137 results on '"Huttner, Eric"'
Search Results
2. An Egg Apparatus-Specific Enhancer of Arabidopsis, Identified by Enhancer Detection
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Yang, Wei, Jefferson, Richard A., Huttner, Eric, Moore, James M., Gagliano, Wendy B., and Grossniklaus, Ueli
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- 2005
3. Diversity Arrays Technology (DArT) for Whole-Genome Profiling of Barley
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Wenzl, Peter, Carling, Jason, Kudrna, David, Jaccoud, Damian, Huttner, Eric, Kleinhofs, Andris, Kilian, Andrzej, and Phillips, Ronald L.
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- 2004
4. AINTEGUMENTA, an APETALA2-Like Gene of Arabidopsis with Pleiotropic Roles in Ovule Development and Floral Organ Growth
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Elliott, Robert C., Betzner, Andreas S., Huttner, Eric, Oakes, Marie P., Gerentes, Denise, Perez, Pascual, and Smyth, David R.
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- 1996
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5. Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative
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Langridge, Peter, primary, Alaux, Michael, additional, Almeida, Nuno Felipe, additional, Ammar, Karim, additional, Baum, Michael, additional, Bekkaoui, Faouzi, additional, Bentley, Alison R., additional, Beres, Brian L., additional, Berger, Bettina, additional, Braun, Hans-Joachim, additional, Brown-Guedira, Gina, additional, Burt, Christopher James, additional, Caccamo, Mario Jose, additional, Cattivelli, Luigi, additional, Charmet, Gilles, additional, Civáň, Peter, additional, Cloutier, Sylvie, additional, Cohan, Jean-Pierre, additional, Devaux, Pierre J., additional, Doohan, Fiona M., additional, Dreccer, M. Fernanda, additional, Ferrahi, Moha, additional, Germán, Silvia E., additional, Goodwin, Stephen B., additional, Griffiths, Simon, additional, Guzmán, Carlos, additional, Handa, Hirokazu, additional, Hawkesford, Malcolm John, additional, He, Zhonghu, additional, Huttner, Eric, additional, Ikeda, Tatsuya M., additional, Kilian, Benjamin, additional, King, Ian Philip, additional, King, Julie, additional, Kirkegaard, John A., additional, Lage, Jacob, additional, Le Gouis, Jacques, additional, Mondal, Suchismita, additional, Mullins, Ewen, additional, Ordon, Frank, additional, Ortiz-Monasterio, Jose Ivan, additional, Özkan, Hakan, additional, Öztürk, İrfan, additional, Pereyra, Silvia A., additional, Pozniak, Curtis J., additional, Quesneville, Hadi, additional, Quincke, Martín C., additional, Rebetzke, Greg John, additional, Christoph Reif, Jochen, additional, Saavedra-Bravo, Teresa, additional, Schurr, Ulrich, additional, Sharma, Shivali, additional, Singh, Sanjay Kumar, additional, Singh, Ravi P., additional, Snape, John W., additional, Tadesse, Wuletaw, additional, Tsujimoto, Hisashi, additional, Tuberosa, Roberto, additional, Willis, Tim G., additional, and Zhang, Xueyong, additional
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- 2022
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6. Crop improvement and management: Timor-Leste cassava ball with coconut
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Erskine, William and Huttner, Eric
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- 2017
7. Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
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Saradadevi, Renu, primary, Mukankusi, Clare, additional, Li, Li, additional, Amongi, Winnyfred, additional, Mbiu, Julius Peter, additional, Raatz, Bodo, additional, Ariza, Daniel, additional, Beebe, Steve, additional, Varshney, Rajeev K., additional, Huttner, Eric, additional, Kinghorn, Brian, additional, Banks, Robert, additional, Rubyogo, Jean Claude, additional, Siddique, Kadambot H. M., additional, and Cowling, Wallace A., additional
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- 2021
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8. Characterization of Mobile Endogenous Copia-Like Transposable Elements in the Genome of Solanaceae
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Grandbastien, Marie-Angèle, Spielmann, Albert, Pouteau, Sylvie, Huttner, Eric, Longuet, Michèle, Kunert, Karl, Meyer, Christian, Rouzé, Pierre, Caboche, Michel, Herrmann, R. G., editor, and Larkins, B. A., editor
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- 1991
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9. Development of DArT markers for a linkage map of flue-cured tobacco
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Lu, XiuPing, Gui, YiJie, Xiao, BingGuang, Li, YongPing, Tong, ZhiJun, Liu, Yun, Bai, XueFei, Wu, WeiRen, Xia, Ling, Huttner, Eric, Kilian, Adrzej, and Fan, LongJiang
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- 2013
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10. Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane
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Heller-Uszynska, Katarzyna, Uszynski, Grzegorz, Huttner, Eric, Evers, Margaret, Carlig, Jason, Caig, Vanessa, Aitken, Karen, Jackson, Phillip, Piperidis, George, Cox, Mike, Gilmour, Ross, D’Hont, Angelique, Butterfield, Mike, Glaszmann, Jean-Christophe, and Kilian, Andrzej
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- 2011
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11. Reconstruction of the synthetic W7984 x Opata M85 wheat reference population
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Sorrells, Mark E., Gustafson, J. Perry, Somers, Daryl, Chao, Shiaoman, Benscher, David, Guedira-Brown, Gina, Huttner, Eric, Kilian, Andrezj, McGuire, Patrick E., Ross, Kathleen, Tanaka, James, Wenzl, Peter, Williams, Keith, and Qualset, Calvin O.
