Copyright (c) 2011 All rights reserved. http://works.bepress.com/robert_henry Recent documents in Robert J Henry en-us Thu, 17 Feb 2011 01:32:33 PST 3600 http://works.bepress.com/robert_henry/846 http://works.bepress.com/robert_henry/846 Tue, 15 Feb 2011 21:54:40 PST Breeding for wood quality is limited by the long generation times and the delay before wood quality can be measured reliably. Association studies allow links between phenotype and genotype to be made, and are a prelude to accelerated domestication of trees by molecular breeding approaches. This study uses association genetics to identify DNA polymorphisms that correlate with solid wood properties of Eucalyptus pilularis Smith (blackbutt). We undertook extensive phenotyping of dimensional stability, growth and structural wood properties on a nine-year-old progeny trial established by Forests NSW at Hannam Vale, near Port Macquarie in NSW. A subset of 372 phenotyped individuals representing 284 families collected from 37 provenances was used as the association population for genotypic assessment. Fifty-two out of 127 novel DNA polymorphisms were surveyed within four candidate genes, CCR, CAD, MYB1 and MYB2. Several putative associations between wood quality traits and selected DNA polymorphisms are reported, along with the likely mechanism of action on wood quality. Association studies such as this will facilitate non-destructive DNA tests for heritable wood properties that can be used to enrich breeding populations at any developmental stage with desirable alleles. Keywords: wood properties; phenotypic variation; genetic variation; molecular markers; selection; marker-aided selection; Eucalyptus pilularis Timothy R. Sexton http://works.bepress.com/robert_henry/845 http://works.bepress.com/robert_henry/845 Tue, 15 Feb 2011 21:54:37 PST Simple sequence repeat (SSR) or microsatellite markers were examined for polymorphisms among the parents of 12 barley mapping populations. Of 259 SSRs screened, 149 were mapped on 1 or more of the 12 doubled haploid populations studied. The relative genetic positions of the 149 mapped SSR markers on Australian varieties are presented in the form of a consensus map. A database was created based on the results of screenings of barley varieties with a series of SSR markers. Details of the markers are at: http://www.scu.edu.au/ research/ cpcg/Barley/index.php. A procedure is suggested for mapping new populations with microsatellites using this information and information available on other databases. These 12 populations have been mapped with SSR markers that act as 'anchors' for other types of genetic markers and for traits of interest. Some challenges in mapping SSRs were detailed. Multi-locus markers can cause confusion since one marker can map at different locations. Polymorphisms should be confirmed in new mapping varieties since some variation of allele size is seen in different sources of varieties of the same name, possibly due to differences in sources of germplasm. Lack of standardisation between laboratories or between analytical systems may also lead to differences in called allele sizes. SSRs proved to be adaptable to several technologies and economical, providing a preferred marker system for mapping new barley populations and to 'anchor' other types of markers. Gary A. Ablett http://works.bepress.com/robert_henry/844 http://works.bepress.com/robert_henry/844 Tue, 15 Feb 2011 21:54:34 PST Timothy Sexton http://works.bepress.com/robert_henry/843 http://works.bepress.com/robert_henry/843 Tue, 21 Sep 2010 20:42:31 PDT Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost-effective options for genome comparisons on a much larger scale. Universal PCR amplification of chloroplast sequences or isolation of pure chloroplast fractions, however, are nontrivial. We now propose the analysis of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost-effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present chloroplast genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The chloroplast genome may be the elusive single-locus DNA barcode for plants. Catherine J. Nock http://works.bepress.com/robert_henry/842 http://works.bepress.com/robert_henry/842 Wed, 14 Jul 2010 22:14:38 PDT Dale A. Shelton http://works.bepress.com/robert_henry/841 http://works.bepress.com/robert_henry/841 Sun, 11 Jul 2010 18:44:45 PDT Geographically distributed genetic variation is expected in species like Eucalyptus pilularis that have wide latitudinal and habitat ranges. Coastal and inland ecotypes of this tall forest tree have been distinguished