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Scaming: An Efficient High Throughput Approach To Discovery And Analysis Of Snps For Genotyping Of Tropical Crop Species, Frances G. Eliott, Giovanni M. Cordeiro, Nicole F. Rice, James K. Cronin, Daniel Le Waters, Peter C. Bundock, Stirling Bowen, Robert J. Henry Jan 2006

Scaming: An Efficient High Throughput Approach To Discovery And Analysis Of Snps For Genotyping Of Tropical Crop Species, Frances G. Eliott, Giovanni M. Cordeiro, Nicole F. Rice, James K. Cronin, Daniel Le Waters, Peter C. Bundock, Stirling Bowen, Robert J. Henry

Southern Cross Plant Science

Model organisms have well established genetic marker tools. However, genotyping of the wide range of agricultural and food species requires the discovery of genetic variations in each species that can be used to distinguish genotypes. Single Nucleotide Polymorphisms (SNPs) are the basis of most high throughput genetic analysis technologies. We have developed a generic approach to the discovery and analysis of SNPs in non-model organisms. SNP Characterisation and Mapping in Genomes (SCAMinG) has been developed from mutation detection based on enzymatic cleavage of DNA heteroduplexes as applied to naturally occurring genetic variation (ecoTILLinG). Our protocol involves application of high throughput ...


Induced Plant Mutation And Molecular Analysis As A Route To Genetic Improvement Of Specific Grain Quality Traits, L Slade Lee, Liz Izquierdo, Gary A. Ablett, Nicole F. Rice, Robert J. Henry Jan 2006

Induced Plant Mutation And Molecular Analysis As A Route To Genetic Improvement Of Specific Grain Quality Traits, L Slade Lee, Liz Izquierdo, Gary A. Ablett, Nicole F. Rice, Robert J. Henry

Southern Cross Plant Science

No abstract provided.


The Mature Cereal Seed Transcriptome, Toni Pacey-Miller, Loraine Watson, Jessica F. White, Allison C. Crawford, Peter C. Bundock, Giovanni M. Cordeiro, Daniel Barbary, Glen P. Fox, Shane Mcintosh, Robert J. Henry Jan 2006

The Mature Cereal Seed Transcriptome, Toni Pacey-Miller, Loraine Watson, Jessica F. White, Allison C. Crawford, Peter C. Bundock, Giovanni M. Cordeiro, Daniel Barbary, Glen P. Fox, Shane Mcintosh, Robert J. Henry

Southern Cross Plant Science

Understanding the gene expression profile of the dry seed of both barley and wheat is important to fully understand the physiological interactions occurring within the seed. Although a vast amount of knowledge has been accumulated on seed dormancy and germination, many of the processes involved remain a mystery. By examining the types of transcripts expressed at any time in the cell and the level of expression, it is possible to determine which genes and their related proteins are being expressed at that moment in time. SAGE (Serial Analysis of Gene Expression) is a technique that allows rapid, detailed analysis of ...


Improving Rice For Human Health, Daniel Le Waters, Shane R. Mcintosh, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry Jan 2006

Improving Rice For Human Health, Daniel Le Waters, Shane R. Mcintosh, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry

Southern Cross Plant Science

No abstract provided.


Competitive Allele Specific Pcr Molecular Markers For Rice [Oryza Sativa] Starch Gelatinisation Temperature, Daniel Le Waters, Robert J. Henry, Russell F. Reinke Jan 2006

Competitive Allele Specific Pcr Molecular Markers For Rice [Oryza Sativa] Starch Gelatinisation Temperature, Daniel Le Waters, Robert J. Henry, Russell F. Reinke

Southern Cross Plant Science

No abstract provided.


Using Longsage To Study Cereal Gene Expression During Grain Development And Germination, Peter C. Bundock, Allison C. Crawford, Jessica F. White, Shane R. Mcintosh, Giovanni M. Cordeiro, Toni Pacey-Miller, Lee Rooke, Linh Nguyen, Gary A. Ablett, Loraine Watson, Robert J. Henry Jan 2006

Using Longsage To Study Cereal Gene Expression During Grain Development And Germination, Peter C. Bundock, Allison C. Crawford, Jessica F. White, Shane R. Mcintosh, Giovanni M. Cordeiro, Toni Pacey-Miller, Lee Rooke, Linh Nguyen, Gary A. Ablett, Loraine Watson, Robert J. Henry

Southern Cross Plant Science

Many methods of studying gene expression rely on previous knowledge of gene sequences to quantify transcript levels. However the SAGE method samples whatever transcripts are present in a given tissue and time point. In one set of experiments we targeted the development of wheat grain using longSAGE. Developing wheat caryopses were sampled for SAGE analysis at five time points - the first at eight days post anthesis and the last being mature grain (40 dpa). A total of approximately 240,000 longSAGE tags were sequenced across these five time points. In another experiment we have targeted germinating barley grain during the ...