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Genetic markers -- Research ,Wheat -- Genetic aspects -- Research ,Genetic populations -- Research ,Chromosome mapping -- Usage ,Biological sciences - Abstract
Reference populations are valuable resources in genetics studies for determining marker order, marker selection, trait mapping, construction of large-insert libraries, cross-referencing marker platforms, and genome sequencing. Reference populations can be propagated indefinitely, they are polymorphic and have normal segregation. Described are two new reference populations who share the same parents of the original wheat reference population Synthetic W7984 (Altar84/Aegilops tauschii (219) CIGM86.940) X Opata M85, an Fi-derived doubled haploid population (SynOpDH) of 215 inbred lines and a recombinant inbred population (SynOpRIL) of 2039 F6 lines derived by single-plant self-pollinations. A linkage map was constructed for the SynOpDH population using 1446 markers. In addition, a core set of 42 SSR markers was genotyped on SynOpRIL. A new approach to identifying a core set of markers used a step-wise selection protocol based on polymorphism, uniform chromosome distribution, and reliability to create nested sets starting with one marker per chromosome, followed by two, four, and six. It is suggested that researchers use these markers as anchors for all future mapping projects to facilitate cross-referencing markers and chromosome locations. To enhance this public resource, researchers are strongly urged to validate line identities and deposit their data in GrainGenes so that others can benefit from the accumulated information. Key words: reference populations, mapping, core collections, molecular markers. Les populations de reference constituent une ressource precieuse en genetique pour determiner l'ordre des marqueurs, ou encore pour le choix des marqueurs, la cartographie de caracteres, la construction de banques de grands inserts, la comparaison croisee de technologies de marqueurs et le sequencage d'un genome. Il est possible de propager indefiniment des populations de reference, elles sont polymorphes et presentent une segregation normale. Les auteurs decrivent deux nouvelles populations de reference qui ont en commun les parents de la population de reference originale W7984 (Altar84/Aegilops tauschii (219) CIGM86,940) x Opata M85, soit une population haploi'de doublee derivee en [F.sub.1] et composee de 215 individus HD (SynOpDH) ainsi qu'une population de 2039 lignees recombinantes fixees en [F.sub.6] (SynOpRIL) obtenues par autofecondation de plantes individuelles. Une carte genetique a ete produite pour la population SynOpDH a l'aide de 1446 marqueurs. De plus, un jeu de base de 42 marqueurs SSR a ete genotype sur la population SynOpRIL. Une nouvelle approche pour choisir les marqueurs composant un jeu de base a ete developpee en faisant appel a une demarche systematique s'appuyant sur le polymorphisme, l'uniformite de la distribution chromosomique ainsi que la reproductibilite afin de creer des jeux emboites commencant avec un marqueur par chromosome, suivis de deux et de six. Il est suggere que les chercheurs utilisent ces marqueurs comme points d'ancrage pour tous les futurs travaux de cartographie afin de faciliter la comparaison des marqueurs et des positions chromosomiques. Afin d'ameliorer cette ressource publique, les chercheurs sont encourages a valider l'identite de leurs lignees et de deposer les donnees au sein de GrainGenes de maniere a permettre aux autres de beneficier de l'information ainsi collectee. Mots-cles : populations de reference, cartographie, collections nucleates, marqueurs moleculaires. [Traduit par la Redaction], Introduction Historical aspects In the late 1980s, the International Maize and Wheat Improvement Center (CIMMYT), Mexico, and Cornell University, Ithaca, New York, collaborated to survey polymorphism levels among a large [...]
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- 2011
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12. Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley
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Li, Haobing, Kilian, Andrzej, Zhou, Meixue, Wenzl, Peter, Huttner, Eric, Mendham, Neville, McIntyre, Lynne, and Vaillancourt, René E.
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- 2010
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13. Isolated chromosomes as a new and efficient source of DArT markers for the saturation of genetic maps
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Wenzl, Peter, Suchánková, Pavla, Carling, Jason, Šimková, Hana, Huttner, Eric, Kubaláková, Marie, Sourdille, Pierre, Paul, Edie, Feuillet, Catherine, Kilian, Andrzej, and Doležel, Jaroslav
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- 2010
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14. Development and assessment of Diversity Arrays Technology for high-throughput DNA analyses in Musa
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Risterucci, Ange-Marie, Hippolyte, Isabelle, Perrier, Xavier, Xia, Ling, Caig, Vanessa, Evers, Margaret, Huttner, Eric, Kilian, Andrzej, and Glaszmann, Jean-Christophe
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- 2009
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15. An integrated DArT-SSR linkage map of durum wheat
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Mantovani, Paola, Maccaferri, Marco, Sanguineti, Maria Corinna, Tuberosa, Roberto, Catizone, Ilaria, Wenzl, Peter, Thomson, Brent, Carling, Jason, Huttner, Eric, DeAmbrogio, Enzo, and Kilian, Andrzej
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- 2008
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16. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome
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Akbari, Mona, Wenzl, Peter, Caig, Vanessa, Carling, Jason, Xia, Ling, Yang, Shiying, Uszynski, Grzegorz, Mohler, Volker, Lehmensiek, Anke, Kuchel, Haydn, Hayden, Mathew J., Howes, Neil, Sharp, Peter, Vaughan, Peter, Rathmell, Bill, Huttner, Eric, and Kilian, Andrzej
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- 2006
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17. Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology
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Yang, Shiying, Pang, Wen, Ash, Gavin, Harper, John, Carling, Jason, Wenzl, Peter, Huttner, Eric, Zong, Xuxiao, and Kilian, Andrzej
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- 2006
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18. Diversity Arrays Technology: A Generic Genome Profiling Technology on Open Platforms
