Genome interplay in the grain transcriptome of hexaploid bread wheat
Matthias Pfeifer
(1)
,
Karl G. Kugler
(1)
,
Simen R. Sandve
(2)
,
Bujie Zhan
(2)
,
Heidi Rudi
(2)
,
Torgeir R. Hvidsten
(3)
,
Klaus F. X. Mayer
(1)
,
Jane Rogers
(4)
,
Jaroslav Doležel
(5)
,
Curtis Pozniak
(6)
,
Kellye Eversole
(4)
,
Catherine Feuillet
(7)
,
Bikram B. Gill
(8)
,
Bernd Friebe
(8)
,
Adam J. Lukaszewski
(9)
,
Pierre Sourdille
(10)
,
Takashi R. Endo
(11)
,
Marie Kubaláková
(12)
,
Jarmila Číhalíková
,
Zdeňka Dubská
,
Jan Vrána
(13)
,
Romana Šperková
,
Hana Šimková
,
Melanie Febrer
,
Leah Clissold
,
Kirsten Mclay
,
Kuldeep Singh
(14)
,
Parveen Chhuneja
,
Nagendra K Singh
(15)
,
Jitendra Khurana
,
Eduard Akhunov
(16)
,
Frédéric Choulet
(10)
,
Adriana A. Alberti
(17)
,
Valérie Barbe
(18)
,
Patrick Wincker
(17)
,
Hiroyuki Kanamori
(19)
,
Fuminori Kobayashi
(19)
,
Takeshi Itoh
(20)
,
Takashi Matsumoto
(21)
,
Hiroaki Sakai
(20)
,
Tsuyoshi Tanaka
(22)
,
Jianzhong Wu
(19)
,
Yasunari Ogihara
,
Hirokazu Handa
(19)
,
P Ron Maclachlan
,
Andrew Sharpe
(23)
,
Darrin Klassen
,
David Edwards
(24)
,
Jacqueline Batley
(24)
,
Odd-Arne Olsen
(25)
,
Sigbjørn Lien
(26)
,
Burkhard Steuernagel
(27)
,
Brande Wulff
,
Mario Caccamo
(28)
,
Sarah Ayling
(28)
,
Ricardo H Ramirez-Gonzalez
(29)
,
Bernardo J Clavijo
,
Jonathan Wright
(30)
,
Manuel Spannagl
(31)
,
Mihaela M Martis
(32)
,
Martin Mascher
(33)
,
Jarrod Chapman
(34)
,
Jesse A Poland
,
Uwe Scholz
(33)
,
Kerrie Barry
(35)
,
Robbie Waugh
(36)
,
Daniel S Rokhsar
(35)
,
Gary J Muehlbauer
,
Nils Stein
(33)
,
Heidrun H. Gundlach
(37)
,
Matthias Zytnicki
(38)
,
Véronique Jamilloux
(39)
,
Hadi Quesneville
(39)
,
Thomas Wicker
(40)
,
Primetta Faccioli
,
Moreno Colaiacovo
,
Antonio Michele Stanca
,
Hikmet Budak
(41)
,
Luigi Cattivelli
(42)
,
Natasha Glover
(10)
,
Lise Pingault
,
Etienne Paux
(10)
,
Sapna Sharma
(43)
,
Rudi Appels
(44)
,
Matthew Bellgard
(45)
,
Brett Chapman
,
Thomas Nussbaumer
(46)
,
Kai Christian Bader
(47)
,
Hélène Rimbert
(10)
,
Shichen Wang
(48)
,
Ron Knox
,
Andrzej Kilian
(49)
,
Michael M. Alaux
(39)
,
Françoise Alfama
(39)
,
Loïc Couderc
(39)
,
Nicolas N. Guilhot
(10)
,
Claire Viseux
,
Mikael Loaec
(39)
,
Beat Keller
(40)
,
Sébastien Praud
(50)
1
PGSB -
Plant Genome and Systems Biology
2 Centre for Integrative Genetics
3 Department of Chemistry, Biotechnology and Food Science
4 Eversole Associates
5 Centre of Plant Structural and Functional Genomics
6 U of S - University of Saskatchewan [Saskatoon]
7 Bayer Crop Science
8 Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA
9 Department of Botany and Plant Sciences [Riverside]
10 GDEC - Génétique Diversité et Ecophysiologie des Céréales
11 Graduate School of Agriculture, Kyoto University, Kyoto, Japan
12 CRH - Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký]
13 Centre of the Region Haná for Biotechnological and Agricultural Research
14 Fraunhofer IAIS - Fraunhofer Institute for Intelligent Analysis and Information Systems
15 National Research Centre Plant Biotechnology
16 Dept Plant Pathol
17 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
18 *
19 ICS CAAS - Institute of Crop Sciences of CAAS [Beijing]
20 NIAS - National Institute of Agrobiological Sciences
