteria. The bacterial populations were around 1010-11 cells g-1 soil before planting, 1012 cells at 1.5 months after planting (MAP) and 108 cells after harvest. For P- solubilizing bacteria, their populations were 1010 cells before planting, 1012 cells at 1.5 MAP and 1011 cells g-1 soil after harvest. The soil C/N ratio of the transgenic plot was not statistically different compared to non-transgenic plot, i.e. 12-15 before planting, 10-11 at 1.5 MAP, and 10 after harvest in non-spray plot. Pests and diseases such as Alternaria solani, Liriomyza, potato tubber moth, aphid and mites on the transgenic and non-transgenic plots were statistically not different. The resistance score for A. solani was 7.2 (parental tansgenic) and 7.6 (parental non-transgenic); for Liriomyza it was 2.07 (parental transgenic) and 2.32 insect per plant (parental non-transgenic), the PTM was 0.63 (parental transgenic) and 0.73 insect per plant (parental non-transgenic), aphid and mites were 0.75 (parental transgenic) and 1.68 insects per plant (parental non-transgenic). The study indicated that LBR potato hybrids did not have any negative impacts on non-target organisms.

65-70

Authors: I Nyoman Widiarta, Adolf Bastian, Syahrir Pakki

Green leafhopper (GLH), Nephotettix virescens, is the most efficient vector of rice tungro virus disease. The disease is endemic in some provinces of Indonesia and commonly con-trolled using resistant varieties. Resistance of rice varieties to tungro could be classified into resistance to a virus and a vector. The history of GLH resistant varieties adoption affected the GLH adaptation in an area. The study was conducted in the period of 2009-2011 to evaluate the resistance status of five GLH resistant rice variety groups (T0-T4) using survival and transmission test. The GLH populations were collected from 15 tungro endemic provinces in Indonesia. The GLH was then reared in the greenhouse before used for the test. The degree of resistance to tungro viruses was calculated by adding the value of survival (weight x score of survival rate) and virus transmission rate (weight x score of transmission rate). The weights for survival and transmission rate were set to 40 and 60, respectively. The results showed that the rank of resistant variety groups in decreasing order of resistance were T4, T1, T2 and T3. Five variations in GLH transmission efficiency were identified, i.e. 170, 070, 050, 030 and 010. GLH populations from Bali and West Nusa Tenggara were the most efficient vector for rice tungro virus. We concluded that there were diversities in the degree of resistance among GLH resistant varieties. Variation in virus transmission efficiency (biotype) among GLH populations collected from various tungro endemic areas closely related to the history of adoption of rice varieties.

79-85

Authors: Siti Dewi Indrasari, Shinta Dewi Ardhiyanti, Buang Abdullah

Rice is an important source of vitamin B1 and folic acid, but cultivated rice cultivars contain low of these nutrient. Breeding program had been conducted and several advanced lines with a high vitamin B and folic acid contents were found. This research aimed to study the contents of vitamin B1 and folic acid in the brown rice and milled rice of fifteen promising lowland rice lines. Dried paddy (14% moisture content) were husked in the mini husker (Satake THU 35A) to obtain brown rice and milled rice by using abrasive-type mini polisher (Satake TM-05, 1,450 RPM for 2 minutes). Vitamin B1 and folic acid in the brown rice and milled rice were determined by using HPLC equipped with fluorescence detector for vitamin B1 and UV detector for folic acid. Four out of fifteen rice lines studied showed a unique characteristic of vitamin B1 content in the brown rice and milled rice. Rice lines which have highest vitamin B1 in the brown rice were B10267-4-PN-6-2-3-2-2-2-3-3-2 (3.03 mg 100 g-1), B10876H-MR-2 (2.13 mg 100 g-1), B10531E-KN-1-2-PN-1-4-2 (1.33 mg 100 g-1) and B12411E-RS*-1-2-1 (1.21 mg 100 g-1). However after milling, 43-92% of their vitamin B1 were lost; the least loss was observed in B12411E-RS*-1-2-1 (1.21 mg 100 g-1) which was only 4%. Three out of fifteen rice lines studied has highest folic acid in brown rice, i.e. BP400G-PN-12-3-6 (158.5 µg 100 g-1), B10876H-MR-2 (152.0 µg 100 g-1), and B11742-RS*-2-3-MR-5-5-1-Si-1-3 (100.0 µg 100 g-1). After milling the line B10876H-MR-2 had the highest folic acid content (52.0 µg 100 g-1), much higher than that of Ciherang variety as a control. This study indicates the importance of having a suitable milling instrument to minimize loss of vitamin B1 and folic acid. The study also suggests the importance of creating new rice cultivars that have high nutrient and resistant to milling process.

