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3. Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato

Author

Clot, Corentin R., primary, Vexler, Lea, additional, Leyva-Perez, Maria de La O, additional, Bourke, Peter M., additional, Engelen, Christel J.M., additional, Hutten, Ronald C.B., additional, de Belt, José van, additional, Wijnker, Erik, additional, Milbourne, Dan, additional, Visser, Richard G.F., additional, Juranić, Martina, additional, and Eck, Herman J. van, additional

Published
2023
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12. Potato

Author

Milbourne, Dan, Pande, Barnaly, Bryan, Glenn J., and Kole, Chittaranjan, editor

Published
2007
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23. Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

Author

Visser, Richard G. F., Bachem, Christian W. B., de Boer, Jan M., Bryan, Glenn J., Chakrabati, Swarup K., Feingold, Sergio, Gromadka, Robert, van Ham, Roeland C. H. J., Huang, Sanwen, Jacobs, Jeanne M. E., Kuznetsov, Boris, de Melo, Paulo E., Milbourne, Dan, Orjeda, Gisella, Sagredo, Boris, and Tang, Xiaomin

Published
2009
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27. Construction, characterization, and preliminary BAC-end sequencing analysis of a bacterial artificial chromosome library of white clover (Trifolium repens L.)

Author

Febrer, Melanie, Cheung, Foo, Town, Christopher D., Cannon, Steven B., Young, Nevin D., Abberton, Michael T., Jenkins, Glyn, and Milbourne, Dan

Subjects
Clover -- Chemical properties, Clover -- Genetic aspects, Genomic libraries -- Authorship, Genetic markers -- Discovery and exploration, Biological sciences
Abstract

Abstract: White clover (Trifolium repens L.) is a forage legume widely used in combination with grass in pastures because of its ability to fix nitrogen. We have constructed a bacterial [...]

Published
2007

28. Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map

Author

van Os, Hans, Andrzejewski, Sandra, Bakker, Erin, Barrena, Imanol, Bryan, Glenn J., Caromel, Bernard, Ghareeb, Bilal, Isidore, Edwige, de Jong, Walter, van Koert, Paul, Lefebvre, Veronique, Milbourne, Dan, Ritter, Enrique, van der Voort, Jeroen N.A.M. Rouppe, Rousselle-Bourgeois, Francoise, van Vliet, Joke, Waugh, Robbie, Visser, Richard G.F., Bakker, Jaap, and van Eck, Herman J.

Subjects
Chromosome mapping -- Analysis, Genetic recombination -- Research, Potatoes -- Genetic aspects, Biological sciences
Abstract

An ultradense genetic linkage map with > 10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in 'skeleton bin maps,' which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in 'bins.' A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).

Published
2006

30. Toward a marker-dense meiotic map of the potato genome: lessons from linkage group I

Author

Isidore, Edwige, van Os, Hans, Andrzejewski, Sandra, Bakker, Jaap, Barrena, Imanol, Bryan, Glenn J., Caromel, Bernard, van Eck, Herman, Ghareeb, Bilal, de Jong, Walter, van Koert, Paul, Lefebvre, Veronique, Milbourne, Dan, Ritter, Enrique, van der Voort, Jeroen Rouppe, Rousselle-Bourgeois, Francoise, van Vliet, Joke, and Waugh, Robbie

Subjects
Genetics -- Research, Biological sciences
Abstract

Segregation data were obtained for 1260 potato linkage group I-specific AFLP loci from a heterozygous diploid potato population. Analytical tools that identified potential typing errors and/or inconsistencies in the data and that assembled cosegregating markers into bins were applied. Bins contain multiple-marker data sets with an identical segregation pattern, which is defined as the bin signature. The bin signatures were used to construct a skeleton bin map that was based solely on observed recombination events. Markers that did not match any of the bin signatures exactly (and that were excluded from the calculation of the skeleton bin map) were placed on the map by maximum likelihood. The resulting maternal and paternal maps consisted of 95 and 101 bins, respectively. Markers derived from EcoRI/MseI, PstI/Msel, and SacI/ MseI primer combinations showed different genetic distributions. Approximately three-fourths of the markers placed into a bin were considered to fit well on the basis of an estimated residual 'error rate' of 0-3%. However, twice as many PstI-based markers fit badly, suggesting that parental PstI-site methylation patterns had changed in the population. Recombination frequencies were highly variable across the map. Inert, presumably centromeric, regions caused extensive marker clustering while recombination hotspots (or regions identical by descent) resulted in empty bins, despite the level of marker saturation.

