How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Background: Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. Results: The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci ( 1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. Conclusion: The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

Pre-maps : An Educational Programme for Reading Tactile Maps

It is demanding for children with visual impairment to become aware of the world beyond their immediate experience. They need to learn to control spatial experiences as a whole and understand the relationships between objects, surfaces and themselves. Tactile maps can be an excellent source of information for depicting space and environment. By means of tactile maps children can develop their spatial understanding more efficiently than through direct travel experiences supplemented with verbal explanations. Tactile maps can help children when they are learning to understand environmental, spatial, and directional concepts. The ability to read tactile maps is not self-evident; it is a skill, which must be learned. The main research question was: can children who are visually impaired learn to read tactile maps at the preschool age if they receive structural teaching? The purpose of this study was to develop an educational program for preschool children with visual impairment, the aim of which was to teach them to read tactile maps in order to strengthen their orientation skills and to encourage them to explore the world beyond their immediate experience. The study is a multiple case study describing the development of the map program consisting of eight learning tasks. The program was developed with one preschooler who was blind, and subsequently the program was implemented with three other children. Two of the children were blind from birth, one child had lost her vision at the age of two, and one child had low vision. The program was implemented in a normal preschool. Another objective of the pre-map program was to teach the preschooler with visual impairment to understand the concept of a map. The teaching tools were simple, map-like representations called pre-maps. Before a child with visual impairment can read a comprehensive tactile map, it is important to learn to understand map symbols, and how a three-dimensional model changes to a two-dimensional tactile map. All teaching sessions were videotaped; the results are based on the analysis of the videotapes. Two of the children completed the program successfully, and learned to read a tactile map. The two other children felt happy during the sessions, but it was problematic for them to engage fully in the instruction. One of the two eventually completed the program, while the other developed predominantly emerging skills. The results of the children's performances and the positive feedback from the teachers, assistants and the parents proved that this pre-map program is appropriate teaching material for preschool children who are visually impaired. The program does not demand high-level expertise; also parents, preschool teachers, and school assistants can carry out the program.

Scalloped Hammerhead microsatellite genotypes (eight loci) representing five regions on Australia's east coast and one location in central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Milkshark (Rhizoprionodon acutus) microsatellite genotype data (six loci) from samples collected from five locations in eastern Australia and central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Lobster aquaculture development in Indonesia, Vietnam and Australia

This project will support the sustainable development of lobster farming in Indonesia to meet global demand for tropical lobsters at high prices (>$US60 /kg). It will also address sustainability issues for the lobster farming industry in Vietnam and provide verification of lobster growout at commercial scale in Australia. The project will adapt technologies developed in Vietnam and apply them in Indonesia to establish a village-based industry for impoverished coastal communities. The Australian component will assess land-based growout systems to prepare for the likely availability of hatchery-reared lobster seed. Hatchery technology is currently being commercialised in Queensland through a partnership between DEEDI and Lobster Harvest Pty Ltd.

Improving production of cows and fattening cattle in Indonesia and north Australia

To increase numbers and reproduction in Ongole and Bali cows by as much as 60% in Indonesia requires use of rice straw for maintenance of cows and higher quality feed and crop by-products for growth and fattening of calves. These feedstuffs exist in large quantities. The project will couple feeding systems with management (controlled mating with a selected bull, weaning, compost production), previously developed by the project team, in village-based adaptive research across the main cattle regions of Indonesia, with emphasis on East Java. The project will link with research on nutrition interactions with reproduction of cows in indigenous pastoral systems in north Australia.

