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Last update: May 2021

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wheatgenome

Physical Maps

Physical Maps
The IWGSC has coordinated and endorsed projects delivering BAC-based physical maps anchored to genetic maps for each of the 21 bread wheat chromosomes (T. aestivum cv Chinese Spring). The physical maps for all chromosomes were completed by the end of 2015.

All physical maps generated by the IWGSC are publicly available to browse and download at the URGI data repository.

1AL

Project Leader: Hikmet Budak, Sabanci University, TR

Publications:

1AS

Project Leader: Beat Keller, University of Zurich, CH

Publication:

  • Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, et al. (2013) A Physical Map of the Short Arm of Wheat Chromosome 1A. PLoS ONE 8(11): e80272. doi:10.1371/journal.pone.0080272

1BL

Project Leader: Catherine Feuillet, INRA, FR

Publication:

  • Philippe, R., Paux, E., Bertin, I., Sourdille, P., Choulet, F., Laugier, C., Simkova, H., Safar, J., Bellec, A., Vautrin, S., Frenkel, Z., Cattonaro, F., Magni, F., Scalabrin, S., Martis, M.M., Mayer, K.F., Korol, A., Berges, H., Dolezel, J., and Feuillet, C., A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol 2013 Jun, 14(6):R64 Pubmed: 23800011

1BS

Project Leader: Abraham Korol, Haifa University, IL

Publication:

  • Raats, D., Frenkel, Z., Krugman, T., Dodek, I., Sela, H., Šimkova, H., magni, F., Cattonaro, F., vautrin, S., Bergès, H., Wicker, T., Keller, B., Leroy, P., Philippe, R., Paux, E., Doložel, J., Feuillet, C., Korol, A., Fahima, T. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biology 2013, 14:R138 doi:10.1186/gb-2013-14-12-r138

1D 4D
6D

Project Leader: Bikram Gill, Kansas State University, US

2A

Project Leader: Kuldeep Singh, Punjab Agricultural University, IN

2D

Project team: Mario Caccamo, The Genome Analysis Centre, UK

3A

Project Leader: Bikram Gill, Kansas State University, US

Publication:

  • Sehgal SK, Li W, Rabinowicz PD, Chan A, Šimková H, Doležel J, Gill BS (2012) Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat. BMC Plant Biology12:64 http://www.biomedcentral.com/1471-2229/12/64/

3B

Project Leader: Etienne Paux, INRA, FR

Publication:

  • Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Bergès H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C (2008). A physical map of the 1-gigabase bread wheat chromosome 3B . Science, 322, 101-104

3DL

Project Leader: Neil McKenzie, John Innes Centre, UK

3DS

Project Leader: Jaroslav Dolezel, Institute of Experimental Botany, CZ

Publication:

  • Holušová, K., J. Vrána, J. Šafář, H. Šimková, B. Balcárková, Z. Frenkel, B. Darrier, E. Paux, F. Cattonaro, H. Berges, T. Letellier, M. Alaux, J. Doležel, and J. Bartoš. 2017. Physical Map of the Short Arm of Bread Wheat Chromosome 3D. Plant Genome 10. doi:10.3835/plantgenome2017.03.0021

4A

Project Leader: Miroslav Valarik, Institute of Experimental Botany, CZ

Publications:

  • Hernandez, P., Martis, M., Dorado, G., Pfeifer, M., Schaaf, S., Jouve, N., Šimková, H., Valárik, M., Doložel, J., Mayer, K.F. Next generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 2012 69(3):377-86. DOI 10.1111/j.1365-313X.2011.04808.x
  • Randhawa, M., Bansai, U., Valárik, M., Klocová, B., Doložel, J., Bariana, H. Molecular mapping of stripe rust resistance gene Yr51 in chromosome 4AL of wheat. Theor Appl Genet. 2014 127(2):317-24. DOI 10.1007/s00122-013-2220-8
  • Tsõmbalova, J., Karafiátová, M., Vrána, J., Kubaláková, M., Peuša, H., Jakobson, I., Järve, M., Valárik, M., Doložel, J., Järve, K. A haplotype specific to North European wheat (Triticum aestivum L.) Genetic Resources and Crop Evolution; March 2016. DOI 10.1007/s10722-016-0389-9
  • Shorinola, O., Balcárková, B., Hyles, J., Tibbits, JFG., Hayden, MJ., Holušova, K., Valárik, M., Distelfeld, A., Torada, A., Barrero, JM., Uauy, C. Haplotype Analysis of the Pre-harvest Sprouting Resistance Locus Phs-A1 Reveals a Causal Role of TaMKK3-A in Global Germplasm. Front Plant Sci. 2017; 8:1555. doi: 10.3389/fpls.2017.01555

5A

Project Leader: Luigi Cattivelli, CREA – Genomics Research Centre, IT

Publication:

  • Delfina Barabaschi, Federica Magni, Andrea Volante, Agata Gadaleta, Hana Šimková, Simone Scalabrin, Maria Lucia Prazzoli, Paolo Bagnaresi, Katia Lacrima, Vania Michelotti, Francesca Desiderio, Luigi Orrù, Valentina Mazzamurro, Agostino Fricano, AnnaMaria Mastrangelo, Paola Tononi, Nicola Vitulo, Irena Jurman, Zeev Frenkel, Federica Cattonaro, Michele Morgante, Antonio Blanco, Jaroslav Doležel, Massimo Delledonne, Antonio M. Stanca, Luigi Cattivelli and Giampiero Valè. Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach. The Plant Genome, 8(1) 2015, doi: 10.3835/plantgenome2015.03.0011

5B

Project Leader: Elena Salina, Institute Cytology and Genetics, RU

Publications:

  • Nesterov M.A., Afonnikov D.A., Sergeeva E.M., Miroshnichenko L.A., Bragina M.K., Bragin A.O., Vasiliev G.V., Salina E.A. Identification of microsatellite loci according to BAC sequencing data and their physical mapping to the bread wheat 5B chromosome. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2015;19(6):707-714. doi: 10.18699/VJ15.08
  • Kiseleva A. A., Shcherban A.B., Leonova I.N., Frenkel Z., Salina E.A. Identification of new heading date determinants in wheat 5B chromosome. BMC Plant Biology 2016, 16 (Suppl 1):8 doi: 10.1186/s12870-015-0688-x .
  • Salina E.A., Nesterov M.A., Frenkel Z., Kiseleva A. A., Timonova E. M., Magni F., Vrána J., Šafář J., Šimková H., Doležel J., Korol A.and Sergeeva E.M. Features of the organization of bread wheat chromosome 5BS based on physical mapping. BMC Genomics 2018 19(Suppl 3):80 doi.org/10.1186/s12864-018-4470-y

5D

Project Leader: Hikmet Budak, Sabanci University, TR

Publication:

  • Akpinar BA, Magni F, Yuce M, Stuart J, Lucas SJ, Šimková H, Šafář J, Vautrin S, Bergès H, Cattonaro F, Doležel J, Budak H., The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements, BMC Genomics 2015, 16:453

6A

Project Leader: Thorsten Schnurbusch, IPK, DE

Publication:

  • Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A. Poursebani, N., Nussbaumer, T., Šimkova, H., Witsenboer, H., van Oeveren, J., Mayer, K.F.X., N. Stein, Schnurbusch, T. Plant Journal 2014 79:334-347. Doi: 10.1111/tpj.12550

6B

Project Leader: Hirokazu Handa, National Institute of Agrobiological Sciences, JP

Publication:

  • A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B. Kobayashi, Fuminori; Wu, Jianzhong; Kanamori, Hiroyuki; Tanaka, Tsuyoshi; Katagiri, Satoshi et al. (2015) BMC genomics vol. 16 (1) p. 595

7A

Project Leader: Rudi Appels, Murdoch University, AU

7B

Project Leader: Simen Sandve, Norwegian University of Life Sciences, NO

Publication:

  • Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome. Tatiana Belova, Lars Grønvold, Ajay Kumar, Shahryar Kianian, Xinyao He, Morten Lillemo, Nathan M. Springer, Sigbjørn Lien, Odd-Arne Olsen, Simen R. Sandve (2014). Theoretical and Applied Genetics 127(9): 2029-2040. Doi 10.1007/s00122-014-2358-z

7DL

Project Leader: Song Weining, Northwest A&F University, CN

7DS

Project Leader: Hana Simkova, Institute of Experimental Botany, CZ

Publication:

  • Staňková, H., Hastie, A.R., Chan, S., Vrána, J., Tulpová, Z., Kubaláková, M., Visendi, P., Hayashi, S., Luo, M., Batley, J., Edwards, D., Doležel, J. and Šimková, H. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnol. J. (2015), doi: 10.1111/pbi.12513

Related projects:

BCS-IWGSC Tags

1A, 1B, 1D, 2A, 3A, 3D, 4A, 4D, 5A, 5BS, 5DS, 6D, 7A, 7B, 7D

Project Leader: John Jacobs, Bayer CropScience, BE

Project description:

To accelerate the process of associating genes with specific BACs and gene isolation /cloning ahead of the full reference sequences becoming available, WGPTM tag sequences were generated for the MTP BACs identified for sequencing on chromosomes for which WGPTM was not used to generate physical maps (13 chromosomes and 2 chromosome arms).

BCS-IWGSC Whole Genome Profiling

2B, 4B, 2D, 5BL, 5DL

Project Leader: John Jacobs, Bayer CropScience, BE

Project description:

To accelerate the delivery of the bread wheat reference genome sequence, Bayer CropScience (BCS) provided funding for the production of physical maps for chromosomes 2B, 4B, 5BL, and 5DL, as well as the completion of the physical map of chromosome 2D.