Copyright (c) 2010 All rights reserved. http://works.bepress.com/slade_lee Recent documents in L Slade Lee en-us Tue, 09 Nov 2010 21:08:57 PST 3600 http://works.bepress.com/slade_lee/174 http://works.bepress.com/slade_lee/174 Tue, 23 Feb 2010 22:03:46 PST The pericarp and aleurone layer of cereal grains are associated with the accumulation of anti-nutritional factors, vitamins, high-value proteins and trace elements. Variations in these tissues may be associated with important differences in the nutritional and functional value of cereals as human or animal feeds. Wild crop relatives (WCR) have been successfully utilised in breeding programs to improve agronomic traits such as dwarfism and pest and disease resistance. Australia’s undomesticated grass species (Poaceae) provide a unique and genetically diverse array of WCRs and therefore the grains of 17 Australian WCRs were examined by scanning electron microscopy (SEM). Aleurone of each WCR was compared with that of its nearest domesticated cereal relative, with little significant morphological variation observed to this structure. A novel subaleurone morphology was observed in the Sorghum WCRs which had the appearance of being a very dense protein matrix only sparsely embedded with small starch granules or completely lacking starch granules. Histochemical analysis of a subsample of the specimens confirmed that the described morphology was lacking starch granules and had a proteinaceous matrix. Such morphological variations within Australian wild crop relatives of commercial cereals may provide novel sources of genetic diversity for future grain improvement programs. Frances M. Shapter http://works.bepress.com/slade_lee/173 http://works.bepress.com/slade_lee/173 Wed, 03 Feb 2010 16:01:05 PST L Slade Lee http://works.bepress.com/slade_lee/172 http://works.bepress.com/slade_lee/172 Wed, 09 Dec 2009 13:32:12 PST L Slade Lee http://works.bepress.com/slade_lee/171 http://works.bepress.com/slade_lee/171 Wed, 09 Dec 2009 13:32:10 PST The Australian Agriculture Research Institute is embarking on a large-scale grape EST analysis project. cDNA libraries are being prepared from a range of tissues, developmental stages and cultivars with the aim of producing a data base of up to 50,000 sequences, covering a high proportion of grape genes. 2,466 sequences have been obtained from a leaf cDNA library, and 2,438 from a berry library. Analysis of the leaf and berry EST’s indicate 59% of clones have significant homology with known plant genes, 16% with more distant organisms and 25% may represent novel genes (no BLAST 2 match or match to EST’s of unknown function). Redundancy levels in the leaf library are about 42%, and 39% in the berry library. Overall both libraries may yield more than 3,000 unique sequences. We are using expression in Arabidopsis to investigate the function of 58 EST’s that match to 26 different transcription factors with unknown function in plants, and 330 EST’s with no homology to known genes or other plant EST’s. The inserts from the cDNA clones of interest are being cloned into pKMB and pSMB (1). Arabidopsis plants will be transformed with each construct to either over-express or knock out the cloned grape gene of interest. Transformed seeds will be germinated and the plants studied to determine phenotypic changes produced by the altered expression of the grape gene. The functional analysis in Arabidopsis of novel grape genes identified as EST’s will provide a powerful new resource for discovering genes with the potential to improve table and wine grapes. (1) Mylne, J., and Botella, J.R. (1998) Binary Vectors for sense and antisense expression of Arabidopsis EST’s. Plant Mol. Biol. Reporter 16, 257-262. Effie M. Ablett http://works.bepress.com/slade_lee/170 http://works.bepress.com/slade_lee/170 Wed, 09 Dec 2009 13:32:09 PST Daniel LE Waters http://works.bepress.com/slade_lee/169 http://works.bepress.com/slade_lee/169 Wed, 09 Dec 2009 13:32:07 PST The grape genome is relatively small (approximately 500Mbp) making it an attractive target for genomics. The grape genome is thus similar in size to the rice genome but is composed of a larger number of small chromosomes amenable to physical mapping. Grapes