in genecological studies, but patterns of regionally distributed quantitative variation are weak. At the coarsest level, variation at microsatellite markers (n=12) divided a range-wide sample of 424 E. pilularis trees into two zones, the region to the south of Sydney forming one zone distinct from regions to the north. Genetic structuring did not correspond with ecotypes but rather with a biogeographic division suggesting an imprint of historical isolation. Typical and uniform levels of genetic diversity (He = 0.78 (0.02) mean (SE)) were found across 10 geographic regions. Structuring into regions (PhiRT = 3%), localities within regions (PhiPT = 2%), between coastal and inland provenances (PhiPT = 2%), or due to isolation by distance, was subtle. These factors, along with the lack of evidence for bottlenecks, suggested cohesion within zones due to gene flow and large population sizes historically. Recent colonisation and adaptation better explained the low levels of diversity and poor growth performance of the Fraser Island ecotype rather than genetic isolation as there was no evidence of inbreeding. Mervyn Shepherd http://works.bepress.com/robert_henry/840 http://works.bepress.com/robert_henry/840 Tue, 04 May 2010 16:03:24 PDT The level of genetic variation throughout the entire worldwide range of the mangrove species Avicennia marina (Forsk.) Vierh. was examined using microsatellite markers. Three microsatellite loci detected high levels of allelic diversity (70 alleles in total), essential for an accurate estimation of population genetic parameters. The informativeness of the microsatellite loci tended to increase with increasing average number of repeats. The levels of heterozygosity detected for each population, over all loci, ranged from 0.0 to 0.8, with an average of 0.407, indicating that some populations had little or no genetic variation, whereas others had a large amount. Populations at the extremes of the distribution range showed reduced levels of heterozygosity, and significant levels of inbreeding. This is not unexpected as these populations may be subject to founder effects and environmental constraints. The presence of genetic structure was tested in A. marina populations using three models: (i) a single panmictic model; (ii) the discrete subpopulation model; and (iii) the isolation by distance model. The discrete subpopulations model was supported by the overall measures of population differentiation based on the infinite alleles model (F-statistics), and the stepwise mutation model (R statistics). In addition, an analysis of molecular variance (amova), using both theoretical models, found that most of the variation was between populations (41–71%), and within individuals in the total population (31–49%). There was little variation among individuals within populations (0–10%). There was no significant isolation by distance. The high levels of genetic differentiation observed among populations of A. marina may be due to environmental and ecological factors, particularly past sea level and climatic changes. Tina L. Maguire http://works.bepress.com/robert_henry/839 http://works.bepress.com/robert_henry/839 Mon, 05 Apr 2010 19:44:14 PDT Fragrance in rice has been shown to result from deletions that cause the loss of function of betaine aldehyde dehydrogenase 2 (BADH2). In many plant species, BADHs play a role in abiotic stress tolerance; in some plants the mechanism by which this occurs is the accumulation of glycinebetaine (GB) from betaine aldehyde. However, rice does not accumulate GB. Rice BADH2 has only moderate activity on betaine aldehyde, with much higher activity on gamma aminobutyraldehyde (GABald). It has been proposed that the primary role of rice BADH2 in vivo is the metabolism of gamma-amino butyric acid (GABA) from GABald. Gamma-amino butyric acid has been shown to perform a range of roles in plants, including assisting in the response to abiotic stress.Recently it has been shown that non-fragrant rice lines with specifically inhibited BADH2 are more susceptible to salt stress than wild type with normal BADH2 expression. This strongly suggests that BADH2 has a role in protecting rice from the effects of salt. To investigate whether cultivated fragrant rice varieties are less tolerant of salt than cultivated non-fragrant rice varieties due to the absence of functional BADH2, the growth to harvest of fragrant and non-fragrant rice plants under salt treatment was observed in a glasshouse-scale experiment. A highly statistically significant difference in the ability of rice plants to