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168 results on '"Dolferus, Rudy"'

5. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

Author

Wang, Shichen, Wong, Debbie, Forrest, Kerrie, Allen, Alexandra, Chao, Shiaoman, Huang, Bevan E, Maccaferri, Marco, Salvi, Silvio, Milner, Sara G, Cattivelli, Luigi, Mastrangelo, Anna M, Whan, Alex, Stephen, Stuart, Barker, Gary, Wieseke, Ralf, Plieske, Joerg, Consortium, International Wheat Genome Sequencing, Lillemo, Morten, Mather, Diane, Appels, Rudi, Dolferus, Rudy, Brown‐Guedira, Gina, Korol, Abraham, Akhunova, Alina R, Feuillet, Catherine, Salse, Jerome, Morgante, Michele, Pozniak, Curtis, Luo, Ming‐Cheng, Dvorak, Jan, Morell, Matthew, Dubcovsky, Jorge, Ganal, Martin, Tuberosa, Roberto, Lawley, Cindy, Mikoulitch, Ivan, Cavanagh, Colin, Edwards, Keith J, Hayden, Matthew, and Akhunov, Eduard

Subjects
Biological Sciences, Ecology, Genetics, Human Genome, Biotechnology, Alleles, Chromosome Mapping, Cluster Analysis, Gene Frequency, Genetic Loci, Genetic Markers, Genetic Variation, Genome, Plant, Genotype, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Polyploidy, Triticum, single nucleotide polymorphism, polyploid wheat, wheat iSelect array, genotyping, high-density map, genetic diversity, International Wheat Genome Sequencing Consortium, Genetic diversity, Genotyping, High-density map, Polyploid wheat, Single nucleotide polymorphism, Wheat iSelect array, Technology, Medical and Health Sciences, Agricultural biotechnology, Plant biology
Abstract

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Published
2014

6. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

Author

Wang, Shichen, Wong, Debbie, Forrest, Kerrie, Allen, Alexandra, Chao, Shiaoman, Huang, Bevan E, Maccaferri, Marco, Salvi, Silvio, Milner, Sara G, Cattivelli, Luigi, Mastrangelo, Anna M, Whan, Alex, Stephen, Stuart, Barker, Gary, Wieseke, Ralf, Plieske, Joerg, International Wheat Genome Sequencing Consortium, Lillemo, Morten, Mather, Diane, Appels, Rudi, Dolferus, Rudy, Brown-Guedira, Gina, Korol, Abraham, Akhunova, Alina R, Feuillet, Catherine, Salse, Jerome, Morgante, Michele, Pozniak, Curtis, Luo, Ming-Cheng, Dvorak, Jan, Morell, Matthew, Dubcovsky, Jorge, Ganal, Martin, Tuberosa, Roberto, Lawley, Cindy, Mikoulitch, Ivan, Cavanagh, Colin, Edwards, Keith J, Hayden, Matthew, and Akhunov, Eduard

Subjects
International Wheat Genome Sequencing Consortium, Triticum, Genetic Markers, Oligonucleotide Array Sequence Analysis, Cluster Analysis, Chromosome Mapping, Gene Frequency, Genotype, Polyploidy, Polymorphism, Single Nucleotide, Alleles, Genome, Plant, Genetic Variation, Genetic Loci, genetic diversity, genotyping, high-density map, polyploid wheat, single nucleotide polymorphism, wheat iSelect array, Genetic diversity, Genotyping, High-density map, Polyploid wheat, Single nucleotide polymorphism, Wheat iSelect array, Biotechnology, Technology, Biological Sciences, Medical and Health Sciences
Abstract

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Published
2014

21. Enhancing the Anaerobic Response

Author

DOLFERUS, RUDY, KLOK, ERIK JAN, DELESSERT, CHRISTIAN, WILSON, SARAH, ISMOND, KATHLEEN P., GOOD, ALLEN G., PEACOCK, W. JAMES, and DENNIS, ELIZABETH S.

Published
2003

28. Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen

Author

Hoeren, Frank U., Dolferus, Rudy, Wu, Yingru, Peacock, W. James, and Dennis, Elizabeth S.