are a woody perennial and thus differ from other species that have been analyzed in detail. We have sequenced cDNA libraries from vegetative tissues and fruits to generate an EST database. Analysis of the first 5000 sequences (2500 from each library) indicated that most ESTs obtained have homology to known genes. The clones had homology to plant genes (68%) and to genes from other organisms (14%). Approximately 18% did not show homology to any sequence of known function in the databases. The two libraries had 275 genes in common. Redundancy was 42% in the leaf library and 39% in the berry library. Functional analysis may identify genes controlling many unique traits in this. Robert J. Henry http://works.bepress.com/slade_lee/168 http://works.bepress.com/slade_lee/168 Wed, 09 Dec 2009 13:32:06 PST Robert J. Henry http://works.bepress.com/slade_lee/167 http://works.bepress.com/slade_lee/167 Wed, 09 Dec 2009 13:32:05 PST Margaret A. Wheeler http://works.bepress.com/slade_lee/165 http://works.bepress.com/slade_lee/165 Sun, 08 Nov 2009 21:54:01 PST CEL I endonuclease cleavage of heteroduplex DNA is noted as an efficient, high-throughput technique for scanning homologous sequences for subtle variations. A significant shortcoming of the CEL I technique, however, is the poor signal-to-noise ratio obtained when using a PCR-based, 5’-end-fluorophore-labelled detection platform. Normally, the sensitivity of fluorescent-based PAGE/CE is many fold superior to the UV visualization of intercalated dyes following agarose electrophoresis. Recent literature, however, reports that maximum pooling capacities are overall similar, when comparing sophisticated fluorophore-labelled detection platforms with more basic ethidium-stained techniques. CEL I has been hypothesized to reduce signal strength of end-labelled amplicon fragments via non-specific exonucleolytic activity, which acts to cleave off 5’-end bases and their covalently-linked fluorophores. Typical CEL I protocols involve only short digestion times in an attempt to limit the loss of true-nicked signal via any undesired exonucleolytic activity. Our research provides strong evidence to support the ‘exonucleolytic cleavage’ hypothesis on CEL I’s activity. We investigate alternative dye-labelling strategies and report a simple, improved technique for CEL I mutation scanning using an Applied Biosystems 3730 DNA Analyzer. Increased sensitivity is achieved, with higher throughputs being enabled via a greater capacity to pool amplified DNA. The CEL I-scanning protocol is suitable for detecting more than one unique mutant allele per pool. Our method was developed and tested in rice across a range of cultivars highly characterized for their SNP content in exon 8 of Starch Sythase IIa. Michael J. Cross http://works.bepress.com/slade_lee/163 http://works.bepress.com/slade_lee/163 Tue, 03 Nov 2009 18:51:26 PST L Slade Lee http://works.bepress.com/slade_lee/162 http://works.bepress.com/slade_lee/162 Tue, 03 Nov 2009 18:51:24 PST L Slade Lee http://works.bepress.com/slade_lee/161 http://works.bepress.com/slade_lee/161 Tue, 03 Nov 2009 18:51:23 PST Maurizio Rossetto http://works.bepress.com/slade_lee/155 http://works.bepress.com/slade_lee/155 Sat, 31 Oct 2009 00:36:25 PDT Melaleuca alternifolia is grown for commercial production of Tea Tree oil which is used for pharmaceutical and cosmetic purposes. Considerable differences in oil yield and composition are of particular concern to commercial producers, and suggest significant genotypic variability. Microsatellite markers were developed using advanced enrichment techniques. Repeat sequences from digested tea tree DNA were hybridised to membrane-bound selected oligonucleotides. The plasmid-vector microsatellite library so enriched, is being used to analyse the genetic variation in tea tree within and between 630 individual samples from 42 populations throughout the entire range of the species, in north-eastern New South Wales, Australia. The aim of the project is to develop an understanding of the population genetics of M. alternifolia. This will indicate the most important plants to preserve for genetic variation in wild populations, and to harness in future varietal improvement