Spiny lobster aquaculture development in eastern Indonesia, Vietnam and Australia

The project was successful across all objectives, making demonstrable progress in support of establishing tropical lobster farming in Indonesia. The industry remains most active in Lombok where lobster seed resources are most abundant, and impact has been greatest there. Nevertheless, project activities have established activity and interest in lobster farming in other provinces and particularly Aceh and, South and Southeast Sulawesi. The project met all of its 23 milestones with the exception of publishing a production manual, which has been held over until 2017. For several milestone activities, further research will be required to build on the outcomes generated and reach practical commercial outputs. The research was instigated to address the opportunity to establish a significant small-holder based industry in Indonesia that could alleviate poverty in coastal communities. The premise was that such an industry – lobster farming, had been established in Vietnam, with ACIAR involvement, and it could be replicated in Indonesia where the availability of necessary basic requirements had been confirmed through a previous ACIAR project focussed in Vietnam (FIS/2001/058). The broad aim was to assess, develop and expand the resources of naturally settling lobster seed (puerulus), and develop grow out of those seed to meet export market demand. This was to be achieved by adapting and transferring to Indonesia technology from Vietnam, where lobster farming had become a successful industry producing 1,500 tonnes of export quality lobsters valued at $A100 million.

Sustainable productivity improvements in allium and solanaceous vegetable crops in Indonesia and sub-tropical Australia

The most important vegetable crops grown in Indonesia, and particularly lowland coastal production, are the true shallot and chilli. These crops are usually grown in rotation with rice but are far more valuable crops and are increasingly in high demand. They offer an opportunity for small farmers to generate extra income, increase farm profitability and shift away from subsistence production. However, the yield and profitability of shallot and chilli production is severely limited by a range of agronomic constraints. This project aims towards raising the productivity of allium (shallot and garlic) and chilli/capsicum cropping systems. The methodology will include a benchmarking survey and review of grower practices. This will be supplemented with physical surveys of crops for disease incidence and efficiency of fertiliser use. Once surveys are completed in Indonesia and the important pathogens identified, recommendations can be made for disease management. This will include review of chemical usage in Indonesia and Australia to provide best management guidelines for the application of insecticides, fungicides and other chemicals.

Social Audit Regulation Within the NGO Sector: Practices of NGOs Operating in Bangladesh and Indonesia

Social audit is one of those important mechanisms for strengthening NGOs’ accountability to poor communities (as NGOs’ key beneficiaries). However, conducting social audits within the NGO sector often rests on the individual interests and priorities of donors or NGOs themselves, effectively resulting in self-selection bias, and limiting the effectiveness and usefulness of social audits as a control and evaluation mechanism. The purpose of this chapter is to identify the prevalence, scale, and scope of social audits within the NGO sector, particularly NGOs engaging in microenterprise development programs. Accordingly, this study examined 20 NGOs operating in two countries - Bangladesh and Indonesia. Data were collected from publicly available sources and in-depth interviews with senior executives of the participating NGOs. Further, 10 interviews were conducted with a small sample of beneficiaries (individuals or groups from four of the participating NGOs) in order to gain an understanding of beneficiaries’ perceptions of the NGOs’ social audit mechanism. The findings reveal a range of approaches to social audit among NGOs, as well as the usefulness and limitations of this mechanism for strengthening NGO accountability, particularly to beneficiaries. Findings highlight that within the NGOs investigated the conduct of social audits remained voluntary and was strongly dependant on donors’ requirements. As social audit regulation within the NGO sector is minimal, the findings provide regulators with valuable guidance for better understanding the value of social audit as a mechanism to strengthen accountability of the NGO sector, particularly accountability to beneficiaries.

ACIAR Productivity and profitability enhancing tropical pulses in Indonesia and Australia

The project aims at improving the productivity and profitability of mung beans, soy beans and peanuts.