Methods For Snp Identification And Analysis In The Sugarcane Genome, Giovanni M. Cordeiro, Frances G. Eliott, C Lynne Mcintyre, Robert J. Henry Jan 2006

Methods For Snp Identification And Analysis In The Sugarcane Genome, Giovanni M. Cordeiro, Frances G. Eliott, C Lynne Mcintyre, Robert J. Henry

Southern Cross Plant Science

The sugarcane genome poses the challenge of being highly polyploid and requiring ingenuity to overcome impediments of straightforward genome analyses methods that are often taken for granted in simpler genomes and inbred species. We have developed and evaluated a number of technologies to accurately locate and score the level of frequency of a SNP at any individual locus.


Genotyping Of The Fragrance Allele In Rice, Louis Mt Bradbury, Robert J. Henry, Qingsheng Jin, Russell F. Reinke, Daniel Le Waters Jan 2006

Genotyping Of The Fragrance Allele In Rice, Louis Mt Bradbury, Robert J. Henry, Qingsheng Jin, Russell F. Reinke, Daniel Le Waters

Southern Cross Plant Science

We have previously determined that fragrance in rice, a recessive trait, is due to a large deletion (8bp) and 3 SNP’s in a gene on chromosome 8 which encodes a putative betaine aldehyde dehydrogenase 2 (BAD2). This mutation results in the formation of a truncated BAD2 enzyme because of the creation of an in-frame termination signal 800bp before that of the wild type. Because this truncated BAD2 is missing key binding domains, it is unlikely that it is capable of acting upon the target substrate and this leads to an accumulation of the principal fragrant molecule, 2-acetyl-1-pyrroline. Here we ...


Characterization Of A Quinolizidine Alkaloid O-Tigloyltransferase Gene In Wild And Domestic White Lupin (L. Albus), Yihua Chen, L Slade Lee, D J. Luckett Jan 2006

Characterization Of A Quinolizidine Alkaloid O-Tigloyltransferase Gene In Wild And Domestic White Lupin (L. Albus), Yihua Chen, L Slade Lee, D J. Luckett

Southern Cross Plant Science

No abstract provided.


Targeted Mutagenesis In Sorghum Using An Improved High-Throughput Screening Platform – A Reverse Genetics Strategy To Complement The Sorghum Genomics Effort, Michael J. Cross, L Slade Lee, Nicole F. Rice, Robert J. Henry Jan 2006

Targeted Mutagenesis In Sorghum Using An Improved High-Throughput Screening Platform – A Reverse Genetics Strategy To Complement The Sorghum Genomics Effort, Michael J. Cross, L Slade Lee, Nicole F. Rice, Robert J. Henry

Southern Cross Plant Science

As a natural complement to the Sorghum Genomics effort, our group has undertaken a reverse genetics strategy involving point-mutagenesis, followed by CEL I mismatch screening. EMS-mutated populations have been generated in four white Sorghum lines. Our research has further developed the mutation screening technique of ‘CEL I mismatch detection’. Our modified technique is a significant improvement on the standard protocols (originally optimized for slab gel systems). Our protocol benefits from the increased sensitivity offered by a capillary electrophoresis platform, enabling a larger degree of sample pooling. Throughput has also been improved via a significant reduction in the amount of background ...


Improving Cereals For Human Health, Shane R. Mcintosh, Daniel Le Waters, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry Jan 2006

Improving Cereals For Human Health, Shane R. Mcintosh, Daniel Le Waters, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry

Southern Cross Plant Science

No abstract provided.


Plant Dna Banks And The Role In Plant Genomics, Nicole F. Rice, Loraine Watson, Robert J. Henry Jan 2006

Plant Dna Banks And The Role In Plant Genomics, Nicole F. Rice, Loraine Watson, Robert J. Henry

Southern Cross Plant Science

No abstract provided.


Rice Genome Sequence Accelerates The Discovery Of Commercially Important Genes And Polymorphisms, Daniel Le Waters, Louis Mt Bradbury, Russell F. Reinke, Melissa A. Fitzgerald, Qingsheng Jin, Robert J. Henry Jan 2006

Rice Genome Sequence Accelerates The Discovery Of Commercially Important Genes And Polymorphisms, Daniel Le Waters, Louis Mt Bradbury, Russell F. Reinke, Melissa A. Fitzgerald, Qingsheng Jin, Robert J. Henry

Southern Cross Plant Science

Traditionally, identification of genes which control important traits has been labour intensive and time consuming. We have demonstrated the annotated rice genome sequence used in combination with re-sequencing by PCR greatly facilitates the discovery of both genes and polymorphisms within genes, which control commercially important traits. Identification of the gene which controls fragrance was achieved using a relatively small mapping population of 168 F2 individuals. Analysis of the recombination data and the relatively large tract (385 kbp) of annotated genome sequence between the flanking markers revealed a candidate gene in this region which plausibly explained the known biochemistry of fragrance ...