1-10

Authors: Nurindah, Dwi Adi Sunarto

Cotton production nationally is low due to various constraints, including pests. Two main pests commonly found in cotton plantation in rain fed fields are cotton leafhopper (Amrasca biguttula) and cotton bollworm (Helicoverpa armigera). The study aimed to evaluate four packages of integrated pest management (IPM) techniques to control cotton leafhopper and cotton bollworm in rain fed fields. The experiment was conducted in farmers’ fields at Asembagus, East Java, between January and July 2012. Four packages of IPM evaluated were cotton varieties, i.e. Kanesia 10 or Kanesia 13, and seed treatment with synthetic insecticide (imidacloprid) before sowing or spraying molasses (10 ml L-1 water) as food for natural enemies. The cotton plants were intercropped with groundnut and sprayed with neem seed extract (NSE) at the action threshold level for pest control. These packages were compared among themselves and also with the methods usually used by farmers, i.e. planting cotton variety Kanesia 8 intercropped with groundnut and pest control using synthetic chemical insecticides. Twenty five plants were sampled randomly per plot and measured for their growth, leafhopper and bollworm populations, as well as cotton seed yield per plot. Observations were made weekly, starting at 30 days after planting (DAP) until 120 DAP. The results showed that the use of Kanesia 10 or Kanesia 13 intercropped with groundnut and spraying molasses to conserve natural enemies was the best pest management practice and superior to farmers’ practices. Conserving natural enemies is not only profitable (saving production cost of IDR1,150,000 to IDR1,500,000 ha-1 season-1), but also safe for the environment (no need to spray chemical insecticides).

17-28

Authors: Puspi Eko Wiranthi, Heny Kuswanti Suwarsinah, Andriyono Kilat Adhi

Indonesian Food Security Council in 2009 issued a Food Security and Vulnerability Atlas (FSVA) which stated that there were 100 districts in Indonesia which were most vulnerable to food insecurity and 79% of which were located in eastern region. By using Susenas regular data in 2008, this study aimed to analyze determinants of household food security in eastern compared to western region. The ordered logistic regression model was employed to investigate the determinants of household food security. The result showed that most of households in Indonesia were vulnerable to food insecurity (41.76%). The percentage in eastern region (48.56%) was higher than that in western region (41.76%). Increase in expenditure equivalent, age and education level of household head, female household head, small household size, household head’s occupation in non-agriculture and urban household would increase the probability of a household to become food secure in both regions. The difference was in the factor of access to electricity in eastern and access to safe drinking water and loan in western region. Policies which aim to increase education, credit access, and intensive family planning have big roles in improving household food security.

35-45

Authors: Eni Maftu’ah, Azwar Ma'as, Benito Heru Purwanto

Peat soil is characterized by poor nitrogen (N) availability. Ameliorants are expected to rectify this problem. This research aimed to study the effect of ameliorant on N availability and N uptake by sweet corn plant in degraded peatland. The experiment was conducted in the greenhouse in May-July 2011 and on peatland of Kalampangan Village, Palangkaraya, Central Kalimantan in September-December 2011. Burnt peat soil of Kalampangan was used in the greenhouse experiment and sweet corn was used as an indicator plant. The treatments consisted of two factors, i.e. compositions of ameliorants by weight (A1 = 80% chicken manure + 20% dolomite; A2 = 80% local farm weed + 20% dolomite; A3 = 80% mineral soil + 20% dolomite; A4 = 20% chicken manure + 20% local farm weed + 20% residue of Chinese water chestnut (Eleocharis dulcis) + 20% mineral soil + 20% dolomite; and A5 = 19% chicken manure + 71.5% mineral soil + 9.5% dolomite) and rates of those ameliorants (5, 10, 15, 20 and 25 t ha-1). The experiment was arranged in a completely randomized block design with three replications. Data were collected every two weeks for five times. Observations were made on soil pH, available N (NH4+, NO3-), plant height, and N uptake in root and shoot. The results showed that treatment A1 increased soil pH and availability of NH4+ and NO3- in peat soils at the maximum vegetative stage. Treatment A1 provided the highest N availability and N uptake by the plant. Field experiment showed that N uptake increased with the plant yield. Optimum yield of fresh corn cob was obtained from treatment A1 at the rate of 20 t ha-1. This research reconfirms the effectiveness of chicken manure and dolomite as peat soil ameliorant.