programs. The level of outcrossing and the variation in oil yield and quality characteristics will also be determined. Microsatellite markers will be related to oil quality characteristics of various genotypes. Furthermore, a genetic map will be generated from a population produced by crossing individuals of diverse oil phenotypes. L Slade Lee http://works.bepress.com/slade_lee/154 http://works.bepress.com/slade_lee/154 Sat, 31 Oct 2009 00:36:08 PDT Kirsten D. Scott http://works.bepress.com/slade_lee/153 http://works.bepress.com/slade_lee/153 Sat, 31 Oct 2009 00:35:52 PDT Tea tree oil production from leaves of Melaleuca alternifolia is a significant agricultural industry with the establishment in recent years of large plantation crops in Australia and several other countries. The oil is highly valued in the pharmaceutical and cosmetic industries for its broad-spectrum germicidal properties. Considerable differences in oil yield and composition are of particular interest to commercial producers, and suggest significant genotypic variability. However, apart from some limited varietal selection, little breeding work has been conducted. Sampling of M. alternifolia leaf material was undertaken from 40 sites throughout the geographic range of the species, which is endemic to north-eastern New South Wales and far south-east Queensland, Australia. Genotypic diversity within the species was studied utilising specifically developed microsatellite DNA markers. These were used to study the genotypic distribution within the species population and between subpopulations. Oil yield and quality analyses were conducted from more than 600 samples in order to identify superior varieties for future commercial production. More importantly, data from the research provides the foundation for a tea tree breeding program to pursue further varietal improvement. Analysis of the microsatellite genotype distributions and the oil phenotypes has facilitated the development of an optimal breeding strategy aimed at parent selection for efficient generation of elite tea tree varieties. The research also lends itself to the future possibility of marker-assisted breeding. L Slade Lee http://works.bepress.com/slade_lee/152 http://works.bepress.com/slade_lee/152 Sat, 31 Oct 2009 00:35:35 PDT In recent times microsatellite analysis has become a favourite tool for a multitude of genetic related projects. However, one of the major drawbacks of this technology is that characterisation of useful loci relies on DNA sequence knowledge. As a result, the amount of resources required does not justify the development of these markers for all species. A potential alternative to taxon specific characterisation, is cross species amplification of microsatellite loci. Initially thought to be less successful in plants than in animals, recent research is increasingly showing otherwise. In this study, we have investigated the transferrability of microsatellite loci in angiosperms, both dicots (Myrtaceae) and monocots (Poaceae), and gymnosperms (Pinus). Thirty five primer pairs developed for tea tree (Melaleuca alternifolia - Myrtaceae), were tested on seven other Myrtaceae including other economically important species such as eucalypts. Success was over 80% within members of the same genus and over 20% for more distant species. Similar studies have been carried out with microsatellites developed for Saccharum spp. and Pinus spp. showing reasonable amounts of cross-transferability. The results suggest that cross-transferability of microsatellites can be a viable alternative to specific characterisation, especially for studies requiring a limited number of hypervariable loci such as population genetics studies. Maurizio Rossetto http://works.bepress.com/slade_lee/151 http://works.bepress.com/slade_lee/151 Sat, 31 Oct 2009 00:35:17 PDT Robert J. Henry http://works.bepress.com/slade_lee/150 http://works.bepress.com/slade_lee/150 Sat, 31 Oct 2009 00:35:00 PDT L Slade Lee http://works.bepress.com/slade_lee/149 http://works.bepress.com/slade_lee/149 Sat, 31 Oct 2009 00:34:42 PDT Kirsten D. Scott http://works.bepress.com/slade_lee/148 http://works.bepress.com/slade_lee/148 Sat, 31 Oct 2009 00:34:24 PDT Effie M. Ablett