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Kilian, Andrzej, primary, Wenzl, Peter, additional, Huttner, Eric, additional, Carling, Jason, additional, Xia, Ling, additional, Blois, Hélène, additional, Caig, Vanessa, additional, Heller-Uszynska, Katarzyna, additional, Jaccoud, Damian, additional, Hopper, Colleen, additional, Aschenbrenner-Kilian, Malgorzata, additional, Evers, Margaret, additional, Peng, Kaiman, additional, Cayla, Cyril, additional, Hok, Puthick, additional, and Uszynski, Grzegorz, additional
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- 2012
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19. Expression of the tobacco Tnt1 retrotransposon promoter in heterologous species
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Pauls, Peter K., Kunert, Karl, Huttner, Eric, and Grandbastien, Marie-Angèle
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- 1994
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20. DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum
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Kumar Ajay, Bassi Filippo M, Paux Etienne, Al-Azzam Omar, de Jimenez Monika, Denton Anne M, Gu Yong Q, Huttner Eric, Kilian Andrzej, Kumar Sachin, Goyal Aakash, Iqbal Muhammad J, Tiwari Vijay K, Dogramaci Munevver, Balyan Harindra S, Dhaliwal Harcharan S, Gupta Pushpendra K, Randhawa Gursharn S, Feuillet Catherine, Pawlowski Wojciech P, and Kianian Shahryar F
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Non homologous end joining ,Physical mapping ,Gamma radiation ,Deletion mutant ,Chromatin ,Wheat chromosome 3B ,Radiation hybrid ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps. Results A high density RH map with 541 marker loci anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 fold higher and ii) six fold more uniform. A significant interaction (r = 0.879 at p = 0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells. Conclusions The RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.
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- 2012
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21. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas
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Matsumoto Takashi, Mbéguié-A-Mbéguié Didier, Pappas Georgios J, Miller Robert NG, Khan Imtiaz A, Piffanelli Pietro, Argout Xavier, Carreel Françoise, Perrier Xavier, Jenny Christophe, Risterucci Ange-Marie, Rivallan Ronan, Gardes Laetitia, Seguin Marc, Bakry Frederic, Hippolyte Isabelle, De Bernardinis Veronique, Huttner Eric, Kilian Andrzej, Baurens Franc-Christophe, D'Hont Angélique, Cote François, Courtois Brigitte, and Glaszmann Jean-Christophe
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Botany ,QK1-989 - Abstract
Abstract Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p < 0.05) from the expected Mendelian ratios. These skewed markers were distributed in different linkage groups for each parent. To solve some complex ordering of the markers on linkage groups, we associated tools such as tree-like graphic representations, recombination frequency statistics and cytogenetical studies to identify structural rearrangements and build parsimonious linkage group order. An illustration of such an approach is given for the P. Lilin parent. Conclusions We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.
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- 2010
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22. DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum
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Huttner Eric, Wenzl Peter, Berry Simon, Kanyuka Kostya, Bayon Carlos, Jing Hai-Chun, Kilian Andrzej, and E Hammond-Kosack Kim
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Triticum monococcum (2n = 2x = 14) is an ancient diploid wheat with many useful traits and is used as a model for wheat gene discovery. DArT (Diversity Arrays Technology) employs a hybridisation-based approach to type thousands of genomic loci in parallel. DArT markers were developed for T. monococcum to assess genetic diversity, compare relationships with hexaploid genomes, and construct a genetic linkage map integrating DArT and microsatellite markers. Results A DArT array, consisting of 2304 hexaploid wheat, 1536 tetraploid wheat, 1536 T. monococcum as well as 1536 T. boeoticum representative genomic clones, was used to fingerprint 16 T. monococcum accessions of diverse geographical origins. In total, 846 polymorphic DArT markers were identified, of which 317 were of T. monococcum origin, 246 of hexaploid, 157 of tetraploid, and 126 of T. boeoticum genomes. The fingerprinting data indicated that the geographic origin of T. monococcum accessions was partially correlated with their genetic variation. DArT markers could also well distinguish the genetic differences amongst a panel of 23 hexaploid wheat and nine T. monococcum genomes. For the first time, 274 DArT markers were integrated with 82 simple sequence repeat (SSR) and two morphological trait loci in a genetic map spanning 1062.72 cM in T. monococcum. Six chromosomes were represented by single linkage groups, and chromosome 4Am was formed by three linkage groups. The DArT and SSR genetic loci tended to form independent clusters along the chromosomes. Segregation distortion was observed for one third of the DArT loci. The Ba (black awn) locus was refined to a 23.2 cM region between the DArT marker locus wPt-2584 and the microsatellite locus Xgwmd33 on 1Am; and the Hl (hairy leaf) locus to a 4.0 cM region between DArT loci 376589 and 469591 on 5Am. Conclusion DArT is a rapid and efficient approach to develop many new molecular markers for genetic studies in T. monococcum. The constructed genetic linkage map will facilitate localisation and map-based cloning of genes of interest, comparative mapping as well as genome organisation and evolution studies between this ancient diploid species and other crops.
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- 2009
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23. Transfer RNA-mediated suppression of amber stop codons in transgenic Arabidopsis thaliana
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Betzner, Andreas S., Oakes, Marie P., and Huttner, Eric
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- 1997
24. DArT markers: diversity analyses and mapping in Sorghum bicolor
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Parh Dipal K, Halloran Kirsten, Jordan David R, Xia Ling, Mace Emma S, Huttner Eric, Wenzl Peter, and Kilian Andrzej
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm. Results A genotyping array was developed representing approximately 12,000 genomic clones using PstI+BanII complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a diverse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a diversity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM. Conclusion We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.