Published
2003

32. Genome sequence and analysis of the tuber crop potato

Author

Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Zhang, Bo, Mu, Desheng, Ni, Peixiang, Zhang, Gengyun, Yang, Shuang, Li, Ruiqiang, Wang, Jun, Orjeda, Gisella, Guzman, Frank, Torres, Michael, Lozano, Roberto, Ponce, Olga, Martinez, Diana, De la Cruz, Germán, Chakrabarti, S. K., Patil, Virupaksh U., Skryabin, Konstantin G., Kuznetsov, Boris B., Ravin, Nikolai V., Kolganova, Tatjana V., Beletsky, Alexey V., Mardanov, Andrei V., Di Genova, Alex, Bolser, Daniel M., Martin, David M. A., Li, Guangcun, Yang, Yu, Kuang, Hanhui, Hu, Qun, Xiong, Xingyao, Bishop, Gerard J., Sagredo, Boris, Mejía, Nilo, Zagorski, Wlodzimierz, Gromadka, Robert, Gawor, Jan, Szczesny, Pawel, Huang, Sanwen, Zhang, Zhonghua, Liang, Chunbo, He, Jun, Li, Ying, He, Ying, Xu, Jianfei, Zhang, Youjun, Xie, Binyan, Du, Yongchen, Qu, Dongyu, Bonierbale, Merideth, Ghislain, Marc, del Rosario Herrera, Maria, Giuliano, Giovanni, Pietrella, Marco, Perrotta, Gaetano, Facella, Paolo, O’Brien, Kimberly, Feingold, Sergio E., Barreiro, Leandro E., Massa, Gabriela A., Diambra, Luis, Whitty, Brett R., Vaillancourt, Brieanne, Lin, Haining, Massa, Alicia N., Geoffroy, Michael, Lundback, Steven, DellaPenna, Dean, Buell, Robin C., Sharma, Sanjeev Kumar, Marshall, David F., Waugh, Robbie, Bryan, Glenn J., Destefanis, Marialaura, Nagy, Istvan, Milbourne, Dan, Thomson, Susan J., Fiers, Mark, Jacobs, Jeanne M. E., Nielsen, Kåre L., Sønderkær, Mads, Iovene, Marina, Torres, Giovana A., Jiang, Jiming, Veilleux, Richard E., Bachem, Christian W. B., de Boer, Jan, Borm, Theo, Kloosterman, Bjorn, van Eck, Herman, Datema, Erwin, te Lintel Hekkert, Bas, Goverse, Aska, van Ham, Roeland C. H. J., and Visser, Richard G. F.

Published
2011
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42. Additional file 3: Figure S1. of Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

Author

Foito, Alexandre, Hackett, Christine, Stewart, Derek, Velmurugan, Janaki, Milbourne, Dan, Byrne, Stephen, and Barth, Susanne

Abstract

Principal component analysis (PCA) based on the correlation matrix of 26 polar metabolites of parents and F1 samples of the Lolium mapping population. Red = P_m maternal line; blue = P_f paternal line; black = F1. (PDF 9 kb)

Published
2017
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43. Additional file 4: Figure S2. of Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

Author

Foito, Alexandre, Hackett, Christine, Stewart, Derek, Velmurugan, Janaki, Milbourne, Dan, Byrne, Stephen, and Barth, Susanne

Abstract

Principal component analysis (PCA) based on the correlation matrix of 26 polar metabolites of parents, F1 and F2 samples of the Lolium mapping population. Red = P_m maternal line; blue = P_f paternal line; black = F1; green = F2. (PDF 35 kb)

Published
2017
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44. Additional file 1: Table S1. of Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

Author

Foito, Alexandre, Hackett, Christine, Stewart, Derek, Velmurugan, Janaki, Milbourne, Dan, Byrne, Stephen, and Barth, Susanne

Abstract

Selection of polar metabolites quantified using GC-MS grouped by retention index with listing of selection ions for the integration of peaks and identification based on comparison with the mass spectra of authentic standards derivatised as described in Materials and Methods. Alternatively, compounds were tentatively annotated based on comparison with the metabolomics gold standard ( http://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:amdis ). (DOCX 15Â kb)

Published
2017
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47. Additional file 4 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

Author

Arojju, Sai, Barth, Susanne, Milbourne, Dan, Conaghan, Patrick, Velmurugan, Janaki, Hodkinson, Trevor, and Byrne, Stephen

Abstract

Figure S4. Heatmap of perennial ryegrass LG5 over six full-sib families. A Kruskal-Wallis test was performed on each marker to identify significant regions for heading. Using the perennial ryegrass genome zipper [26, 30] we identified a putative gene order for markers on LG5. These data were used to construct the heatmap for each family. A perennial ryegrass transcriptome-based genetic linkage map upon which GenomeZipper was based was used as reference to construct LG5 [26, 27] and placed above the heatmap. Each bar in the heatmap represents region between two genetic markers from the linkage map. The median Kruskal-Wallis test statistic was calculated for markers binned between markers on the genetic linkage map and used to construct the heatmap. Color of the heatmap illustrates the test-statistic of the Kruskal-wallis analysis. (PDF 32 kb)

Published
2016
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48. Additional file 9 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

Author

Arojju, Sai, Barth, Susanne, Milbourne, Dan, Conaghan, Patrick, Velmurugan, Janaki, Hodkinson, Trevor, and Byrne, Stephen

Abstract

Figure S9. Phylogenetic tree of candidate heading gene SOC1. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [67]. The tree is mid-point rooted, drawn to scale, with branch lengths proportional to the number of substitutions per site. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA 6.06 [66]. All the associated Lolium and Arabidopsis proteins were highlighted. (PDF 42 kb)

Published
2016
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49. Additional file 11 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

Author

Arojju, Sai, Barth, Susanne, Milbourne, Dan, Conaghan, Patrick, Velmurugan, Janaki, Hodkinson, Trevor, and Byrne, Stephen

Abstract

Figure S11. Phylogenetic tree of candidate heading gene GI. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [67]. The tree is mid-point rooted, drawn to scale, with branch lengths proportional to the number of substitutions per site. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA 6.06 [66]. Associated Lolium and Arabidopsis proteins were highlighted. (PDF 37 kb)

Published
2016
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50. Additional file 8 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

Author

Arojju, Sai, Barth, Susanne, Milbourne, Dan, Conaghan, Patrick, Velmurugan, Janaki, Hodkinson, Trevor, and Byrne, Stephen

Abstract

Figure S8. Phylogenetic tree of candidate heading gene PRR37. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [67]. The tree is mid-point rooted, drawn to scale, with branch lengths proportional to the number of substitutions per site. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA 6.06 [66]. All the associated Lolium and rice proteins were highlighted. (PDF 38 kb)

Published
2016
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