Sage Of The Developing Wheat Caryopsis, Shane Mcintosh, Loraine Watson, Peter C. Bundock, Allison C. Crawford, Jessica F. White, Giovanni M. Cordeiro, Daniel Barbary, Lee Rooke, Robert J. Henry Jan 2006

Sage Of The Developing Wheat Caryopsis, Shane Mcintosh, Loraine Watson, Peter C. Bundock, Allison C. Crawford, Jessica F. White, Giovanni M. Cordeiro, Daniel Barbary, Lee Rooke, Robert J. Henry

Southern Cross Plant Science

Understanding the development of the cereal caryopsis holds the future for metabolic engineering in the interests of enhancing global food production. We have developed a Serial Analysis of Gene Expression (SAGE) data platform to investigate the developing wheat (Triticum aestivum) caryopsis. LongSAGE libraries have been constructed at five time-points post-anthesis to coincide with key processes in caryopsis development. More than 90 000 LongSAGE tags have been sequenced generating 29 261 unique tag sequences across all five libraries. Tag abundance, generated from cumulative tag counts, provides insight into the redundancy and diversity of each library. Annotation of the 500 most abundant ...


Malting Quality Improvement Using Sage, Toni Pacey-Miller, Loraine Watson, Jessica F. White, Allison C. Crawford, Peter C. Bundock, Giovanni M. Cordeiro, Daniel Barbary, Shane R. Mcintosh, Robert J. Henry Jan 2006

Malting Quality Improvement Using Sage, Toni Pacey-Miller, Loraine Watson, Jessica F. White, Allison C. Crawford, Peter C. Bundock, Giovanni M. Cordeiro, Daniel Barbary, Shane R. Mcintosh, Robert J. Henry

Southern Cross Plant Science

No abstract provided.


Population Panmixia In A Spotted Gum Species Complex (Mytaceae): Implications For Association Mapping, Joel W. Ochieng, Peter R. Baverstock, Robert J. Henry, Mervyn Shepherd Jan 2006

Population Panmixia In A Spotted Gum Species Complex (Mytaceae): Implications For Association Mapping, Joel W. Ochieng, Peter R. Baverstock, Robert J. Henry, Mervyn Shepherd

Southern Cross Plant Science

No abstract provided.


Predicting Extractives, Lignin, And Cellulose Contents Using Near Infrared Spectroscopy On Solid Wood In Eucalyptus Globulus, Carolyn A. Raymond, Fiona S. Poke Jan 2006

Predicting Extractives, Lignin, And Cellulose Contents Using Near Infrared Spectroscopy On Solid Wood In Eucalyptus Globulus, Carolyn A. Raymond, Fiona S. Poke

Southern Cross Plant Science

Near infrared reflectance (NIR) spectroscopy can be used to reliably predict both the physical and chemical wood properties of Eucalyptus. However, studies have been based on ground wood, which is costly and time-consuming to obtain. Predicting wood traits from NIR spectral data taken from solid wood would greatly increase the speed and cost-effectiveness of this procedure. Existing ground wood calibrations were evaluated for the prediction of wood chemistry from NIR spectral data taken from solid wood. Extractives, acid-soluble lignin, and Klason lignin contents were poorly predicted. Total lignin and cellulose contents showed moderate relationships between laboratory values and the NIR ...


Improving Productivity In Mixed-Species Plantations, Mila Bristow, J Doland Nichols, Jerome K. Vanclay Jan 2006

Improving Productivity In Mixed-Species Plantations, Mila Bristow, J Doland Nichols, Jerome K. Vanclay

School of Environment, Science and Engineering Papers

Mixed species plantations are often promoted as being environmentally preferable to monocultures, but are rarely considered operationally viable by commercial forest growers. Despite many publications documenting benefits demonstrated in research studies (e.g., Kelty 2006; Forrester et al. 2006b; Wood and Vanclay 1995), and despite continuing calls from a wide range of advocates for mixed-species plantations, polyculture remains the exception rather than the rule in industrial plantation forestry (Nichols et al 2006)...


Spatially-Explicit Competition Indices And The Analysis Of Mixed-Species Plantings With The Simile Modelling Environment, Jerome K. Vanclay Jan 2006

Spatially-Explicit Competition Indices And The Analysis Of Mixed-Species Plantings With The Simile Modelling Environment, Jerome K. Vanclay

School of Environment, Science and Engineering Papers

Individual-based modelling and analysis of forest experiments has been made more accessible to researchers with the advent of modelling environments like Simile from www.simulistics.com. Individual-based analyses of tree growth data offer insights not possible with plot-based analyses, especially when the original experimental design has been compromised by mortality or other unforeseen events. The paper illustrates how Simile can be used for individual-based analyses of mixed plantings, and how it can be used to explore the consequences of the resulting statistical models. A mixed-species planting of Eucalyptus pellita and Acacia peregrina is used to illustrate possibilities.