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- 2008
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25. A DArT platform for quantitative bulked segregant analysis
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Wang Junping, Raman Harsh, Wenzl Peter, Zhou Meixue, Huttner Eric, and Kilian Andrzej
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Bulked segregant analysis (BSA) identifies molecular markers associated with a phenotype by screening two DNA pools of phenotypically distinct plants for markers with skewed allele frequencies. In contrast to gel-based markers, hybridization-based markers such as SFP, DArT or SNP generate quantitative allele-frequency estimates. Only DArT, however, combines this advantage with low development and assay costs and the ability to be deployed for any plant species irrespective of its ploidy level. Here we investigate the suitability of DArT for BSA applications using a barley array as an example. Results In a first test experiment, we compared two bulks of 40 Steptoe/Morex DH plants with contrasting pubescent leaves (mPub) alleles on chromosome 3H. At optimized levels of experimental replication and marker-selection threshold, the BSA scan identified 433 polymorphic markers. The relative hybridization contrast between bulks accurately reflected the between-bulk difference in the frequency of the mPub allele (r = 0.96). The 'platform noise' of DArT assays, estimated by comparing two identical aliquots of a DNA mixture, was significantly lower than the 'pooling noise' reflecting the binomial sampling variance of the bulking process. The allele-frequency difference on chromosome 3H increased in the vicinity of mPub and peaked at the marker with the smallest distance from mPub (4.6 cM). In a validation experiment with only 20 plants per bulk we identified an aluminum (Al) tolerance locus in a Dayton/Zhepi2 DH population on chromosome 4H with < 0.8 cM precision, the same Al-tolerance locus that had been mapped before in other barley populations. Conclusion DArT-BSA identifies genetic loci that influence phenotypic characters in barley with at least 5 cM accuracy and should prove useful as a generic tool for high-throughput, quantitative BSA in plants irrespective of their ploidy level.
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- 2007
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26. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits
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Wang Junping, Poulsen David, Cakir Mehmet, Ovesná Jaroslava, Caig Vanessa, Xia Ling, Maier Christina, Hearnden Phillippa, Paul Edie, Raman Harsh, Zhou Meixue, Carling Jason, Li Haobing, Wenzl Peter, Raman Rosy, Smith Kevin P, Muehlbauer Gary J, Chalmers Ken J, Kleinhofs Andris, Huttner Eric, and Kilian Andrzej
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.
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- 2006
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27. Digital Technologies to Modernize Effective and Efficient Use of Plant Genetic Resources
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Huttner, Eric, primary
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- 2016
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28. Cloning of DNA fragments complementary to tobacco nitrate reductase mRNA and encoding epitopes common to the nitrate reductases from higher plants
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Calza, Roger, Huttner, Eric, Vincentz, Michel, Rouzé, Pierre, Galangau, Fabienne, Vaucheret, Hervé, Chérel, Isabelle, Meyer, Christian, Kronenberger, Jocelyne, and Caboche, Michel
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- 1987
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29. Diversity arrays technology (DArT) and statistical tools for genome profile-based molecular breeding of sugarcane : [Abstract W305]
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Heller-Uszynska, Katarzyna, Uszynski, Grzegorz, Evers, Margaret, Huttner, Eric, Carlig, Jason, Caig, Vanessa, Detering, Frank, Aitken, Karen S., Jackson, Phil A., Hermann, Scott, Cox, Mike, D'Hont, Angélique, Butterfield, Mike, Glaszmann, Jean-Christophe, and Kilian, Andrzej
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Saccharum officinarum ,human activities ,F30 - Génétique et amélioration des plantes - Abstract
Diversity Arrays Technology (DArT) combines the ability to identify various types of DNA polymorphism with the low cost and high throughput platforms DArT offers several-fold gain over other technologies in terms of marker throughput and assay cost and was successfully deployed in over 50 organisms including those with complex, polyploid genomes (www.DiversityArrays.com). We will report the current status of technology development of DArT for sugarcane, one of the most genetically complex crops. Several effective methods of genome complexity reduction were established leading to creation of genotyping array containing 7.680 probes. All markers on the array were sequenced. The analysis of sequence data shows that similarly to other crops sugarcane DArT markers are highly enriched for the genic, low copy number, sequences, enabling effective comparison against sorghum genome assembly. The genotyping array was successfully used for diversity analysis of cultivated materials and ancestral lines as well as for genetic mapping in several populations. The good genome coverage afforded by DArT array enabled efficient discovery of significant marker-trait associations and informed decisions on initiating molecular breeding of sugarcane in Australia. Several challenges identified in the course of technology development and application as well as some novel approaches to dealing with molecular marker and phenotypic data will be presented. (Texte intégral)
