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Shifting the Limits in Wheat Research and Breeding Using a Fully Annotated Reference Genome

International Wheat Genome Sequencing Consortium (IWGSC)IWGSC RefSeq principal investigators:Rudi Appels  1   2 Kellye Eversole  3   4 Catherine Feuillet  5 Beat Keller  6 Jane Rogers  7 Nils Stein  8   9 IWGSC whole-genome assembly principal investigators:Curtis J Pozniak  10 Nils Stein  8   9 Frédéric Choulet  11 Assaf Distelfeld  12 Kellye Eversole  3   4 Jesse Poland  13 Jane Rogers  7 Gil Ronen  14 Andrew G Sharpe  15 Whole-genome sequencing and assembly:Curtis Pozniak  10 Gil Ronen  14 Nils Stein  8   9 Omer Barad  14 Kobi Baruch  14 Frédéric Choulet  11 Gabriel Keeble-Gagnère  16 Martin Mascher  17   18 Andrew G Sharpe  15 Gil Ben-Zvi  14 Ambre-Aurore Josselin  11 Hi-C data-based scaffolding:Nils Stein  8   9 Martin Mascher  17   18 Axel Himmelbach  17 Whole-genome assembly quality control and analyses:Frédéric Choulet  11 Gabriel Keeble-Gagnère  16 Martin Mascher  17   18 Jane Rogers  7 François Balfourier  11 Juan Gutierrez-Gonzalez  19 Matthew Hayden  16 Ambre-Aurore Josselin  11 ChuShin Koh  15 Gary Muehlbauer  19 Raj K Pasam  16 Etienne Paux  11 Curtis J Pozniak  10 Philippe Rigault  20 Andrew G Sharpe  15 Josquin Tibbits  16 Vijay Tiwari  21 Pseudomolecule assembly:Frédéric Choulet  11 Gabriel Keeble-Gagnère  16 Martin Mascher  17   18 Ambre-Aurore Josselin  11 Jane Rogers  7 RefSeq genome structure and gene analyses:Manuel Spannagl  22 Frédéric Choulet  11 Daniel Lang  22 Heidrun Gundlach  22 Georg Haberer  22 Gabriel Keeble-Gagnère  16 Klaus F X Mayer  22   23 Danara Ormanbekova  22   24 Etienne Paux  11 Verena Prade  22 Hana Šimková  25 Thomas Wicker  6 Automated annotation:Frédéric Choulet  11 Manuel Spannagl  22 David Swarbreck  26 Hélène Rimbert  11 Marius Felder  22 Nicolas Guilhot  11 Heidrun Gundlach  22 Georg Haberer  22 Gemy Kaithakottil  26 Jens Keilwagen  27 Daniel Lang  22 Philippe Leroy  11 Thomas Lux  22 Klaus F X Mayer  22   23 Sven Twardziok  22 Luca Venturini  26 Manual gene curation:Rudi Appels  1   2 Hélène Rimbert  11 Frédéric Choulet  11 Angéla Juhász  2   28 Gabriel Keeble-Gagnère  16 Subgenome comparative analyses:Frédéric Choulet  11 Manuel Spannagl  22 Daniel Lang  22 Michael Abrouk  25   29 Georg Haberer  22 Gabriel Keeble-Gagnère  16 Klaus F X Mayer  22   23 Thomas Wicker  6 Transposable elements:Frédéric Choulet  11 Thomas Wicker  6 Heidrun Gundlach  22 Daniel Lang  22 Manuel Spannagl  22 Phylogenomic analyses:Daniel Lang  22 Manuel Spannagl  22 Rudi Appels  1   2 Iris Fischer  22 Transcriptome analyses and RNA-seq data:Cristobal Uauy  30 Philippa Borrill  30 Ricardo H Ramirez-Gonzalez  30 Rudi Appels  1   2 Dominique Arnaud  31 Smahane Chalabi  31 Boulos Chalhoub  32   31 Frédéric Choulet  11 Aron Cory  10 Raju Datla  33 Mark W Davey  34 Matthew Hayden  16 John Jacobs  34 Daniel Lang  22 Stephen J Robinson  35 Manuel Spannagl  22 Burkhard Steuernagel  30 Josquin Tibbits  16 Vijay Tiwari  21 Fred van Ex  34 Brande B H Wulff  30 Whole-genome methylome:Curtis J Pozniak  10 Stephen J Robinson  35 Andrew G Sharpe  15 Aron Cory  10 Histone mark analyses:Moussa Benhamed  36 Etienne Paux  11 Abdelhafid Bendahmane  36 Lorenzo Concia  36 David Latrasse  