School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemOn assessing some of the net effects of IPM(Australian Agricultural and Resource Economics Society, 1996)The potential costs and benefits, private and external, of a shift to Integrated Pest Management (IPM) are considered. A method is developed to estimate the private net returns of IPM in particular farm situations. This method is then applied to compare the financial characteristics of IPM and conventional systems in apple and grain legume production in Victoria. A key finding is that in a 'typical year' of a 'typical operation' the annual net returns of a shift to IPM, in both crops, could be positive. Externalities associated with IPM may be positive or negative depending on the circumstances.
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ItemAn economic evaluation of alternative pest management strategies in Northern Victorian peach orchards(Australian Agricultural Economics Society, 1994)
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ItemThe tax Australia has to have(Australian Agricultural Economics Society, 1994)
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ItemThe decision to invest in lime for acid soils(Australian Agricultural Economics Society, 1994)This study is about how to make long-term farm management decisions effectively when the amount of information available is extremely limited. Long-term decisions rely on judgements of input responses and outcomes which are uncertain or unknown. This is the reality of farm management decision-making. Complex decisions have to be based, in part, on some very ‘soft’ data. Therefore, good decision-making relies on good judgement. Judgement derives from lessons from experience (old information), and from the assimilation of new information generated by analysis of all the available information. In this study, information about liming acid soils in north-eastern Victoria is used, along with farm management information, to generate further information, and thus facilitate the making of some judgements about the economic merit of investing in lime on a particular farm. Soil acidity is a physical phenomenon which has the potential to lower agricultural production and reduce farm profitability. The potential of soil acidity to lower agricultural production has led to it being described as a serious problem for agricultural activities in south-eastern Australia (Coventry 1985; Coventry et. al. 1987a; Cregan 1980; Ellington 1984b; Evans 1991; Helyar et. al. 1990; Reeves and Ellington 1985; and Williams 1980). Making long-term farm management decisions with the limited information which is available requires finding a way to analyse and assimilate the available and new information, and then presenting it in such a way that sound judgements can be made about the likelihood of the possible outcomes actually eventuating. In this study, the standard farm management investment technique discounted cash flow analysis is used. To facilitate making sound judgements about the likelihood of outcomes, a break-even method is developed and applied to the major unknown parameter. The break-even level of the critical factor in the investment provides the decision-maker, who is looking ahead in a world of very uncertain input responses and outcomes, with something concrete on which to focus. Judgements can be formed about the likelihood of this critical level of the critical variable being achieved. The analysis of liming as an investment provides information on the yields required for an investment in lime on the case study farm to break-even, that is, to cover all costs, including the opportunity cost of capital. The judgement made as to whether such yields are achievable will determine whether liming is a worthwhile investment on the case study farm and, implicitly, whether soil acidity is a problem requiring action by the case study farmer at this stage.
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ItemNo Preview AvailableSix-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene(NATL ACAD SCIENCES, 2007-01-23)Increased seed production has been a common goal during the domestication of cereal crops, and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype, with additional, strictly rudimentary, lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently, the origin of the six-rowed phenotype remained unknown. In the present study, we isolated vrs1 (six-rowed spike 1), the gene responsible for the six-rowed spike in barley, by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes, suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly, at different times and in different regions, through independent mutations of Vrs1.
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ItemNo Preview AvailableAnalysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of rice-barley micro collinearity by a transposition(SPRINGER, 2007-05)In cultivated barley (Hordeum vulgare ssp. vulgare), six-rowed spikes produce three times as many seeds per spike as do two-rowed spikes. The determinant of this trait is the Mendelian gene vrs1, located on chromosome 2H, which is syntenous with rice (Oryza sativa) chromosomes 4 and 7. We exploited barley-rice micro-synteny to increase marker density in the vrs1 region as a prelude to its map-based cloning. The rice genomic sequence, covering a 980 kb contig, identified barley ESTs linked to vrs1. A high level of conservation of gene sequence was obtained between barley chromosome 2H and rice chromosome 4. A total of 22 EST-based STS markers were placed within the target region, and the linear order of these markers in barley and rice was identical. The genetic window containing vrs1 was narrowed from 0.5 to 0.06 cM, which facilitated covering the vrs1 region by a 518 kb barley BAC contig. An analysis of the contig sequence revealed that a rice Vrs1 orthologue is present on chromosome 7, suggesting a transposition of the chromosomal segment containing Vrs1 within barley chromosome 2H. The breakdown of micro-collinearity illustrates the limitations of synteny cloning, and stresses the importance of implementing genomic studies directly in the target species.