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- 2010
30. Musa genetic mapping
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Hippolyte, Isabelle, Seguin, Marc, Bakry, Frédéric, Gardes, Laëtitia, Baurens, Franc-Christophe, Miller, Roberto Neil Gerard, Khan, Imtiaz A., Jenny, Christophe, Carreel, Françoise, Huttner, Eric, Xavier PERRIER, Kilian, Andrzej, Risterucci, Ange-Marie, and Glaszmann, Jean-Christophe
- Subjects
Musa acuminata ,F30 - Génétique et amélioration des plantes - Abstract
We report a reference map of Musa acuminata from 180 individuals of BORLI population. This F1 population derived from the cross between M.a. "Borneo" x M.a. "Pisang Lilin" which was chosen for mapping mainly because of the great heterozygosity of both parents (76 % each). For map construction we genotyped 180 SSR markers on 180 individuals, 12 RGA-RFLP probes on 112 individuals and 380 DArT markers on 92 individuals. Using the software Joinmap 4 at LOD 5, Kosambi calculation distance and the regression mapping algorithm, we defined 11 main linkage groups, as expected, on Borneo parent and 10 on Pisang lilin due to one translocation event in the male parent. Despite structural differences between the parents, a consensus map was built. In order to check genotyping results and to analyse structural rearrangements, we developed an original method using Neighbor Joining algorithm implemented in the genetic diversity software Darwin5. It allows visualizing graphically disruptions in alignments arising from these structural rearrangements. (Texte intégral)
- Published
- 2008
31. Establishment of diversity arrays technology for whole-genome profiling of banana
- Author
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Huttner, Eric, Risterucci, Ange-Marie, Hippolyte, Isabelle, Caig, Vanessa, Carlig, Jason, Evers, Margaret, Uszynski, Grzegorz, Wenzl, Peter, Glaszmann, Jean-Christophe, and Kilian, Andrzej
- Subjects
food and beverages ,U30 - Méthodes de recherche ,human activities ,F30 - Génétique et amélioration des plantes - Abstract
The genetic improvement of ¿orphan¿ crops is going to benefit from modern breeding methods underpinned by molecular marker technologies. Establishing reliable associations between complex traits and genomic regions requires both accurate and comprehensive phenotypic characterization of the germplasm and cost-effective, high-density genotyping methods. Whole-genome, molecular profiles also enable breeders and scientists to better manage and utilize the available genetic diversity. Since many marker systems such as SSR and SNP depend on sequence information, marker discovery is still expensive and limits the development of whole-genome profiling tools for ¿orphan¿ crops. Diversity Arrays Technology (DArT) circumvents the need for sequence information and accelerates marker discovery and typing, both at a very low cost. We have established DArT for the Musa genus. Two arrays of 6,000 clones each are now available. On each array, 700 to 800 polymorphic markers were discovered in a broad survey of Musa genotypes. The majority of the markers separate the A and the B genomes, but subsets of markers resolve the diversity within each genome. A few markers also identify genetic heterogeneity within clones of cultivated banana. The low cost of DArT assays opens new opportunities for germplasm characterization and trait mapping in banana and plantain. In addition, the phenotypic effects of DNA methylation polymorphisms can now be identified and studied. The density of DArT molecular profiles will also benefit applications in Musa genomics. (Texte intégral)
- Published
- 2007
32. Validation of diversity arrays technology (DArT) as a plateform for whole-genome profiling in orphan crops
- Author
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Wongtiem, Prapit, Perera, Chandrika, Risterucci, Ange-Marie, Xia, Ling, Patarapuwadol, Sujin, Carlig, Jason, Caig, Vanessa, Evers, Margaret, Uszynski, Grzegorz, Huttner, Eric, Wenzl, Peter, Fregene, Martin, De Vicente, M. Carmen, Glaszmann, Jean-Christophe, and Kilian, Andrzej
- Subjects
Génie génétique ,Génome ,F30 - Génétique et amélioration des plantes ,Variation génétique ,Carte génétique ,Marqueur génétique ,U30 - Méthodes de recherche ,Plante de culture ,Technique analytique - Published
- 2006
33. DArT, a whole genome profiling method for high-troughput genotyping of Musa
- Author
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Risterucci, Ange-Marie, Hippolyte, Isabelle, Caig, Vanessa, Carling, J., Evers, Margaret, Uszynski, Grzegorz, Wenzl, Peter, Xia, L., Huttner, Eric, Glaszmann, Jean-Christophe, and Kilian, Andrzej
- Subjects
food and beverages ,F30 - Génétique et amélioration des plantes - Abstract
Genetic analysis of adaptation in plants is of primary interest in the case of crops as well as natural populations, for the sake of sustainable agriculture and ecological resource management. Both accurate assessment of the right phenotypic features and fast and affordable high throughput genotyping are necessary. If we manage to make the latter no longer limiting, we open a wider range of opportunities to produce valuable genetic information using materials with phenotypic description derived from diverse and rich experiments and protocols. The sequential nature of gel-based markers entails a limitation in throughput. Many marker systems such as SNP and SSR depend on sequence information. Diversity Arrays Technology (DArT) circumvents these limitations and enables high-throughput genome profiling at low cost even for crops with no sequence information available. Musa