Shifting the limits in wheat research and breeding using a fully annotated reference genome-Reference-Cited by-同舟云学术

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Published:2018-08-17 Issue:6403 Volume:361 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

,Appels Rudi¹²,Eversole Kellye³⁴,Stein Nils⁵⁶,Feuillet Catherine⁷,Keller Beat⁸,Rogers Jane⁹,Pozniak Curtis J.¹⁰,Choulet Frédéric¹¹,Distelfeld Assaf¹²,Poland Jesse¹³,Ronen Gil¹⁴,Sharpe Andrew G.¹⁵,Barad Omer¹⁴,Baruch Kobi¹⁴,Keeble-Gagnère Gabriel¹,Mascher Martin⁵¹⁶,Ben-Zvi Gil¹⁴,Josselin Ambre-Aurore¹¹,Himmelbach Axel⁵,Balfourier François¹¹,Gutierrez-Gonzalez Juan¹⁷,Hayden Matthew¹,Koh ChuShin¹⁵,Muehlbauer Gary¹⁷,Pasam Raj K.¹,Paux Etienne¹¹,Rigault Philippe¹⁸,Tibbits Josquin¹,Tiwari Vijay¹⁹,Spannagl Manuel²⁰,Lang Daniel²⁰,Gundlach Heidrun²⁰,Haberer Georg²⁰,Mayer Klaus F. X.²⁰²¹,Ormanbekova Danara²⁰²²,Prade Verena²⁰,Šimková Hana²³,Wicker Thomas⁸,Swarbreck David²⁴,Rimbert Hélène¹¹,Felder Marius²⁰,Guilhot Nicolas¹¹,Kaithakottil Gemy²⁴,Keilwagen Jens²⁵,Leroy Philippe¹¹,Lux Thomas²⁰,Twardziok Sven²⁰,Venturini Luca²⁴,Juhász Angéla²²⁶,Abrouk Michael²³²⁷,Fischer Iris²⁰,Uauy Cristobal²⁸,Borrill Philippa²⁸,Ramirez-Gonzalez Ricardo H.²⁸,Arnaud Dominique²⁹,Chalabi Smahane²⁹,Chalhoub Boulos³⁰²⁹,Cory Aron¹⁰,Datla Raju³¹,Davey Mark W.³²,Jacobs John³²,Robinson Stephen J.³³,Steuernagel Burkhard²⁸,van Ex Fred³²,Wulff Brande B. H.²⁸,Benhamed Moussa³⁴,Bendahmane Abdelhafid³⁴,Concia Lorenzo³⁴,Latrasse David³⁴,Bartoš Jan²³,Bellec Arnaud³⁵,Berges Hélène³⁵,Doležel Jaroslav²³,Frenkel Zeev³⁶,Gill Bikram¹³,Korol Abraham³⁶,Letellier Thomas³⁷,Olsen Odd-Arne³⁸,Singh Kuldeep³⁹,Valárik Miroslav²³,van der Vossen Edwin⁴⁰,Vautrin Sonia³⁵,Weining Song⁴¹,Fahima Tzion³⁶,Glikson Vladimir⁴²,Raats Dina²⁴,Číhalíková Jarmila²³,Toegelová Helena²³,Vrána Jan²³,Sourdille Pierre¹¹,Darrier Benoit¹¹,Barabaschi Delfina⁴³,Cattivelli Luigi⁴³,Hernandez Pilar⁴⁴,Galvez Sergio⁴⁵,Budak Hikmet⁴⁶,Jones Jonathan D. G.⁴⁷,Witek Kamil⁴⁷,Yu Guotai²⁸,Small Ian⁴⁸,Melonek Joanna⁴⁸,Zhou Ruonan⁵,Belova Tatiana³⁸,Kanyuka Kostya⁴⁹,King Robert⁵⁰,Nilsen Kirby¹⁰,Walkowiak Sean¹⁰,Cuthbert Richard⁵¹,Knox Ron⁵¹,Wiebe Krysta¹⁰,Xiang Daoquan³¹,Rohde Antje⁵²,Golds Timothy³²,Čížková Jana²³,Akpinar Bala Ani⁴⁶,Biyiklioglu Sezgi⁴⁶,Gao Liangliang¹³,N’Daiye Amidou¹⁰,Kubaláková Marie²³,Šafář Jan²³,Alfama Françoise³⁷,Adam-Blondon Anne-Françoise³⁷,Flores Raphael³⁷,Guerche Claire³⁷,Loaec Mikaël³⁷,Quesneville Hadi³⁷,Condie Janet³¹,Ens Jennifer¹⁰,Maclachlan Ron¹⁰,Tan Yifang³¹,Alberti Adriana⁵³,Aury Jean-Marc⁵³,Barbe Valérie⁵³,Couloux Arnaud⁵³,Cruaud Corinne⁵³,Labadie Karine⁵³,Mangenot Sophie⁵³,Wincker Patrick⁵³⁵⁴⁵⁵,Kaur Gaganpreet¹³,Luo Mingcheng⁵⁶,Sehgal Sunish⁵⁷,Chhuneja Parveen³⁹,Gupta Om Prakash³⁹,Jindal Suruchi³⁹,Kaur Parampreet³⁹,Malik Palvi³⁹,Sharma Priti³⁹,Yadav Bharat³⁹,Singh Nagendra K.⁵⁸,Khurana Jitendra P.⁵⁹,Chaudhary Chanderkant⁵⁹,Khurana Paramjit⁵⁹,Kumar Vinod⁵⁸,Mahato Ajay⁵⁸,Mathur Saloni⁵⁹,Sevanthi Amitha⁵⁸,Sharma Naveen⁵⁹,Tomar Ram Sewak⁵⁸,Holušová Kateřina²³,Plíhal Ondřej⁶⁰,Clark Matthew D.²⁴⁶¹,Heavens Darren²⁴,Kettleborough George²⁴,Wright Jon²⁴,Balcárková Barbora²³,Hu Yuqin⁵⁶,Salina Elena⁶²,Ravin Nikolai⁶³⁶⁴,Skryabin Konstantin⁶³⁶⁴,Beletsky Alexey⁶³,Kadnikov Vitaly⁶³,Mardanov Andrey⁶³,Nesterov Michail⁶²,Rakitin Andrey⁶³,Sergeeva Ekaterina⁶²,Handa Hirokazu⁶⁵,Kanamori Hiroyuki⁶⁵,Katagiri Satoshi⁶⁵,Kobayashi Fuminori⁶⁵,Nasuda Shuhei⁶⁶,Tanaka Tsuyoshi⁶⁵,Wu Jianzhong⁶⁵,Cattonaro Federica⁶⁷,Jiumeng Min⁶⁸,Kugler Karl²⁰,Pfeifer Matthias²⁰,Sandve Simen⁶⁹,Xun Xu⁷⁰,Zhan Bujie³⁸,Batley Jacqueline⁷¹,Bayer Philipp E.⁷¹,Edwards David⁷¹,Hayashi Satomi⁷²,Tulpová Zuzana²³,Visendi Paul⁷³,Cui Licao⁴¹,Du Xianghong⁴¹,Feng Kewei⁴¹,Nie Xiaojun⁴¹,Tong Wei⁴¹,Wang Le⁴¹

