Background Long read sequencing allows the analysis of full-length transcripts in plants without the challenges of reliable transcriptome assembly. Long read sequencing of transcripts from plant genomes has often utilized sized transcript... more
Background Long read sequencing allows the analysis of full-length transcripts in plants without the challenges of reliable transcriptome assembly. Long read sequencing of transcripts from plant genomes has often utilized sized transcript libraries. However, the value of including libraries of differing sizes has not been established. Methods A comprehensive transcriptome of the leaves of Jojoba (Simmondsia chinensis) was generated from two different PacBio library preparations: standard workflow (SW) and long workflow (LW). Results The importance of using both transcript groups in the analysis was demonstrated by the high proportion of unique sequences (74.6%) that were not shared between the groups. A total of 37.8% longer transcripts were only detected in the long dataset. The completeness of the combined transcriptome was indicated by the presence of 98.7% of genes predicted in the jojoba male reference genome. The high coverage of the transcriptome was further confirmed by BUSC...
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See next page for additional authors ePublications@ SCU is an electronic repository administered by Southern Cross University Library. Its goal is to capture and preserve the intellectual output of Southern Cross University authors and... more
See next page for additional authors ePublications@ SCU is an electronic repository administered by Southern Cross University Library. Its goal is to capture and preserve the intellectual output of Southern Cross University authors and researchers, and to increase visibility and impact through open access to researchers around the world. For further information please contact epubs@ scu. edu. au.
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SAGE and the Mysteries of Malting Toni Pacey-Miller, Jessica White, Allison Crawford, Giovanni Cordeiro, Daniel Barbary, Peter Bundock and Robert Henry Grain Foods CRC, Ltd., Centre for Plant Conservation Genetics, Southern Cross... more
SAGE and the Mysteries of Malting Toni Pacey-Miller, Jessica White, Allison Crawford, Giovanni Cordeiro, Daniel Barbary, Peter Bundock and Robert Henry Grain Foods CRC, Ltd., Centre for Plant Conservation Genetics, Southern Cross University, Lismore Australia 2480 ...
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Abstract Wild barley (Hordeum spontaneum) represents a significant genetic resource for crop improvement in barley (Hordeum vulgare) and for the study of the evolution and domestication of plant populations. The Isa gene from barley has a... more
Abstract Wild barley (Hordeum spontaneum) represents a significant genetic resource for crop improvement in barley (Hordeum vulgare) and for the study of the evolution and domestication of plant populations. The Isa gene from barley has a putative role in plant defense. We identified 16 Single Nucleotide Polymorphisms (SNPs) in the coding region of the Isa locus of 189 wild barley accessions from 8 sites that were characterized for 16 ecogeographical variables. The pattern of SNPs suggested a large number of ...
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Abstract: Serial Analysis of Gene Expression (SAGE) is a technique that allows genome-wide expression studies based on the sequencing of unique gene tags. This method produces a comprehensive and quantitative picture of an RNA transcript... more
Abstract: Serial Analysis of Gene Expression (SAGE) is a technique that allows genome-wide expression studies based on the sequencing of unique gene tags. This method produces a comprehensive and quantitative picture of an RNA transcript population. The principle that a short nucleotide sequence, or tag, can effectively identify the original gene transcript from whence it came, allows these tags to be linked together for rapid sequencing. The tags are extracted from the raw sequence and the frequency of a particular tag ...
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Ablett, GA, Ablett, EM, Bundock, PC, Kennedy, BG, Rice, NF & Henry, RJ 2002, 'Emerging molecular technology for rapid variety identification and detection of variety contamination', in CK Black, J Panozzo, CW Wrigley, IL... more
Ablett, GA, Ablett, EM, Bundock, PC, Kennedy, BG, Rice, NF & Henry, RJ 2002, 'Emerging molecular technology for rapid variety identification and detection of variety contamination', in CK Black, J Panozzo, CW Wrigley, IL Batey & N Larsen (eds), Cereals 2002: Proceedings of the 52nd Australian Cereal Chemistry Conference, Christchurch, New Zealand, 9-12 September, Cereal Chemistry Division, Royal Australian Chemical Institute, North Melbourne. Vic.