is one of the world's most important crop genera with 73 million tons of banana and 33 million tons of plantain fruits produced in 2005. It features several genomes in various combinations. We have now established two libraries of 6,000 DArT clones using a complexity reduction method based on restriction enzymes Pstl as a primary cutter and Taql or BstNl as a secondary cutter. Between 700 and 800 markers were identified in each of these libraries. Initial analysis of 187 diverse banana and plantain accessions showed that while the majority of the markers separated the A and the B genome, the array also resolves diversity within each genome. This current set of arrays will be applied to extend the current genetic map of banana, explore applications of DArTs for ordering BAC libraries and for anchoring the genetic and physical maps. (Texte intégral)
- Published
- 2006
34. Diversity arrays technology (DArT) : An efficient plateform for whole-genome profiling of crops
- Author
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Wongtiem, Prapit, Perera, Chandrika, Risterucci, Ange-Marie, Xia, Ling, Patarapuwadol, Sujin, Carlig, Jason, Caig, Vanessa, Evers, Margaret, Uszynski, Grzegorz, Wenzl, Peter, Huttner, Eric, Fregene, Martin, De Vicente, M. Carmen, Glaszmann, Jean-Christophe, and Kilian, Andrzej
- Subjects
Génome ,Manihot esculenta ,Oryza ,Musa ,F30 - Génétique et amélioration des plantes ,Variation génétique ,Carte génétique ,U30 - Méthodes de recherche ,Technique analytique ,Sorghum ,Cocos nucifera - Published
- 2006
35. Ribozyme genes protecting transgenic melon plants against potyviruses
- Author
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Huttner, Eric, Tucker, William, Agnè, Vermeulen, s, Fré, dé, Ignart, ric, Sawyer, Brett, and Birch, Robert
- Subjects
medicine.medical_specialty ,Transgene ,Genetically modified crops ,Plant disease resistance ,Genes, Reporter ,Molecular genetics ,Plant virus ,Gene expression ,medicine ,RNA, Catalytic ,Gene ,Genetics ,biology ,business.industry ,fungi ,Ribozyme ,food and beverages ,Agriculture ,General Medicine ,Potyviridae ,Plants, Genetically Modified ,Ribozyme Genes Protecting Transgenic Melon Plants Against Potyviruses ,Biotechnology ,Cucurbitaceae ,biology.protein ,business ,Genetic Engineering - Abstract
Potyviruses are the most important viral pathogens of crops worldwide. Under a contract with Gene Shears Pty Limited, we are using ribozyme genes to protect melon plants against two potyviruses: WMV2 and ZYMV. Different polyribozyme genes were designed, built and introduced into melons plants. Transgenic melon plants containing a resistance gene were obtained and their progeny was challenged by the appropriate virus. Most of the genes tested conferred some degree of resistance to the viruses in glasshouse trials. Melon plants from one family containing one gene directed against WMV2 were also field-trialed on small plots under natural infection pressure and were found immune to WMV2. Field trial is in progress for plants containing genes against ZYMV. Some of the ribozyme genes used in the plants were also assayed in a transient expression system in tobacco cells. This enabled us to study the sequence discrimination capacity of the ribozyme in the case of one ribozyme target site. We found that a mutated target GUG (non cleavable) was less susceptible to inhibition by the ribozyme gene than the corresponding wild type target GUA (cleavable). Work is now in progress to incorporate multiple resistance genes in melon plants, in constructs designed in compliance with the evolving European regulations concerning transgenic plants. The use of ribozyme genes to protect plants against viruses provides an alternative to the technologies currently used for protecting crops against viruses, based on the concept of Pathogen Derived Resistance (see for example 14). In the light of concerns expressed by some plant virologists (13) about the use of viral genes in transgenic plants, it may be that ribozyme genes will find many uses in this area of agricultural biotechnology.
- Published
- 2001
36. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas
- Author
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Hippolyte, Isabelle, Bakry, Frédéric, Seguin, Marc, Gardes, Laëtitia, Rivallan, Ronan, Risterucci, Ange-Marie, Jenny, Christophe, Perrier, Xavier, Carreel, Françoise, Argout, Xavier, Piffanelli, Pietro, Khan, Imtiaz A., Miller, Roberto Neil Gerard, Pappas Junior, Georgios, Mbéguié-A-Mbéguié, Didier, Matsumoto, Takashi, De Bernardinis, Véronique, Huttner, Eric, Kilian, Andrzej, Baurens, Franc-Christophe, D'Hont, Angélique, Côte, François-Xavier, Courtois, Brigitte, Glaszmann, Jean-Christophe, Hippolyte, Isabelle, Bakry, Frédéric, Seguin, Marc, Gardes, Laëtitia, Rivallan, Ronan, Risterucci, Ange-Marie, Jenny, Christophe, Perrier, Xavier, Carreel, Françoise, Argout, Xavier, Piffanelli, Pietro, Khan, Imtiaz A., Miller, Roberto Neil Gerard, Pappas Junior, Georgios, Mbéguié-A-Mbéguié, Didier, Matsumoto, Takashi, De Bernardinis, Véronique, Huttner, Eric, Kilian, Andrzej, Baurens, Franc-Christophe, D'Hont, Angélique, Côte, François-Xavier, Courtois, Brigitte, and Glaszmann, Jean-Christophe
- Abstract
Background: The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results: An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p < 0.05) from the expected Mendelian ratios. These skewed markers were distributed in different linkage groups for each parent. To solve some complex ordering of the markers on linkage groups, we associated tools such as tree-like graphic representations, recombination frequency statistics and cytogenetical studies to identify structural rearrangements and build parsimonious linkage group order. An illustration of such an approach is given for the P. Lilin parent. Conclusions: We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose tw