Liveweight gain and feed intake of weaned Bali cattle fed a range of diets in Central Sulawesi, Indonesia

Three experiments were conducted to determine liveweight (W) gain and feed and water intake of weaned Bali cattle offered a range of feed types. In each experiment, 18 weaned entire male Bali cattle were allocated to three treatment groups in a completely randomised block design, with six replicates (animals) per treatment. The dietary treatments were: Experiment 1, native grass fed ad libitum, native grass supplemented with rice bran at 10 g dry matter (DM)/kg W.day and native grass supplemented with a mixture of rice bran and copra meal in equal proportions fed at 10 g DM/kg W.day; Experiment 2, elephant grass hay fed ad libitum, elephant grass supplemented with gliricidia at 10 g DM/kg W.day, and gliricidia fed ad libitum; and Experiment 3, corn stover fed ad libitum, corn stover supplemented with gliricidia at 10 g DM/kg W.day, and corn stover supplemented with rice bran/copra meal in equal amounts (w/w) at 10 g DM/kg W.day. Each experiment was 10 weeks in duration, consisting of a 2-week preliminary period for adaptation to diets and an 8-week experimental period for the measurement of W change, feed and water intake and digestibility of the diet. Growth rates of 6-12-month-old, entire male Bali cattle fed a range of local diets ranged from 0.10 and 0.40 kg/day. Lowest growth rates occurred when the cattle were given the basal diets of native grass (0.104 kg/day), elephant grass (0.174 kg/day) and corn stover (0.232 kg/day). With the addition of supplements such as rice bran, rice bran/copra meal or gliricidia to these basal diets liveweight gains increased to between 0.225 and 0.402 kg/day. Forage DM intake was reduced with these supplements by on average 22.6% while total DM intake was increased by an average of 10.5%. The growth rate on gliricidia alone was 0.269 kg/day and feed DM intake was 28.0 g/kg W.day. Water intake was not affected by supplement type or intake. In conclusion, inclusion of small quantities of locally available, high quality feed supplements provide small-holder farmers with the potential to increase growth rates of Bali calves from 0.1 to 0.2 kg/day, under prevailing feeding scenarios, to over 0.4 kg/day.

Nipah Virus in the Fruit Bat Pteropus vampyrus in Sumatera, Indonesia

Nipah virus causes periodic livestock and human disease with high case fatality rate, and consequent major economic, social and psychological impacts. Fruit bats of the genus Pteropus are the natural reservoir. In this study, we used real time PCR to screen the saliva and urine of P. vampyrus from North Sumatera for Nipah virus genome. A conventional reverse transcriptase (RT-PCR) assay was used on provisionally positive samples to corroborate findings. This is the first report of Nipah virus detection in P. vampyrus in Sumatera, Indonesia.

Cover page of a binder for maps of Crimea and Ukraine

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Performance-based contracting for roads – Experiences of Australia and Indonesia

Many countries over the last decade, have used performance-based contracting (PBC) to manage and maintain roads. The implementation of PBC provides additional benefits for the government/public such as cost savings and improved conditions of contracted road assets. In Australia, PBC is already being implemented on all categories of roads: national, state, urban and rural. Australian PBC arrangement is designed to turn over control and responsibility for roadway system maintenance, rehabilitation, and capital improvement projects to private contractors. Contractors’ responsibilities include determination of treatment types, the design, programming and the undertaking of works needed to maintain road networks at predetermined performance levels. Indonesia initiated two PBC pilot projects in 2011, the Pantura Section Demak-Trengguli (7.68 kilometers) in Central Java Province and Section Ciasem-Pamanukan (18.5 kilometers) in West Java Province. Both sections are categorized as national roads. The contract duration for both of these projects is four years. To facilitate a possible way forward, it is proposed to conduct a study to understand Australia's experiences of advancing from pilot projects to nation-wide programs using PBC. The study focuses on the scope of contracts, bidding processes, risk allocation, and key drivers, using relevant PBC case studies from Australia. Recommendations for future PBC deployment nation-wide should be based on more research associated with risk allocation. This will include investigation of standard conditions of contract. Implications of the contract clauses for the risk management strategy to be adopted by contractors. Based on the nature of risks, some are best managed by the project owner. It is very important that all parties involved to be open to the new rules of contract and to convince themselves about the potential increased benefits of the use of PBC. The most recent states of challenging issues were explored and described.