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The processes involved in malting are still somewhat a mystery on a genetic level. SAGE (Serial Analysis of Gene Expression) is a technique that allows rapid, detailed analysis of thousands of transcripts in a cell. The process of SAGE... more
The processes involved in malting are still somewhat a mystery on a genetic level. SAGE (Serial Analysis of Gene Expression) is a technique that allows rapid, detailed analysis of thousands of transcripts in a cell. The process of SAGE relies on two principles. Firstly, a small sequence of nucleotides from the transcript, called a “tag” can effectively identify the original transcript from whence it came. Secondly, linking these tags allows rapid sequencing analysis of multiple transcripts. By examining the transcripts expressed at any ...
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The Isa gene from barley--an intronless gene expressed in maternal tissues of the seed--has a likely role in defence against pathogens. The protein product--bi-functional alpha-amylase/subtilisin inhibitor--inhibits the... more
The Isa gene from barley--an intronless gene expressed in maternal tissues of the seed--has a likely role in defence against pathogens. The protein product--bi-functional alpha-amylase/subtilisin inhibitor--inhibits the seed's own amylase in addition to the bacterial protease subtilisin and fungal xylanase. Sixteen barley genotypes were targeted to amplify and sequence the Isa gene region to detect sequence polymorphisms, since little is known about genetic diversity at this locus. A total of 80 single nucleotide polymorphisms (SNPs) and 23 indels were detected in 2,164 bp of sequence containing the Isa transcript, promoter and 3' non-transcribed region (overall one SNP per 27 bp and one indel per 94 bp), with eight sequence-based haplotypes distinguishable amongst the 16 varieties. Sequencing a polymorphic region in the promoter in an additional 27 barley genotypes increased the number of sequence-based haplotypes discovered to 11. However there is low haplotype diversity amongst the cultivated barley varieties sampled, with most varieties represented by a single haplotype. There was minor amino acid diversity in the protein, with five out of ten SNP sites in the coding region predicted to produce amino acid substitutions. SNP analysis indicated a history of recombination events--a minimum of seven based on the initial eight haplotypes from the whole sequenced region. Most of the recombination events occurred in the highly polymorphic regions, the 3' non-transcribed region and sequences flanking a microsatellite in the Isa promoter.
Research Interests: Genetics, Polymorphism, Biology, Medicine, Gene expression, and 15 moreGenetic Diversity, Biological Sciences, Haplotypes, Plant sciences, Gene, Genotype, Single Nucleotide Polymorphism, Genetic Recombination, Genetic variation, Species Specificity, Amino Acid Sequence, Base Sequence, Amino Acid Substitution Rates, Haplotype, and Molecular Sequence Data
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Establishing an open-source platform for unravelling the genetics of macadamia: integration of linkage and genome maps.
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Sugarcane is genetically complex due to polyploidy, aneuploidy and hybridisation which have led to a large but variable number of copies of each chromosome and a large number of chromosomes overall in the genomes of commercial varieties.... more
Sugarcane is genetically complex due to polyploidy, aneuploidy and hybridisation which have led to a large but variable number of copies of each chromosome and a large number of chromosomes overall in the genomes of commercial varieties. To map genes of interest, ‘single dose’ SNPs are desirable because they are fully informative across the mapping population. However discovery of these
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Barley and its malting potential are of great economical importance worldwide. The processes involved in malting at the genetic level are however still poorly understood. By examining the transcripts expressed at any time in the cell it... more
Barley and its malting potential are of great economical importance worldwide. The processes involved in malting at the genetic level are however still poorly understood. By examining the transcripts expressed at any time in the cell it is possible to determine which genes and ...