- Published
- 2010
37. Development of DArT markers for a linkage map of flue-cured tobacco
- Author
-
Lu, XiuPing, primary, Gui, YiJie, additional, Xiao, BingGuang, additional, Li, YongPing, additional, Tong, ZhiJun, additional, Liu, Yun, additional, Bai, XueFei, additional, Wu, WeiRen, additional, Xia, Ling, additional, Huttner, Eric, additional, Kilian, Adrzej, additional, and Fan, LongJiang, additional
- Published
- 2012
- Full Text
- View/download PDF
38. Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population
- Author
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Sorrells, Mark E., primary, Gustafson, J. Perry, additional, Somers, Daryl, additional, Chao, Shiaoman, additional, Benscher, David, additional, Guedira-Brown, Gina, additional, Huttner, Eric, additional, Kilian, Andrezj, additional, McGuire, Patrick E., additional, Ross, Kathleen, additional, Tanaka, James, additional, Wenzl, Peter, additional, Williams, Keith, additional, and Qualset, Calvin O., additional
- Published
- 2011
- Full Text
- View/download PDF
39. Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane
- Author
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Heller-Uszynska, Katarzyna, primary, Uszynski, Grzegorz, additional, Huttner, Eric, additional, Evers, Margaret, additional, Carlig, Jason, additional, Caig, Vanessa, additional, Aitken, Karen, additional, Jackson, Phillip, additional, Piperidis, George, additional, Cox, Mike, additional, Gilmour, Ross, additional, D’Hont, Angelique, additional, Butterfield, Mike, additional, Glaszmann, Jean-Christophe, additional, and Kilian, Andrzej, additional
- Published
- 2010
- Full Text
- View/download PDF
40. Evaluation and application of a luciferase fusion system for rapidin vivoanalysis of RNAi targets and constructs in plants
- Author
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Birch, Robert G., primary, Shen, Bo, additional, Sawyer, Brett J. B., additional, Huttner, Eric, additional, Tucker, William Q. J., additional, and Betzner, Andreas S., additional
- Published
- 2010
- Full Text
- View/download PDF
41. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas
- Author
-
Hippolyte, Isabelle, primary, Bakry, Frederic, additional, Seguin, Marc, additional, Gardes, Laetitia, additional, Rivallan, Ronan, additional, Risterucci, Ange-Marie, additional, Jenny, Christophe, additional, Perrier, Xavier, additional, Carreel, Françoise, additional, Argout, Xavier, additional, Piffanelli, Pietro, additional, Khan, Imtiaz A, additional, Miller, Robert NG, additional, Pappas, Georgios J, additional, Mbéguié-A-Mbéguié, Didier, additional, Matsumoto, Takashi, additional, De Bernardinis, Veronique, additional, Huttner, Eric, additional, Kilian, Andrzej, additional, Baurens, Franc-Christophe, additional, D'Hont, Angélique, additional, Cote, François, additional, Courtois, Brigitte, additional, and Glaszmann, Jean-Christophe, additional
- Published
- 2010
- Full Text
- View/download PDF
42. DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum
- Author
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Jing, Hai-Chun, primary, Bayon, Carlos, additional, Kanyuka, Kostya, additional, Berry, Simon, additional, Wenzl, Peter, additional, Huttner, Eric, additional, Kilian, Andrzej, additional, and E Hammond-Kosack, Kim, additional
- Published
- 2009
- Full Text
- View/download PDF
43. DArT markers: diversity analyses and mapping in Sorghum bicolor
- Author
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Mace, Emma S, primary, Xia, Ling, additional, Jordan, David R, additional, Halloran, Kirsten, additional, Parh, Dipal K, additional, Huttner, Eric, additional, Wenzl, Peter, additional, and Kilian, Andrzej, additional
- Published
- 2008
- Full Text
- View/download PDF
44. A DArT platform for quantitative bulked segregant analysis
- Author
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Wenzl, Peter, primary, Raman, Harsh, additional, Wang, Junping, additional, Zhou, Meixue, additional, Huttner, Eric, additional, and Kilian, Andrzej, additional
- Published
- 2007
- Full Text
- View/download PDF
45. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits
- Author
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Wenzl, Peter, primary, Li, Haobing, additional, Carling, Jason, additional, Zhou, Meixue, additional, Raman, Harsh, additional, Paul, Edie, additional, Hearnden, Phillippa, additional, Maier, Christina, additional, Xia, Ling, additional, Caig, Vanessa, additional, Ovesná, Jaroslava, additional, Cakir, Mehmet, additional, Poulsen, David, additional, Wang, Junping, additional, Raman, Rosy, additional, Smith, Kevin P, additional, Muehlbauer, Gary J, additional, Chalmers, Ken J, additional, Kleinhofs, Andris, additional, Huttner, Eric, additional, and Kilian, Andrzej, additional
- Published
- 2006
- Full Text
- View/download PDF
46. Diversity Arrays Technology: A Generic Genome Profiling Technology on Open Platforms.
- Author
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Kilian, Andrzej, Wenzl, Peter, Huttner, Eric, Carling, Jason, Xia, Ling, Blois, Hélène, Caig, Vanessa, Heller-Uszynska, Katarzyna, Jaccoud, Damian, Hopper, Colleen, Aschenbrenner-Kilian, Malgorzata, Evers, Margaret, Peng, Kaiman, Cayla, Cyril, Hok, Puthick, and Uszynski, Grzegorz
- Published
- 2012
- Full Text
- View/download PDF
47. Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley.
- Author
-
Haobing Li, Kilian, Andrzej, Meixue Zhou, Wenzl, Peter, Huttner, Eric, Mendham, Neville, McIntyre, Lynne, and Vaillancourt, René E.