36 BAC chromosome MTP IWGSC–Bayer Whole-Genome Profiling (WGP) tags:Jane Rogers  7 John Jacobs  34 Michael Alaux  37 Rudi Appels  1   2 Jan Bartoš  25 Arnaud Bellec  38 Hélène Berges  38 Jaroslav Doležel  25 Catherine Feuillet  5 Zeev Frenkel  39 Bikram Gill  13 Abraham Korol  39 Thomas Letellier  37 Odd-Arne Olsen  40 Hana Šimková  25 Kuldeep Singh  41 Miroslav Valárik  25 Edwin van der Vossen  42 Sonia Vautrin  38 Song Weining  43 Chromosome LTC mapping and physical mapping quality control:Abraham Korol  39 Zeev Frenkel  39 Tzion Fahima  39 Vladimir Glikson  44 Dina Raats  26 Jane Rogers  7 RH mapping:Vijay Tiwari  21 Bikram Gill  13 Etienne Paux  11 Jesse Poland  13 Optical mapping:Jaroslav Doležel  25 Jarmila Číhalíková  25 Hana Šimková  25 Helena Toegelová  25 Jan Vrána  25 Recombination analyses:Pierre SourdilleBenoit Darrier  11 Gene family analyses:Rudi Appels  1   2 Manuel Spannagl  22 Daniel Lang  22 Iris Fischer  22 Danara Ormanbekova  22   24 Verena Prade  22 CBF gene family:Delfina Barabaschi  45 Luigi Cattivelli  45 Dehydrin gene family:Pilar Hernandez  46 Sergio Galvez  47 Hikmet Budak  48 NLR gene family:Burkhard Steuernagel  30 Jonathan D G Jones  49 Kamil Witek  49 Brande B H Wulff  30 Guotai Yu  30 PPR gene family:Ian Small  50 Joanna Melonek  50 Ruonan Zhou  17 Prolamin gene family:Angéla Juhász  2   28 Tatiana Belova  40 Rudi Appels  1   2 Odd-Arne Olsen  40 WAK gene family:Kostya Kanyuka  51 Robert King  52 Stem solidness (SSt1) QTL team:Kirby Nilsen  10 Sean Walkowiak  10 Curtis J Pozniak  10 Richard Cuthbert  53 Raju Datla  33 Ron Knox  53 Krysta Wiebe  10 Daoquan Xiang  33 Flowering locus C (FLC) gene team:Antje Rohde  54 Timothy Golds  34 Genome size analysis:Jaroslav Doležel  25 Jana Čížková  25 Josquin Tibbits  16 MicroRNA and tRNA annotation:Hikmet Budak  48 Bala Ani Akpinar  48 Sezgi Biyiklioglu  48 Genetic maps and mapping:Gary Muehlbauer  19 Jesse Poland  13 Liangliang Gao  13 Juan Gutierrez-Gonzalez  19 Amidou N'Daiye  10 BAC libraries and chromosome sorting:Jaroslav Doležel  25 Hana Šimková  25 Jarmila Číhalíková  25 Marie Kubaláková  25 Jan Šafář  25 Jan Vrána  25 BAC pooling, BAC library repository, and access:Hélène Berges  38 Arnaud Bellec  38 Sonia Vautrin  38 IWGSC sequence and data repository and access:Michael Alaux  37 Françoise Alfama  37 Anne-Françoise Adam-Blondon  37 Raphael Flores  37 Claire Guerche  37 Thomas Letellier  37 Mikaël Loaec  37 Hadi Quesneville  37 Physical maps and BAC-based sequences:1A BAC sequencing and assembly:Curtis J Pozniak  10 Andrew G Sharpe  33   15 Sean WalkowiakHikmet Budak  48 Janet Condie  33 Jennifer Ens  10 ChuShin Koh  15 Ron Maclachlan  10 Yifang Tan  33 Thomas Wicker  6 1B BAC sequencing and assembly:Frédéric Choulet  11 Etienne Paux  11 Adriana Alberti  55 Jean-Marc Aury  55 François Balfourier  11 Valérie Barbe  55 Arnaud Couloux  55 Corinne Cruaud  55 Karine Labadie  55 Sophie Mangenot  55 Patrick Wincker  55   56   57 1D, 4D, and 6D physical mapping:Bikram Gill  13 Gaganpreet Kaur  13 Mingcheng Luo  58 Sunish Sehgal  59 2AL physical mapping:Kuldeep Singh  41 Parveen Chhuneja  41 Om Prakash Gupta  41 Suruchi Jindal  41 Parampreet Kaur  41 Palvi Malik  41 Priti Sharma  41 Bharat Yadav  41 2AS physical mapping:Nagendra K Singh  60 JitendraP Khurana  