47-54

Authors: A. Wihardjaka, S. Djalal Tandjung, B. Hendro Sunarminto, Eko Sugiharto

Rice cultivation is one of the antropogenic sources of nitrous oxide (N2O) emission that is produced by microbiological nitrification-denitrification processes. Incorporating soil amendment in rainfed rice soil attempted to increase soil productivity, while nematicide application aimed to maintain root growth system. Incorporating soil amendment and nematicide application are predicted to suppress N2O production in lowland rice. The objective of this research was to study the interaction of soil organic amendment and nematicide on N2O emission and nitrogen uptake from rainfed lowland rice soils. A field experiment was conducted in rainfed lowland rice soils during 2010/2011 wet season (direct seeded rice) and 2011 dry season (transplanted rice). The 3 x 3 factorial trial was arranged in a randomized completely block design with three replications. The first factor was soil amendment consisted of without rice straw, fresh rice straw and composted rice straw. The second factor was nematicide application consisted of without nematicide, neemcake and carbofuran. Variables measured were N2O flux, rice grain yield and nitrogen uptake. Incorporation of fresh and composted rice straws reduced N2O flux about 49.2% and 59.9% in transplanted rice, and 32.9% and 28.2% in direct seeded rice, respectively. The neemcake application reduced N2O emission about 44-50%, while carbofuran application decreased N2O emission by 23-35%. Neemcake has a good potential as nitrification inhibitor of N2O emission, so the neem trees have a prospect to be cultivated intensively. The reduction of N2O emission was effective in direct seeded rice system with the application of neemcake and fresh rice straw, however, in transplanted rice system it was effective with neemcake and composted rice straw applications.

63-70

Authors: Budi Tangendjaja

Dried distillers grains with solubles (DDGS) is a co-product of ethanol industry made from grains through fermentation process and it can be used for animal feeding especially for dairy cows. A feeding trial on US corn DDGS was conducted at commercial dairy farm in Vietnam during hot condition in 2010. One hundred and fifty six dairy cows in a later stage of milk production were allotted randomly in three groups of 52 cows with similar milk production. Three dietary treatments offered comprised control diet, diet with 7.5% DDGS and diet with 15% DDGS. The diets were formulated to contain similar nutrient profiles and comprised forages (corn, elephant grass and alfalfa hay), brewery waste, soybean curd waste, corn, soybean meal, molasses and commercial dairy supplement. The diet was manufactured locally in total mixed ration system and delivered two times per day. Milk production, feed consump-tion and milk quality were measured for 5 days before the trial and 45 days after the trial. The result demonstrated that feeding DDGS could support higher milk production without affecting feed consumption. Feeding DDGS at 7.5% and 15% resulted in higher milk production of 2 and 4 kg per day respectively compared to cows fed control diet. Feed intake remained unaffected at around 35 kg per day. Milk quality as measured by total solid and fat content was similar in cows fed the control diet and DDGS at 7.5%. Feeding DDGS at 15% tended to have slightly better total solid and fat content. Feeding DDGS was able to reduce cost of the diets; diet cost for control, DDGS 7.5% and DDGS 15% were VND 2537, 2460 and 2399 per kg, respectively. It is concluded that DDGS can be economically used for feeding dairy cows in hot climate condition and improving milk production.

79-86

Authors: Meynarti Sari Dewi Ibrahim, Rr. Sri Hartati, Rubiyo, Agus Purwito, Sudarsono

Propagation of Coffea arabica L. through direct and indirect somatic embryogenesis technique is promising for producing large number of coffee seedlings. The objectives of the research were to evaluate methods for direct and indirect somatic embryo-genesis induction of C. arabica var. Kartika. The explants were the youngest fully expanded leaves of arabica coffee. The evalu-ated medium was modified Murashige and Skoog (MS) medium supplemented with a combination of 2.26 µM 2,4-D + 4.54 or 9.08 µM thidiazuron; 4.52 µM 2,4-D + 4.54 or 9.08 µM thidiazuron; or 9.04 µM 2,4-D + 9.08 µM thidiazuron. Both calli (100 mg) and pre-embryos developed from the edge of leaf explants were subcultured into regeneration medium (half strength MS with modified vitamin, supplemented with kinetine 9.30 µM and adenine sulfate 40 mg L-1). The results showed coffee leaf explant cultured on medium containing 2.26 µM 2,4-D + 4.54 or 9.08 µM thidiazuron to induce direct somatic embriogenesis from explant, while that of 4.52 or 9.04 µM 2,4-D + 9.08 µM thidiazuron to induced indirect somatic embrio-genesis. The medium for calli induction from coffee by explants was medium supplemented with 4.52 or 9.04 µM 2,4-D in combination with 9.08 µM thidiazuron. On the other hand, the best medium for activation of induction of somatic embryos was MS medium supplemented with 9.04 µM 2,4-D + 9.08 µM thidiazuron. Based on this results, the first step for developing micropropagation for coffee has been resolved. The subsequent studies will be directed to evaluate agronomic performance of the derived planting materials.