Subjects
Arabidopsis -- Genetic aspects, Dehydrogenases -- Genetic aspects, Oxygen -- Genetic aspects, Genetic transcription -- Analysis, Nicotiana -- Genetic aspects, Peas -- Genetic aspects, Promoters (Genetics) -- Research, Biological sciences
Abstract

The transcription factor AtMYB2 binds to two sequence motifs in the promoter of the Arabidopsis ADH1 gene. The binding to the GT-motif (5[prime]-TGGTTT-3[prime]) is essential for induction of ADH1 by low oxygen, while binding to the second motif, MBS-2, is not essential for induction. We show that AtMYB2 is induced by hypoxia with kinetics compatible with a role in the regulation of ADH1. Like ADH1, AtMYB2 has root-limited expression. When driven by a constitutive promoter, AtMYB2 is able to transactivate ADH1 expression in transient assays in both Arabidopsis and Nicotiana plumbaginifolia protoplasts, and in particle bombardment of Pisum sativum leaves. Mutation of the GT-motif abolished binding of AtMYB2 and caused loss of activity of the ADH1 promoter in both transient assays and transgenic Arabidopsis plants. These results are consistent with AtMYB2 being a key regulatory factor in the induction of the ADH1 promoter by low oxygen.

Published
1998

32. Determining the Genetic Architecture of Reproductive Stage Drought Tolerance in Wheat Using a Correlated Trait and Correlated Marker Effect Model

Author

Dolferus, Rudy, primary, Thavamanikumar, Saravanan, additional, Sangma, Harriet, additional, Kleven, Sue, additional, Wallace, Xiaomei, additional, Forrest, Kerrie, additional, Rebetzke, Gregory, additional, Hayden, Matthew, additional, Borg, Lauren, additional, Smith, Alison, additional, and Cullis, Brian, additional

Published
2019
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43. Enhanced Low Oxygen Survival in Arabidopsis through Increased Metabolic Flux in the Fermentative Pathway1

Author

Ismond, Kathleen P., Dolferus, Rudy, De Pauw, Mary, Dennis, Elizabeth S., and Good, Allen G.

Subjects
Oxygen, Gene Expression Regulation, Plant, fungi, Fermentation, Pyruvic Acid, Alcohol Dehydrogenase, Arabidopsis, food and beverages, Plants, Genetically Modified, Pyruvate Decarboxylase, Plant Shoots, Research Article
Abstract

We manipulated the enzyme activity levels of the alcohol fermentation pathway, pyruvate decarboxylase (PDC), and alcohol dehydrogenase (ADH) in Arabidopsis using sense and antisense overexpression of the corresponding genes (PDC1, PDC2, and ADH1). Transgenic plants were analyzed for levels of fermentation and evaluated for changes in hypoxic survival. Overexpression of either Arabidopsis PDC1 or PDC2 resulted in improved plant survival. In contrast, overexpression of Arabidopsis ADH1 had no effect on flooding survival. These results support the role of PDC as the control step in ethanol fermentation. Although ADH1 null mutants had decreased hypoxic survival, attempts to reduce the level of PDC activity enough to see an effect on plant survival met with limited success. The combination of flooding survival data and metabolite analysis allows identification of critical metabolic flux points. This information can be used to design transgenic strategies to improve hypoxic tolerance in plants.

Published
2003

50. Cold-induced repression of the rice anther-specific cell wall invertase gene OSINV4 is correlated with sucrose accumulation and pollen sterility

Author

OLIVER, SANDRA N., primary, VAN DONGEN, JOOST T., additional, ALFRED, SANJEEV C., additional, MAMUN, EZAZ A., additional, ZHAO, XIAOCHUN, additional, SAINI, HARGURDEEP S., additional, FERNANDES, SUSSAN F., additional, BLANCHARD, CHRISTOPHER L., additional, SUTTON, BRUCE G., additional, GEIGENBERGER, PETER, additional, DENNIS, ELIZABETH S., additional, and DOLFERUS, RUDY, additional

Published
2005
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