61 Chanderkant Chaudhary  61 Paramjit Khurana  61 Vinod Kumar  60 Ajay Mahato  60 Saloni Mathur  61 Amitha Sevanthi  60 Naveen Sharma  61 Ram Sewak Tomar  60 2B, 2D, 4B, 5BL, and 5DL IWGSC–Bayer Whole-Genome Profiling (WGP) physical maps:Jane Rogers  7 John Jacobs  34 Michael Alaux  37 Arnaud Bellec  38 Hélène Berges  38 Jaroslav Doležel  25 Catherine Feuillet  5 Zeev Frenkel  39 Bikram Gill  13 Abraham Korol  39 Edwin van der Vossen  42 Sonia Vautrin  38 3AL physical mapping:Bikram Gill  13 Gaganpreet Kaur  13 Mingcheng Luo  58 Sunish Sehgal  59 3DS physical mapping and BAC sequencing and assembly:Jan Bartoš  25 Kateřina Holušová  25 Ondřej Plíhal  62 3DL BAC sequencing and assembly:Matthew D Clark  26   63 Darren Heavens  26 George Kettleborough  26 Jon Wright  26 4A physical mapping, BAC sequencing, assembly, and annotation:Miroslav Valárik  25 Michael Abrouk  25   29 Barbora Balcárková  25 Kateřina Holušová  25 Yuqin Hu  58 Mingcheng Luo  58 5BS BAC sequencing and assembly:Elena Salina  64 Nikolai Ravin  65   66 Konstantin Skryabin  65   66 Alexey Beletsky  65 Vitaly Kadnikov  65 Andrey Mardanov  65 Michail Nesterov  64 Andrey Rakitin  65 Ekaterina Sergeeva  64 6B BAC sequencing and assembly:Hirokazu Handa  67 Hiroyuki Kanamori  67 Satoshi Katagiri  67 Fuminori Kobayashi  67 Shuhei Nasuda  68 Tsuyoshi Tanaka  67 Jianzhong Wu  67 7A physical mapping and BAC sequencing:Rudi Appels  1   2 Matthew Hayden  16 Gabriel Keeble-Gagnère  16 Philippe Rigault  20 Josquin Tibbits  16 7B physical mapping, BAC sequencing, and assembly:Odd-Arne Olsen  40 Tatiana Belova  40 Federica Cattonaro  69 Min Jiumeng  70 Karl Kugler  22 Klaus F X Mayer  22   23 Matthias Pfeifer  22 Simen Sandve  71 Xu Xun  72 Bujie Zhan  40 7DS BAC sequencing and assembly:Hana Šimková  25 Michael Abrouk  25   29 Jacqueline Batley  73 Philipp E Bayer  73 David Edwards  73 Satomi Hayashi  74 Helena Toegelová  25 Zuzana Tulpová  25 Paul Visendi  75 7DL physical mapping and BAC sequencing:Song Weining  43 Licao Cui  43 Xianghong Du  43 Kewei Feng  43 Xiaojun Nie  43 Wei Tong  43 Le Wang  43 Figures:Philippa Borrill  30 Heidrun Gundlach  22 Sergio Galvez  47 Gemy Kaithakottil  26 Daniel Lang  22 Thomas Lux  22 Martin Mascher  17   18 Danara Ormanbekova  22   24 Verena Prade  22 Ricardo H Ramirez-Gonzalez  30 Manuel Spannagl  22 Nils Stein  8   9 Cristobal Uauy  30 Luca Venturini  26 Manuscript writing team:Nils Stein  8   9 Rudi Appels  1   2 Kellye Eversole  3   4 Jane Rogers  7 Philippa Borrill  30 Luigi Cattivelli  45 Frédéric Choulet  11 Pilar Hernandez  46 Kostya Kanyuka  51 Daniel Lang  22 Martin Mascher  17   18 Kirby Nilsen  10 Etienne Paux  11 Curtis J Pozniak  10 Ricardo H Ramirez-Gonzalez  30 Hana Šimková  25 Ian Small  50 Manuel Spannagl  22 David Swarbreck  26 Cristobal Uauy  30
Affiliations

Shifting the Limits in Wheat Research and Breeding Using a Fully Annotated Reference Genome

International Wheat Genome Sequencing Consortium (IWGSC) et al. Science.

Abstract

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Comment in

  • Chinese Spring fervour.
    Surridge C. Surridge C. Nat Plants. 2018 Sep;4(9):628. doi: 10.1038/s41477-018-0262-2. Nat Plants. 2018. PMID: 30150617 No abstract available.

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