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Vu G.T.H.,Aberystwyth University | Dear P.H.,Medical Research Council Laboratory of Molecular Biology | Caligari P.D.S.,Sumatra Bioscience | Wilkinson M.J.,Aberystwyth University
PLoS ONE | Year: 2010

Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning ∼ 10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual "BAC-HAPPY-mapping" to convert BAC landing data into BAC linkage contigs is possible. © 2010 Vu et al.

Tohiruddin L.,Sumatra Bioscience | Foster H.L.,Sumatra Bioscience
Journal of Oil Palm Research | Year: 2013

Trials by Sumatra Bioscience have shown that high quality compost can be produced by composting empty oil palm fruit bunches with oil mill effluent in an open windrow system over 25 days. Fifteen tonnes of the final product typically contains 105 kg N, 16 kg P, 168 kg K and 26 kg Mg, which is close to the average nutrient levels applied to oil palm in Sumatra as inorganic fertiliser per year, except for P which is lower in the compost. Thus, compost applied alone clearly has the potential to replace the inorganic fertilizers usually applied to oil palm. Two trials have been carried out to compare the effectiveness of compost and inorganic fertilisers applied to oil palm on a typical volcanic ash soil in North Sumatra and to determine the optimal rate and method of application of the compost. The first trial tested a factorial combination of three rates of compost, urea, rock phosphate and muriate of potash. The highest rate of compost (10 t ha-1 yr-1) applied alone increased the FFB yield from 23.1 up to 26.8 t ha-1 yr-1 over a three-year period, which is an increase of 0.37 t ha -1 yr-1 FFB per tonne of compost applied each year. A similar yield was achieved with 2 kg urea plus 1 kg rock phosphate (there was no response to K fertiliser), which based on the nutrient content of the two materials, indicates that the N and P in the compost were 66% and 37% more effective than the nutrients in the inorganic fertilizer (and confirms that the P content in the compost is more than adequate). The greater efficiency of compost compared to the inorganic fertilisers in supplying N and P to the oil palms was also confirmed by the higher recovery of these nutrients into the palm fronds. The highest yield of 28.7 t ha-1 yr-1 in this trial was achieved with 10 t ha-1 yr-1 compost plus 2 kg urea and 2 kg rock phosphate, indicating that if only compost is applied, the highest rate will be needed to achieve the optimal yield. In the second trial, compost alone was tested at incremental rates of up to 20 t ha-1 yr-1, applied as a patch between the avenues and as 1, 2 and 3 m bands down the avenues. The optimal yield over three years was achieved with 15 t ha -1 yr-1 compost, which increased FFB production from 26.9 to 32.6 t ha-1 yr-1; which is an increase of 0.38 t ha-1 yr-1 FFB per tonne of compost applied per year and this is in very close agreement with the response recorded in the first trial. There were no significant differences due to the different methods of application of the compost. As in the first trial, N and P nutrient contents in the fronds were very significantly increased by the compost, but not K, due to a high K nutrient reserve level in the soil. The cost of producing 1 t of compost by the windrow method and applying it in the field in Lonsum estates has been calculated as USD 10, so the application of 15 t ha-1 of compost in the second trial would cost USD 150. Application of inorganic fertilisers at the same nutrient rates as 15 t compost ha-1 yr-1 at 65% moisture content is approximately twice as expensive as compost. Taking into account the greater efficiency of compost in supplying nutrients, replacement of inorganic fertilisers with compost would save the costs of inorganic fertilisers almost three times as much. However in the trial area, K and Mg fertilisers were not required, so savings by switching to compost at this particular location would be less.

Nasution O.,Sumatra Bioscience | Sitorus A.C.,Sumatra Bioscience | Nelson S.P.C.,Sumatra Bioscience | Forster B.P.,BioHybrids International Ltd. | Caligari P.D.S.,BioHybrids International Ltd.
Journal of Oil Palm Research | Year: 2013

Non-euploid seedlings occur naturally in many plant species including oil palm but at frequencies usually considered too low for practical purposes. A low cytometry method is described that overcomes the diiculty of exploiting such low frequency events and provides a practical plant breeding methodology to identify noneuploids/haploids within large sample sizes. In addition, the eiciency of detecting non-euploid seedlings can also be increased greatly by a pre-screen for abnormal phenotypes. Oil palm is relatively diicult to analyse via low cytometry as tissue disruption initiates secondary metabolite production which interferes with the analyte and data capture. The addition of dithiothreitol and polyvinylpyrrolidone during sample preparation, followed by cold incubation, prior to analysis overcomes these problems. The high-throughput method developed allows the analysis of 1000 samples per day per low cytometer. The number of haploids produced by this method rivals that of other haploid production systems and is currently the only known method of generating haploids in oil palm. Additionally, the method for oil palm is not season dependent and may be performed all year round. The method can be applied to other species and provides a practical means of harvesting naturally occurring non-euploid. The seedlings selected using this methodology can be grown, thus making the method applicable to a range of species and disciplines including evolutionary studies of speciation of polyploids, reproductive biology, embryology and the production of haploids and doubled haploids for genetic studies and plant breeding of oil palm.

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