- Subjects
BARLEY ,MOLECULAR biology ,PLANT genetics ,PLANT populations ,PLANT growth - Abstract
Segregation distortion can negatively impact on gains expected using selection. In order to increase our understanding of genetic factors that may influence the extent and direction of segregation distortion, segregation distortion analyses were conducted in four different doubled haploid (DH) populations. A high-density composite map of barley was then constructed by integrating information from the four populations. The composite map contained 2,111 unique loci, comprising RFLP, SSR and DArT markers and spanned 1,136 cM. In the four populations investigated, the proportion of markers with segregation distortion ranged from 15 to 38%, depending on the population. The highest distortion was observed in populations derived by the microspore culture technique. Distorted loci tended to be clustered, which allowed definition of segregation distortion regions (SDRs). A total of 14 SDRs were identified in the 4 populations. Using the high-density composite map, several SDRs were shown to have consistent map locations in two or more populations; one SDR on chromosome 1H was present in all four populations. The analysis of haplotypes underlying seven SDRs indicated that in three cases the under-represented haplotypes were common across populations, but for four SDRs the under-represented haplotypes varied across populations. Six of the seven centromeric regions harboured SDRs suggesting that genetic processes related to position near a centromere caused the segregation distortion in these SDRs. Other SDRs were most likely due to the methods used to produce the DH populations. The association of the SDRs identified in this study and some of the genes involved in the process of haploid production described in other studies were compared. The composite map constructed in this study provides an additional resource for the barley community via increased genome coverage and the provision of additional marker options. It has also enabled further insights into mechanisms that underpin segregation distortion. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
48. Evaluation and application of a luciferase fusion system for rapid in vivo analysis of RNAi targets and constructs in plants.
- Author
-
Birch, Robert G., Shen, Bo, Sawyer, Brett J. B., Huttner, Eric, Tucker, William Q. J., and Betzner, Andreas S.
- Subjects
RNA viruses ,NUCLEIC acids ,MICROBIAL mutation ,GENE expression ,TRANSGENIC organisms - Abstract
The practical use of RNA-mediated approaches including antisense RNA, ribozymes and siRNAs for specific inhibition of gene expression is limited by lack of simple quantitative methods to rapidly test efficacy in vivo. There have been indications that cotransfer of target::reporter gene fusions with constructs designed against the target sequence, followed by quantification of transient reporter gene activity might be effective. Here, we report detailed testing of the approach in plants, using diverse target::luciferase fusions and antisense or ribozyme constructs. We used quantitative transient luciferase activity (Luc) assays to test antisense constructs against β-glucuronidase, PR glucanase, vacuolar invertase and cucumber mosaic virus, as well as ribozymes against watermelon mosaic virus and tobacco anionic peroxidase. For constructs previously tested in transgenic plants, the results correspond well with those from the transient expression assay. Target susceptibility was generally not strongly influenced by luciferase fusion, and the assay was not highly dependent on target sequence length. Some sequences reduced Luc activity below the level for reliable quantification, but suitable alternative fusions were readily produced. Transcriptional and translation fusions were effective for 5′ target:: luc constructs. Translational fusions were more reliable for luc::target 3′ constructs. With minimal preliminary work to prepare suitable target::luciferase fusions, the approach appears generally applicable for rapid in vivo validation of effectiveness and specificity of constructs designed for RNA-mediated down-regulation of plant genes. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
49. DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum.
- Author
-
Hai-Chun Jing, Bayon, Carlos, Kanyuka, Kostya, Berry, Simon, Wenzl, Peter, Huttner, Eric, Kilian, Andrzej, and Hammond-Kosack, Kim E.
- Subjects
WHEAT genetics ,GENE mapping ,GENOMES ,GENETICS ,GENETIC markers - Abstract
Background: Triticum monococcum (2n = 2x = 14) is an ancient diploid wheat with many useful traits and is used as a model for wheat gene discovery. DArT (Diversity Arrays Technology) employs a hybridisation-based approach to type thousands of genomic loci in parallel. DArT markers were developed for T. monococcum to assess genetic diversity, compare relationships with hexaploid genomes, and construct a genetic linkage map integrating DArT and microsatellite markers. Results: A DArT array, consisting of 2304 hexaploid wheat, 1536 tetraploid wheat, 1536 T. monococcum as well as 1536 T. boeoticum representative genomic clones, was used to fingerprint 16 T. monococcum accessions of diverse geographical origins. In total, 846 polymorphic DArT markers were identified, of which 317 were of T. monococcum origin, 246 of hexaploid, 157 of tetraploid, and 126 of T. boeoticum genomes. The fingerprinting data indicated that the geographic origin of T. monococcum accessions was partially correlated with their genetic variation. DArT markers could also well distinguish the genetic differences amongst a panel of 23 hexaploid wheat and nine T. monococcum genomes. For the first time, 274 DArT markers were integrated with 82 simple sequence repeat (SSR) and two morphological trait loci in a genetic map spanning 1062.72 cM in T. monococcum. Six chromosomes were represented by single linkage groups, and chromosome 4A
m was formed by three linkage groups. The DArT and SSR genetic loci tended to form independent clusters along the chromosomes. Segregation distortion was observed for one third of the DArT loci. The Ba (black awn) locus was refined to a 23.2 cM region between the DArT marker locus wPt-2584 and the microsatellite locus Xgwmd33 on 1Am ; and the Hl (hairy leaf) locus to a 4.0 cM region between DArT loci 376589 and 469591 on 5Am . Conclusion: DArT is a rapid and efficient approach to develop many new molecular markers for genetic studies in T. monococcum. The constructed genetic linkage map will facilitate localisation and map-based cloning of genes of interest, comparative mapping as well as genome organisation and evolution studies between this ancient diploid species and other crops. [ABSTRACT FROM AUTHOR]- Published
- 2009
- Full Text
- View/download PDF
50. Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology.
- Author
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Shiying Yang, Wen Pang, Ash, Gavin, Harper, John, Carling, Jason, Wenzl, Peter, Huttner, Eric, Xuxiao Zong, and Kilian, Andrzej
- Subjects
GENETICS ,SPECIES hybridization ,PIGEON pea ,BIODIVERSITY ,BREEDING ,GENETIC polymorphisms - Abstract
Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea ( Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/ HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/ HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
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