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Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to... more
Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to their locality outside the range of domesticated rice, Australian wild rice populations are a potential source of unique traits for rice breeding. These rice species provide a diverse gene pool for improvement that could be utilized for desirable traits such as stress resistance, disease tolerance, and nutritional qualities. However, they remain poorly characterized. The CRISPR/Cas system has revolutionized gene editing and has improved our understanding of gene functions. Coupled with the increasing availability of genomic information on the species, genes in Australian wild rice could be modified through genome editing technologies to produce new domesticates. Alternatively, beneficial alleles from these rice species could be incorporated into culti...
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The wild rice gene pool, i.e., AA-genome, in Australia is geographically and genetically distinct from that in Asia. Two distinct taxa are found growing together in northern Australia,Oryza meridionalis(including annual and perennial... more
The wild rice gene pool, i.e., AA-genome, in Australia is geographically and genetically distinct from that in Asia. Two distinct taxa are found growing together in northern Australia,Oryza meridionalis(including annual and perennial forms) and anOryza rufipogonlike taxa that have been shown to have a chloroplast genome sequence that is closer to that ofO. meridionalisthan toO. rufipogonfrom Asia. Rare plants of intermediate morphology have been observed in the wild despite a reported reproductive barrier between these two species. We now report the resequencing of plants from 26 populations including both taxa and putative hybrids. A comparison of chloroplast and nuclear genome sequences indicated re-combinations that demonstrated hybridisation in both directions. Individuals with intermediate morphology had high nuclear genome heterozygosity consistent with a hybrid origin. An examination of specific genes (e.g., starch biosynthesis genes) revealed the presence of heterozygotes wi...
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SummaryAllele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each... more
SummaryAllele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, ASEGs were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organell...
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Background The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucrose accumulation,... more
Background The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucrose accumulation, fiber content and stalk number. To expand the understanding of the biological pathways related to these traits, we evaluated gene expression of two groups of genotypes contrasting in biomass composition. Results First visible dewlap leaves were collected from 12 genotypes, six per group, to perform RNA-SEq. We found a high number of differentially expressed genes, showing how hybridization in a complex polyploid system caused extensive modifications in genome functioning. We found evidence that the variation between these groups may be partly due to the expansion of the Saccharum genomes by differential transposition and defense related genes. Genotypes within both biomass groups showed substantial variability in genes involved in photosynthesis. Ho...
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Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity... more
Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after t...
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The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale... more
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Gr...
Research Interests: Bioinformatics, Evolutionary Biology, Developmental Biology, Biology, Evolution, and 15 moreMedicine, Biological Sciences, Molecular, Phylogeny, Genomics and Proteomics, Rice, Plant, Domestication, Crops, Genome, Introgression, Agricultural, Genetic variation, Oryza rufipogon , and Medical and Health Sciences
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Barley is a genotypically variable species and correct identification of barley varieties is vital for quality assurance of goods requiring different grain attributes. For example, the malting and brewing performance of barley is variety... more
Barley is a genotypically variable species and correct identification of barley varieties is vital for quality assurance of goods requiring different grain attributes. For example, the malting and brewing performance of barley is variety dependent, thus sourcing the correct variety is critical to product consistency. In order to facilitate rapid, high throughput identification of barley varieties, we have developed an assay capable of determining variety identity and purity with precision and speed. A comprehensive ...
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See next page for additional authors ePublications@ SCU is an electronic repository administered by Southern Cross University Library. Its goal is to capture and preserve the intellectual output of Southern Cross University authors and... more
See next page for additional authors ePublications@ SCU is an electronic repository administered by Southern Cross University Library. Its goal is to capture and preserve the intellectual output of Southern Cross University authors and researchers, and to increase visibility and impact through open access to researchers around the world. For further information please contact epubs@ scu. edu. au.