21 Natl Inst Agrobiol Sci
22 JST-CREST
23 Global Institute of Food Security
24 School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics
25 NMBU - Norwegian University of Life Sciences
26 Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences
27 TSL - The Sainsbury Laboratory [Norwich]
28 Genome Analysis Centre
29 John Innes Centre [Norwich]
30 ESRF - European Synchrotron Radiation Facility
31 German Research Center for Environmental Health - Helmholtz Center München (GmbH)
32 MIPS/IBIS
33 IPK-Gatersleben - Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
34 DOE Joint Genome Institute [Walnut Creek]
35 United States Department of Energy
36 The James Hutton Institute
37 Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences
38 MIAT INRA - Unité de Mathématiques et Informatique Appliquées de Toulouse
39 URGI - Unité de Recherche Génomique Info
40 Institute of Plant Biology [UZH, Zürich]
41 Fac Engn & Nat Sci
42 Genomics Research Centre
43 York University
44 Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources
45 Centre for Comparative Genomics
46 CUBE Division of Computational Systems Biology
47 Plant Genome and Systems Biology
48 Department of Plant Pathology
49 DArT P/L - Diversity Arrays Technology Pty Ltd
50 Centre de Recherche de Chappes
2 Centre for Integrative Genetics
3 Department of Chemistry, Biotechnology and Food Science
4 Eversole Associates
5 Centre of Plant Structural and Functional Genomics
6 U of S - University of Saskatchewan [Saskatoon]
7 Bayer Crop Science
8 Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA
9 Department of Botany and Plant Sciences [Riverside]
10 GDEC - Génétique Diversité et Ecophysiologie des Céréales
11 Graduate School of Agriculture, Kyoto University, Kyoto, Japan
12 CRH - Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký]
13 Centre of the Region Haná for Biotechnological and Agricultural Research
14 Fraunhofer IAIS - Fraunhofer Institute for Intelligent Analysis and Information Systems
15 National Research Centre Plant Biotechnology
16 Dept Plant Pathol
17 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
18 *
19 ICS CAAS - Institute of Crop Sciences of CAAS [Beijing]
20 NIAS - National Institute of Agrobiological Sciences
21 Natl Inst Agrobiol Sci
22 JST-CREST
23 Global Institute of Food Security
24 School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics
25 NMBU - Norwegian University of Life Sciences
26 Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences
27 TSL - The Sainsbury Laboratory [Norwich]
28 Genome Analysis Centre
29 John Innes Centre [Norwich]
30 ESRF - European Synchrotron Radiation Facility
31 German Research Center for Environmental Health - Helmholtz Center München (GmbH)
32 MIPS/IBIS
33 IPK-Gatersleben - Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
34 DOE Joint Genome Institute [Walnut Creek]
35 United States Department of Energy
36 The James Hutton Institute
37 Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences
38 MIAT INRA - Unité de Mathématiques et Informatique Appliquées de Toulouse
39 URGI - Unité de Recherche Génomique Info
40 Institute of Plant Biology [UZH, Zürich]