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ItemNo Preview AvailableGenetic characterization of Iranian native Bombyx mori strains using amplified fragment length polymorphism markers(OXFORD UNIV PRESS INC, 2007-06)Genetic relationships within and among seven Iranian native silkworm strains was determined by DNA fingerprinting by using amplified fragment length polymorphism (AFLP) markers. In total, 189 informative AFLP markers were generated and analyzed. Estimates of Nei's gene diversity for all loci in individual strains showed a higher degree of genetic similarity within each studied strain. The highest and the least degrees of gene diversity were related to Khorasan Pink (h = 0.1804) and Baghdadi (h = 0.1412) strains, respectively. The unweighted pair-group method with arithmetic average dendrogram revealed seven strains of silkworm, Bombyx mori (L.), resolving into two major clusters. The highest degree of genetic similarity was related to Baghdadi and Harati White, and the least degree was related to Guilan Orange and Harati Yellow. The genetic similarity estimated within and among silkworms could be explained by the pedigrees, historical and geographical distribution of the strains, effective population size, inbreeding rate, selection intensity, and gene flow. This study revealed that the variability of DNA fingerprints within and among silkworm strains could provide an essential basis for breeders in planning crossbreeding strategies to produce potentially hetrotic hybrids in addition to contributing in conservation programs.
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ItemNo Preview AvailableBootstrapping of gene-expression data improves and controls the false discovery rate of differentially expressed genes(E D P SCIENCES, 2004)The ordinary-, penalized-, and bootstrap t-test, least squares and best linear unbiased prediction were compared for their false discovery rates (FDR), i.e. the fraction of falsely discovered genes, which was empirically estimated in a duplicate of the data set. The bootstrap-t-test yielded up to 80% lower FDRs than the alternative statistics, and its FDR was always as good as or better than any of the alternatives. Generally, the predicted FDR from the bootstrapped P-values agreed well with their empirical estimates, except when the number of mRNA samples is smaller than 16. In a cancer data set, the bootstrap-t-test discovered 200 differentially regulated genes at a FDR of 2.6%, and in a knock-out gene expression experiment 10 genes were discovered at a FDR of 3.2%. It is argued that, in the case of microarray data, control of the FDR takes sufficient account of the multiple testing, whilst being less stringent than Bonferoni-type multiple testing corrections. Extensions of the bootstrap simulations to more complicated test-statistics are discussed.
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ItemNo Preview AvailableMapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data(BMC, 2004)A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD) information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC) methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.
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ItemNo Preview AvailableA practical approach for minimising inbreeding and maximising genetic gain in dairy cattle(BMC, 2007)A method that predicts the genetic composition and inbreeding (F) of the future dairy cow population using information on the current cow population, semen use and progeny test bulls is described. This is combined with information on genetic merit of bulls to compare bull selection methods that minimise F and maximise breeding value for profit (called APR in Australia). The genetic composition of the future cow population of Australian Holstein-Friesian (HF) and Jersey up to 6 years into the future was predicted. F in Australian HF and Jersey breeds is likely to increase by about 0.002 and 0.003 per year between 2002 and 2008, respectively. A comparison of bull selection methods showed that a method that selects the best bull from all available bulls for each current or future cow, based on its calf's APR minus F depression, is better than bull selection methods based on APR alone, APR adjusted for mean F of prospective progeny after random mating and mean APR adjusted for the relationship between the selected bulls. This method reduced F of prospective progeny by about a third to a half compared to the other methods when bulls are mated to current and future cows that will be available 5 to 6 years from now. The method also reduced the relationship between the bulls selected to nearly the same extent as the method that is aimed at maximising genetic gain adjusted for the relationship between bulls. The method achieves this because cows with different pedigree exist in the population and the method selects relatively unrelated bulls to mate to these different cows. Selecting the best bull for each current or future cow so that the calf's genetic merit minus F depression is maximised can slow the rate of increase in F in the population.