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Abstract Improving the effective separation of wheat bran from endosperm has important economic ramifications for the milling industry. While physical and mechanical aspects of grain fractionation have been studied, a genome-wide genetic... more
Abstract Improving the effective separation of wheat bran from endosperm has important economic ramifications for the milling industry. While physical and mechanical aspects of grain fractionation have been studied, a genome-wide genetic approach has not been undertaken. We are using the Serial Analysis of Gene Expression (SAGE) technique to study both temporal and spatial differences in gene expression in developing wheat (Triticum aestivum) seeds. The high throughput SAGE approach not only provides a comparison of ...
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Plant breeding systems can have a profound effect on a species ability to persist, colonise new areas and adapt to environmental change. Determining the breeding systems in rare and common congeners may shed light on factors influencing... more
Plant breeding systems can have a profound effect on a species ability to persist, colonise new areas and adapt to environmental change. Determining the breeding systems in rare and common congeners may shed light on factors influencing rarity. Endemic to Australia, the Davidsonia genus comprises three species of rainforest trees. The two sympatric, subtropical species, Davidsonia jerseyana (F.Muell. ex F.M.Bailey) G.Harden & J.B.Williams, and D. johnsonii G.Harden & J.B.Williams, are endangered whereas the tropical D. pruriens F.Muell. is widespread. Other than exclusive clonality in D. johnsonii, the reproductive systems in the genus are unknown. We used segregation analysis of microsatellite loci in open-pollinated progeny arrays to investigate the breeding systems in D. jerseyana and D. pruriens. Reproductive success, under glasshouse conditions, was measured by the proportion of viable seeds, germination rate and seedling growth and survival over 12 months. Davidsonia jerseyana appears to be predominantly selfing with high fecundity. In D. pruriens, polyembryony was common and 89% of the progeny were identical to the heterozygous maternal parent, implying likely apomixis. Overall, fecundity was significantly lower than for D. jerseyana, although survival was higher from D. pruriens polyembryonic than from monoembryonic seed. The high fecundity in D. jerseyana indicates a lack of inbreeding depression and also suggests that it would be less likely to be endangered than the less fecund D. pruriens. This raises the possibility that polyembryony and likely apomixis may provide a reproductive advantage to D. pruriens, which could otherwise share rarity with its congeners.
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SNPs are the basis for many polymorphisms that are detected using systems such as restriction fragment length polymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs). Cleaved... more
SNPs are the basis for many polymorphisms that are detected using systems such as restriction fragment length polymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs). Cleaved amplified polymorphic site (CAPS or PCRRFLP) markers have been adopted by a number of groups to enable mapping of SNP markers identified in ESTs. Because this system relies on each SNP being associated with a restriction enzyme site, only a proportion of SNPs are amenable to CAPS. In addition, the enzyme digest step is both time-consuming and often unreliable. An alternative method is allele-specific PCR (AS-PCR). The reliability of AS-PCR can be increased by the addition of destabilizing mismatches within the allele-specific primer (ASP), reducing the false positive rate, and a parallel positive control PCR reducing false negatives. The positive control PCR takes place in the same tube as the diagnostic PCR, competing with it for access to polymerase and nucleotides and this too may contribute to a reduction in the false positive rate. The outcomes of these experiments allowed the formation of guidelines which were successfully used to design assays for three additional SNPs. Briefly, the guidelines were as follows: (i) the melting temperature (Tm) of the positive control primers should be 20-25°C lower than that of the 300-1000 bp PCR product itself; (ii) the Tm of the inner PCR products should be -35°C lower than the positive control PCR product; and (iii) the annealing temperature should be 20°C below the Tm of the positive control PCR product. The recommended optimization pathway involved alterations to both positive control and ASP concentrations.