produce mature seed under salt treatment was observed between the fragrant and non-fragrant groups. On average, greater than 99% inhibition of mature seed production for fragrant rice plants exposed to 22 mM salt solution (from 11 weeks post-planting) was observed, which is a greater salt sensitivity than previously reported for any rice genotype. These results suggest that human preference for the desirable aroma of fragrant rice has selected plants with salt sensitivity. Timothy L. Fitzgerald http://works.bepress.com/robert_henry/838 http://works.bepress.com/robert_henry/838 Tue, 02 Mar 2010 18:30:10 PST Plant betaine aldehyde dehydrogenases (BADHs) have been the target of substantial research, especially during the last 20 years. Initial characterisation of BADH as an enzyme involved in the production of glycine betaine (GB) has led to detailed studies of the role of BADH in the response of plants to abiotic stress in vivo, and the potential for transgenic expression of BADH to improve abiotic stress tolerance. These studies have, in turn, yielded significant information regarding BADH and GB function. Recent research has identified the potential for BADH as an antibiotic-free marker for selection of transgenic plants, and a major role for BADH in 2-acetyl-1-pyrroline-based fragrance associated with jasmine and basmati style aromatic rice varieties. Timothy L. Fitzgerald http://works.bepress.com/robert_henry/837 http://works.bepress.com/robert_henry/837 Tue, 23 Feb 2010 22:42:03 PST Susan A. Gillies http://works.bepress.com/robert_henry/836 http://works.bepress.com/robert_henry/836 Tue, 23 Feb 2010 22:41:59 PST Automated DNA Extraction, Next Generation Sequencing and high throughput genotyping technologies used in combination allow more tightly targeted approaches to genetic analysis than ever before. It is now possible to quickly acquire genome wide data for a range of key reference varieties which differ by important phenotypes. These data can be quickly converted to high throughput genotyping assays allowing rapid analysis of populations derived from the reference varieties. The same data can be used for cereal variety identification, an important quality control tool. We have optimized a high-throughput multiplexed SNP assay for eight polymorphisms which explain two agronomic and three grain quality traits in rice. Gene fragments coding for the agronomic traits plant height (sd-1) and blast disease resistance (Pi-ta) and the quality traits amylose content (waxy), gelatinisation temperature (alk) and fragrance (fgr) were amplified in a multiplex PCR. A single base extension reaction carried out at the polymorphism responsible for each of these phenotypes within these genes generated extension products which were quantified by a MALDI –TOF system, the Sequenom® MassARRAY®. The assay detects both SNPs and indels and is co-dominant, simultaneously detecting both homozygous and heterozygous samples in a multiplex system. We are extending this approach to the analysis of rice starch biosynthesis genes. Ardashir K. Masouleh http://works.bepress.com/robert_henry/835 http://works.bepress.com/robert_henry/835 Tue, 23 Feb 2010 22:41:55 PST Timothy Sexton http://works.bepress.com/robert_henry/834 http://works.bepress.com/robert_henry/834 Tue, 23 Feb 2010 22:41:51 PST Barley grain from a combined intermediate and advanced barley breeding trial was assessed for grain, feed and malt quality from two sites over two consecutive years, with the objective to ascertain relationships between these traits. Results indicated there were genetic effects for both malt (hot water extract and friability) and “feed” traits (as measured by hardness, acid detergent fibre, starch and in-sacco dry matter digestibility). The feed trait values were generally independent of the malt trait values. However, there were positive relationships between friability, hardness and protein, as well as a negative relationship between extract and husk. Extract also had a positive relationship with test weight but appeared to be independent from the feed traits. Test weight also showed little relationship to the feed traits. Heritability values ranged from low to high for almost all traits. This study details where both malt and cattle feed parameters have been compared and the results indicated that while malt and feed traits do not correlate directly, malt cultivars can exhibit excellent feed characteristics, equal to or better than feed cultivars. This data highlights the benefit of selecting for malt quality even if a breeding program would be interested