Diameter Growth Performance Varies With Species Functional-Group And Habitat Characteristics In Subtropical Rainforests, Maina Kariuki, Margaret Rolfe, R Geoff B. Smith, Jerome K. Vanclay, Robert M. Kooyman Jan 2006

Diameter Growth Performance Varies With Species Functional-Group And Habitat Characteristics In Subtropical Rainforests, Maina Kariuki, Margaret Rolfe, R Geoff B. Smith, Jerome K. Vanclay, Robert M. Kooyman

School of Environment, Science and Engineering Papers

We examined tree diameter growth in 20 plots subjected to various disturbance intensities (natural, low, moderate and intensive logging) in a bid to understand the general tree growth responses in relation to habitat characteristics in subtropical rainforests of north-eastern NSW, Australia. Species-specific regeneration strategy, maximum size and level of shade tolerance were used to classify species into five groups: emergent and shade tolerant main canopy (group 1), shade tolerant mid canopy (2), shade tolerant understoreys (3), moderate shade tolerant (4) and shade intolerant (5) tree species. Data series for trees ‗10 cm diameter at 1.3 m above the ground ...


Regeneration Changes In Tree Species Abundance Diversity And Structure In Logged And Unlogged Subtropical Rainforest Over A 36-Year Period, Maina Kariuki, Robert M. Kooyman, R Geoff B. Smith, Grant Wardell-Johnson, Jerome K. Vanclay Jan 2006

Regeneration Changes In Tree Species Abundance Diversity And Structure In Logged And Unlogged Subtropical Rainforest Over A 36-Year Period, Maina Kariuki, Robert M. Kooyman, R Geoff B. Smith, Grant Wardell-Johnson, Jerome K. Vanclay

School of Environment, Science and Engineering Papers

The long-term effects of logging treatments on rainforest regeneration are difficult to quantify due to compounding interactions with natural dynamics, site characteristics and tree species. The aim of this study was to examine regeneration differences over a 36-year period in stands subjected to various levels of disturbance ranging from natural, through an increasing intensity of individual tree removal to intensive logging. Multivariate and univariate analyses of trees ¡Ý 10 cm diameter at 1.3 m above the ground (dbh) showed that regeneration responses were generally correlated with disturbance gradient. In the undisturbed controls there were gradual changes that had no ...


Growth And Species Interactions Of Eucalyptus Pellita In A Mixed And Monoculture Plantation In The Humid Tropics Of North Queensland, Mila Bristow, Jerome K. Vanclay, Lyndon O. Brooks, Mark Hunt Jan 2006

Growth And Species Interactions Of Eucalyptus Pellita In A Mixed And Monoculture Plantation In The Humid Tropics Of North Queensland, Mila Bristow, Jerome K. Vanclay, Lyndon O. Brooks, Mark Hunt

School of Environment, Science and Engineering Papers

This study investigated whether mixed-species designs can increase the growth of a tropical eucalypt when compared to monocultures. Monocultures of Eucalyptus pellita (E) and Acacia peregrina (A) and mixtures in various proportions (75E:25A, 50E:50A, 25E:75A) were planted in a replacement series design on the Atherton Tablelands of north Queensland, Australia. High mortality in the establishment phase due to repeated damage by tropical cyclones altered the trial design. Effects of experimental designs on tree growth were estimated using a linear mixed effects model with restricted maximum likelihood analysis (REML). Volume growth of individual eucalypt trees were positively affected ...


Mixed Species Plantations: Prospects And Challenges, J Doland Nichols, Mila Bristow, Jerome K. Vanclay Jan 2006

Mixed Species Plantations: Prospects And Challenges, J Doland Nichols, Mila Bristow, Jerome K. Vanclay

School of Environment, Science and Engineering Papers

About 2% of English-language literature on plantations deals with mixed-species plantations, but only a tiny proportion (<0.1%) of industrial plantations are polycultures. Small landholders are more innovative, with 12% of Australia’s farm forestry plantations under mixed-species plantings, and 80% of Queensland’s farm forestry as polycultures. We examine reasons for this discrepancy, and explore the history, silviculture and economics of polycultures. Financial analyses suggest that a yield stimulus of 10%, depending on product and rotation length, may be sufficient to offset increased costs associated with planting and managing a mixed-species plantation, a stimulus that has been demonstrated in many field trials. We conclude that the main obstacle to commercial uptake of polycultures in industrial plantations may be the lack of operational-scale demonstrations coupled with reliable financial analyses.