Research Interests: Genetics, Biology, Single Nucleotide Polymorphisms (SNPs), Plant Breeding, Polymerase Chain Reaction, and 11 moreSingle Nucleotide Polymorphism, Genotyping, Agricultural and Biological Sciences, Genetic Analysis, Allele, Genotypes, Genetic Markers, Starch synthase IIa, Barley (Hordeum vulgare L.), alleles, and Single nucleotide polymorphisms
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ABSTRACT We have developed grainSAGE, a data warehousing facility to store and analyse large sample sets of tag sequences derived from Serial Analysis of Gene Expression (SAGE) for wheat and barley grain. Expression profiles of specific... more
ABSTRACT We have developed grainSAGE, a data warehousing facility to store and analyse large sample sets of tag sequences derived from Serial Analysis of Gene Expression (SAGE) for wheat and barley grain. Expression profiles of specific tag sequences across multiple time point libraries are visualised graphically with SWF.
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Studies of genetic variability in crop plants are often based on polymorphism of DNA markers from anonymous genomic sites using highly polymorphic markers eg. SSRs. However variability at the level of the functional gene has been less... more
Studies of genetic variability in crop plants are often based on polymorphism of DNA markers from anonymous genomic sites using highly polymorphic markers eg. SSRs. However variability at the level of the functional gene has been less studied even though it is a portion of this variability that is likely to create most of the genetically based phenotypic variability utilised by breeders in improvement programs. To determine the distribution, extent and type of variability between barley varieties at this level the asi gene of barley was analysed by sequencing a 2.3kb region comprising the promoter, coding and downstream regions from fourteen barley varieties. The asi gene is an intronless gene whose product functions as an inhibitor of a-amylase and subtilisin. The barley varieties studied were mostly cultivated varieties bred in Australia but included a wild barley (Hordeum spontaneum) and a North African landrace. As expected the wild barley variety had the largest number of SNPs and indels compared to the consensus sequence. However ten of the cultivated barley varieties had identical sequences over the 2.3kb of sequence except for the number of repeats in a microsatellite sequence in the promoter region. To compare the level of polymorphism displayed by the microsatellite with that based on SNP and indel haplotypes a further 36 barley varieties were genotyped for microsatellite length and selected sequence polymorphisms in the promoter and coding region
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Abstract Custom microarrays can be used to examine genes influencing wheat grain quality that are expressed during seed development. Data obtained from previous SAGE (Serial Analysis of Gene Expression) analysis of the wheat genome has... more
Abstract Custom microarrays can be used to examine genes influencing wheat grain quality that are expressed during seed development. Data obtained from previous SAGE (Serial Analysis of Gene Expression) analysis of the wheat genome has been used to developed a custom array containing specific genes of interest. The custom array uses an electrochemical detection system for recognition of hybridisation. A 12K array was designed for each of two time points of the developing wheat grain (14dpa and 30dpa). The arrays ...
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Skip to main content: My Account; Help; About; Home. ePublications@SCU. ePublications@SCU. < Previous; Next >; Home > Plant Science papers > 363. Southern Cross Plant Science. Title. Recombination in the asi gene of barley.... more
Skip to main content: My Account; Help; About; Home. ePublications@SCU. ePublications@SCU. < Previous; Next >; Home > Plant Science papers > 363. Southern Cross Plant Science. Title. Recombination in the asi gene of barley. Authors. PC BundockFollow RJ HenryFollow. Suggested Citation. Interim Citation: Bundock, PC & Henry, RJ 2004, 'Recombination in the asi gene of barley', in Plant and Animal Genomes XII, San Diego CA, USA. Tell a Colleague Print COinS. ...
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Abstract Serial Analysis of Gene Expression (SAGE) has been used to understand more comprehensively the gene expression involved in the growth of a developing wheat grain. SAGE is a technique that allows rapid, detailed analysis of... more
Abstract Serial Analysis of Gene Expression (SAGE) has been used to understand more comprehensively the gene expression involved in the growth of a developing wheat grain. SAGE is a technique that allows rapid, detailed analysis of thousands of transcripts in a cell. The abundance of a particular tag relates directly to the expression level of the gene from which it is derived. The analysis of gene expression of different physiological states provides both qualitative and quantitative information. Seed development is a complex process ...
