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 AvailableMapping of the eibi1 gene responsible for the drought hypersensitive cuticle in wild barley (Hordeum spontaneum)(JAPANESE SOC BREEDING, 2009-03)Segregation analysis showed that eibi1, a drought hypersensitive cuticle wild barley mutant, was monogenic and recessive, and mapped in two F2 populations, one made from a cross between the mutant and a cultivated barley (cv. Morex), and the other between the mutant and another wild barley. A microsatellite marker screen showed that the gene was located on barley chromosome 3H, and a set of markers already assigned to this chromosome, including both microsatellites and ESTs, was used to construct a genetic map. eibi1 co-segregated with barley EST AV918546, and was located to bin 6. The synteny between barley and rice in this region is incomplete, with a large discrepancy in map distances, and the presence of multiple inversions.
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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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ItemAnalysis of Intraspecies Diversity in Wheat and Barley Genomes Identifies Breakpoints of Ancient Haplotypes and Provides Insight into the Structure of Diploid and Hexaploid Triticeae Gene Pools(AMER SOC PLANT BIOLOGISTS, 2009-01)A large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic diversity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes diverged only a few thousand years ago, while some barley and Ae. tauschii haplotypes diverged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.
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ItemNo Preview AvailableMolecular evolution and phylogeny of the RPB2 gene in the genus Hordeum(OXFORD UNIV PRESS, 2009-04)BACKGROUND AND AIMS: It is known that the miniature inverted-repeat terminal element (MITE) preferentially inserts into low-copy-number sequences or genic regions. Characterization of the second largest subunit of low-copy nuclear RNA polymerase II (RPB2) has indicated that MITE and indels have shaped the homoeologous RPB2 loci in the St and H genome of Eymus species in Triticeae. The aims of this study was to determine if there is MITE in the RPB2 gene in Hordeum genomes, and to compare the gene evolution of RPB2 with other diploid Triticeae species. The sequences were used to reconstruct the phylogeny of the genus Hordeum. METHODS: RPB2 regions from all diploid species of Hordeum, one tetraploid species (H. brevisubulatum) and ten accessions of diploid Triticeae species were amplified and sequenced. Parsimony analysis of the DNA dataset was performed in order to reveal the phylogeny of Hordeum species. KEY RESULTS: MITE was detected in the Xu genome. A 27-36 bp indel sequence was found in the I and Xu genome, but deleted in the Xa and some H genome species. Interestingly, the indel length in H genomes corresponds well to their geographical distribution. Phylogenetic analysis of the RPB2 sequences positioned the H and Xa genome in one monophyletic group. The I and Xu genomes are distinctly separated from the H and Xa ones. The RPB2 data also separated all New World H genome species except H. patagonicum ssp. patagonicum from the Old World H genome species. CONCLUSIONS: MITE and large indels have shaped the RPB2 loci between the Xu and H, I and Xa genomes. The phylogenetic analysis of the RPB2 sequences confirmed the monophyly of Hordeum. The maximum-parsimony analysis demonstrated the four genomes to be subdivided into two groups.