41 Fac Engn & Nat Sci
42 Genomics Research Centre
43 York University
44 Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources
45 Centre for Comparative Genomics
46 CUBE Division of Computational Systems Biology
47 Plant Genome and Systems Biology
48 Department of Plant Pathology
49 DArT P/L - Diversity Arrays Technology Pty Ltd
50 Centre de Recherche de Chappes
Catherine Feuillet
- Fonction : Auteur
- PersonId : 1202762
- ORCID : 0000-0003-2991-4001
Pierre Sourdille
- Fonction : Auteur
- PersonId : 749552
- IdHAL : pierre-sourdille
- ORCID : 0000-0002-1027-2224
- IdRef : 139291075
Jarmila Číhalíková
- Fonction : Auteur
Zdeňka Dubská
- Fonction : Auteur
Romana Šperková
- Fonction : Auteur
Hana Šimková
- Fonction : Auteur
Melanie Febrer
- Fonction : Auteur
Leah Clissold
- Fonction : Auteur
Kirsten Mclay
- Fonction : Auteur
Parveen Chhuneja
- Fonction : Auteur
Jitendra Khurana
- Fonction : Auteur
Frédéric Choulet
- Fonction : Auteur
- PersonId : 746269
- IdHAL : frederic-choulet
- ORCID : 0000-0003-1788-7288
- IdRef : 111370639
Adriana A. Alberti
- Fonction : Auteur
- PersonId : 183113
- IdHAL : adriana-alberti
- ORCID : 0000-0003-3372-9423
Valérie Barbe
- Fonction : Auteur
- PersonId : 1187196
- IdHAL : valerie-barbe
- ORCID : 0000-0002-8162-3343
Patrick Wincker
- Fonction : Auteur
- PersonId : 757160
- IdHAL : patrick-wincker
- ORCID : 0000-0001-7562-3454
Takashi Matsumoto
- Fonction : Auteur
- PersonId : 760057
- ORCID : 0000-0003-0639-9262
Yasunari Ogihara
- Fonction : Auteur
P Ron Maclachlan
- Fonction : Auteur
Darrin Klassen
- Fonction : Auteur
David Edwards
- Fonction : Auteur
- PersonId : 929108
Jacqueline Batley
- Fonction : Auteur
- PersonId : 971017
Brande Wulff
- Fonction : Auteur
Bernardo J Clavijo
- Fonction : Auteur
Jonathan Wright
- Fonction : Auteur
- PersonId : 772362
- ORCID : 0000-0002-8217-0884
Martin Mascher
- Fonction : Auteur
- PersonId : 956041
Jesse A Poland
- Fonction : Auteur
Uwe Scholz
- Fonction : Auteur
- PersonId : 956051
Kerrie Barry
- Fonction : Auteur
- PersonId : 776761
- ORCID : 0000-0002-8999-6785
Gary J Muehlbauer
- Fonction : Auteur
Nils Stein
- Fonction : Auteur
- PersonId : 956047
Matthias Zytnicki
- Fonction : Auteur
- PersonId : 748132
- IdHAL : matthias-zytnicki
- ORCID : 0000-0002-4895-8731
Véronique Jamilloux
- Fonction : Auteur
- PersonId : 185138
- IdHAL : veronique-jamilloux
- ORCID : 0000-0002-6898-4910
Hadi Quesneville
- Fonction : Auteur
- PersonId : 736048
- IdHAL : hadi-quesneville
- ORCID : 0000-0003-3001-4908
- IdRef : 137542860
Primetta Faccioli
- Fonction : Auteur
Moreno Colaiacovo
- Fonction : Auteur
Antonio Michele Stanca
- Fonction : Auteur
Lise Pingault
- Fonction : Auteur
Etienne Paux
- Fonction : Auteur
- PersonId : 736306
- IdHAL : etienne-paux
- ORCID : 0000-0002-3094-7129
- IdRef : 083625402
Brett Chapman
- Fonction : Auteur
Hélène Rimbert
- Fonction : Auteur
- PersonId : 746285
- IdHAL : helene-rimbert
- ORCID : 0000-0002-2288-6864
Ron Knox
- Fonction : Auteur
Michael M. Alaux
- Fonction : Auteur
- PersonId : 1207096
- IdHAL : michael-alaux
- ORCID : 0000-0001-9356-4072
Claire Viseux
- Fonction : Auteur
Résumé
Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.