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Abstract We have developed markers for thirty-six single nucleotide polymorphisms (SNPs) found between cultivated barley varieties. The SNPs are present in twenty-eight barley genes and were initially detected in silico from publicly... more
Abstract We have developed markers for thirty-six single nucleotide polymorphisms (SNPs) found between cultivated barley varieties. The SNPs are present in twenty-eight barley genes and were initially detected in silico from publicly available EST sequences. The resulting allele specific PCR markers are simple to assay (requiring only an agarose gel system and thermocycler) and could be used in linkage mapping, pedigree analysis, varietal identification and association studies. Forty-nine likely intervarietal SNP sites identified ...
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Single nucleotide polymorphisms (SNPs) and small DNA insertions and deletions (indels) constitute a highly abundant source of genetic variation that can be utilised to describe varietal differences and hence be used for varietal... more
Single nucleotide polymorphisms (SNPs) and small DNA insertions and deletions (indels) constitute a highly abundant source of genetic variation that can be utilised to describe varietal differences and hence be used for varietal identification. Once discovered, the presence of SNPs and small indels can be assayed routinely using pyrosequencing. Pyrosequencing™ is a sequence-by-synthesis method in which a series of enzymatic reactions yields detectable light that is proportional to the number of incorporated ...
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Abstract Numerous methods have been developed for genotyping SNPs, however many of these depend on expensive equipment for analysis. In addition, as a result of the diversity of assay methods, markers developed in one laboratory are often... more
Abstract Numerous methods have been developed for genotyping SNPs, however many of these depend on expensive equipment for analysis. In addition, as a result of the diversity of assay methods, markers developed in one laboratory are often not transferable to laboratories dedicated to a different method of analysis. An alternative cheap, simple, transferable and robust method of SNP genotyping is based on a three primer nested allele specific PCR. With this method, SNP genotyping can be carried out with a thermocycler ...
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Abstract Rice (Oryza sativa Japonica) was probably domesticated from wild populations of Oryza rufipogon in Asia. Relative to cultivated rice, O. meridionalis, from Australia is the most genetically distant Oryza species with an A genome... more
Abstract Rice (Oryza sativa Japonica) was probably domesticated from wild populations of Oryza rufipogon in Asia. Relative to cultivated rice, O. meridionalis, from Australia is the most genetically distant Oryza species with an A genome (some level of inter breeding with O. sativa is possible) O. rufipogon and O. meridionalis are found in widespread populations across northern Australia. Massively parallel sequencing was used to determine the sequence of the chloroplast genomes of O. rufipogon from Asia and Australia and O. ...
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Long Serial Analysis of Gene Expression (SAGE) is a technique that enables the analysis of a large number of expressed transcripts using a quantitative approach. Efficient analysis of the transcripts is achieved by concatenation of short... more
Long Serial Analysis of Gene Expression (SAGE) is a technique that enables the analysis of a large number of expressed transcripts using a quantitative approach. Efficient analysis of the transcripts is achieved by concatenation of short 21 bp tags into longer clones for ...
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Skip to main content: My Account; Help; About; Home. ePublications@SCU. ePublications@SCU. &amp;lt; Previous; Next &amp;gt;; Home &amp;gt; Plant Science papers &amp;gt; 362. Southern Cross Plant Science. Title. Shotgun... more
Skip to main content: My Account; Help; About; Home. ePublications@SCU. ePublications@SCU. &amp;lt; Previous; Next &amp;gt;; Home &amp;gt; Plant Science papers &amp;gt; 362. Southern Cross Plant Science. Title. Shotgun sequencing and targeted enrichment of sugarcane genome sequences. Authors. PC BundockFollow R. Casu GMM Cordeiro R. J J. HenryFollow. Suggested Citation. Interim Citation: Bundock, PC, Casu, R, Cordeiro, GM &amp;amp; Henry, RJ 2011, &amp;#x27;Shotgun sequencing ...
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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.... more
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 ...
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Abstract 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... more
Abstract 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 ...