Affiliation:

1. AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia.

2. Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.

3. International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA.

4. Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA.

5. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.

6. The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia.

7. Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA.

8. Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.

9. International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK.

10. University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.

11. GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France.

12. School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv 69978, Israel.

13. Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA.

14. NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel.

15. University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada.

16. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.

17. Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA.

18. GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada.

19. Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA.

20. Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.

21. School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany.

22. Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy.

23. Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.

24. Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK.

25. Julius Kühn-Institut, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany.

26. Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary.

27. Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.

28. John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK.

29. Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France.

30. Monsanto SAS, 28000 Boissay, France.

31. National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.

32. Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium.

33. Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.

34. Biology Department, Institute of Plant Sciences–Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France.

35. INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France.

36. University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel.

37. URGI, INRA, Université Paris-Saclay, 78026 Versailles, France.

38. Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway.

39. Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR–National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India.

40. Keygene, N.V., Agro Business Park 90, 6708 PW Wageningen, Netherlands.

41. State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China.

42. MultiQTL Ltd., University of Haifa, Haifa 3498838, Israel.

43. Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d’Arda, Italy.

44. Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain.

45. Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain.

46. Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA.

47. The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK.

48. School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.

49. Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK.

50. Rothamsted Research, Computational and Analytical Sciences, West Common, Harpenden AL5 2JQ, UK.

51. Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada.

52. Bayer CropScience, Breeding and Trait Development, Technologiepark 38, 9052 Gent, Belgium.

53. CEA–Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.

54. CNRS, UMR 8030, CP5706, 91057 Evry, France.

55. Université d’Evry, UMR 8030, CP5706, 91057 Evry, France.

56. Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA.

57. Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA.

58. ICAR–National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India.

59. University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India.

60. Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic.

61. Department of Lifesciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.

62. The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia.

63. Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.

64. Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia.

65. Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.

66. Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.

67. Instituto di Genomica Applicata, Via J. Linussio 51, Udine 33100, Italy.

68. BGI-Shenzhen, BGI Genomics, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.

69. Faculty of Bioscience, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway.

70. BGI-Shenzhen, BGI Genomics, Yantian District, Shenzhen 518083, Guangdong, China.

71. School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia.

72. Queensland University of Technology, Earth, Environmental and Biological Sciences, Brisbane, QLD 4001, Australia.

73. University of Greenwich, Natural Resources Institute, Central Avenue, Chatham, Kent ME4 4TB, UK.

Abstract

Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science , this issue p. eaar7191 ; see also p. eaar6089

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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