at targeting specific feed quality Glen P. Fox http://works.bepress.com/robert_henry/833 http://works.bepress.com/robert_henry/833 Tue, 23 Feb 2010 22:41:47 PST Julie Pattemore http://works.bepress.com/robert_henry/832 http://works.bepress.com/robert_henry/832 Tue, 23 Feb 2010 22:41:44 PST Ian Chivers http://works.bepress.com/robert_henry/831 http://works.bepress.com/robert_henry/831 Tue, 23 Feb 2010 22:41:39 PST Shabana Kasem http://works.bepress.com/robert_henry/830 http://works.bepress.com/robert_henry/830 Tue, 23 Feb 2010 22:41:37 PST Shotgun sequencing plant genomic DNA preparations generates large quantities of sequence data in a single run. Using the Illumina GAII, whole genome shot-gun sequence (WGS) data was generated for Oryza sativa cv Nipponbarre, and the rice wild relatives Oryza meridionalis and Oryza australiensis. Two other grass species were also sequenced, Potamophila parviflora, from the Oryzeae tribe and Microlaena stipoides from the subfamily Ehartoideae. The Illumina Genome Analyser generates short sequence reads of 36 -75 bp. These short reads are usually converted to contiguous DNA sequence data by either de novo assembly or by assembling the data using an existing genome sequence as a scaffold. We used both approaches to retrieve the whole chloroplast sequence of cultivated rice and related species from whole genome sequence data. Assembly and phylogenetic analysis of the sequence data will be discussed with an emphasis on construction of novel chloroplast genomes with and without comparison to a reference genome as a strategy for application in simple, cost-effective phylogenetic analysis, identification and barcoding of plants. Nicole F. Rice http://works.bepress.com/robert_henry/829 http://works.bepress.com/robert_henry/829 Tue, 23 Feb 2010 22:41:33 PST An international consortium of 10 laboratories from 6 countries started the sequencing of the diploid species Coffea canephora during the second semester of 2009. The genus Coffea is a member of the family Rubiaceae, one of the largest among angiosperms, mainly represented in tropical areas, and a member of the Asterid clade. Interestingly, although coffee is the second most valuable commodity exported by developing countries, ours is the first known effort to get a broad view of its genome sequence. Based on deep sequencing technologies, the genome of a double haploid plant was used for performing 12 runs with the Roche Titanium technology and 1 run with the Illumina G2 technology. Available sequences in public data banks were used to help the assembly of the obtained sequences. We expect to obtain an assembly sufficient enough to allow an assessment of the general organization of the genome, to permit comparisons with existing sequenced genomes, and to lead to better understanding of Coffea genome evolution. Identification of the great majority of genes should provide insight into specific metabolic and developmental pathways. A dramatic increase in the quantity of genetic markers will also be provided, permitting the establishment of more dense genetic maps for C. arabica. Identification of transposable elements and analysis of their distribution will also be greatly facilitated. Aldexandre de Kochko http://works.bepress.com/robert_henry/828 http://works.bepress.com/robert_henry/828 Tue, 23 Feb 2010 22:41:29 PST Robert J. Henry http://works.bepress.com/robert_henry/827 http://works.bepress.com/robert_henry/827 Tue, 23 Feb 2010 22:41:25 PST The sequencing of the sugarcane genome to produce a complete assembled sequence will be an important platform for sugarcane research. However, because of the complexity of this genome, assembly of the sequence from the short sequence reads that can now be cost effectively collected remains a significant challenge. Genome sequence may produce more immediate outcomes before complete assembly of the genome is achieved. Deep sequencing of gene rich fractions of the genome from many genotypes will define genetic diversity in sugarcane genes and provide very large numbers of genetic markers. We have obtained random shot gun sequences from the whole genome of several important genotypes and will use those as references to determine the success of genome enrichment systems. The genotype R570 will be used as a source of BAC clones for extensive sequencing of the sugarcane genome. Q165 and IJ76-514 are parents of populations with extensive maps. SP80-3280 is the subject of large scale sequencing. LA purple and Mandalay allow analysis of Saccharum officinarum and S. spontaneum genomes separately. Robert J. Henry