Genome interplay in the grain transcriptome of hexaploid bread wheat

Matthias Pfeifer; Karl G. Kugler; Simen R. Sandve; Bujie Zhan; Heidi Rudi; Torgeir R. Hvidsten; Klaus F.X. Mayer; Odd Arne Olsen; Jane Rogers; Jaroslav Doležel; Curtis Pozniak; Kellye Eversole; Catherine Feuillet; Bikram Gill; Bernd Friebe; Adam J. Lukaszewski; Pierre Sourdille; Takashi R. Endo; Marie Kubaláková; Jarmila Číhalíková; Zdeňka Dubská; Jan Vrána; Romana Šperková; Hana Šimková; Melanie Febrer; Leah Clissold; Kirsten McLay; Kuldeep Singh; Parveen Chhuneja; Nagendra K. Singh; Jitendra Khurana; Eduard Akhunov; Frédéric Choulet; Adriana Alberti; Valérie Barbe; Patrick Wincker; Hiroyuki Kanamori; Fuminori Kobayashi; Takeshi Itoh; Takashi Matsumoto; Hiroaki Sakai; Tsuyoshi Tanaka; Jianzhong Wu; Yasunari Ogihara; Hirokazu Handa; P. Ron Maclachlan; Andrew Sharpe; Darrin Klassen; David Edwards; Jacqueline Batley; Simen Rød Sandve; Sigbjørn Lien; Burkhard Steuernagel; Brande Wulff; Mario Caccamo; Sarah Ayling; Ricardo H. Ramirez-Gonzalez; Bernardo J. Clavijo; Jonathan Wright; Manuel Spannagl; Mihaela M. Martis; Martin Mascher; Jarrod Chapman; Jesse A. Poland; Uwe Scholz; Kerrie Barry; Robbie Waugh; Daniel S. Rokhsar; Gary J. Muehlbauer; Nils Stein; Heidrun Gundlach; Matthias Zytnicki; Véronique Jamilloux; Hadi Quesneville; Thomas Wicker; Primetta Faccioli; Moreno Colaiacovo; Antonio Michele Stanca; Hikmet Budak; Luigi Cattivelli; Natasha Glover; Lise Pingault; Etienne Paux; Sapna Sharma; Rudi Appels; Matthew Bellgard; Brett Chapman; Thomas Nussbaumer; Kai Christian Bader; Hélène Rimbert; Shichen Wang; Ron Knox; Andrzej Kilian; Michael Alaux; Françoise Alfama; Loïc Couderc; Nicolas Guilhot; Claire Viseux; Mikaël Loaec; Beat Keller; Sebastien Praud

doi:10.1126/science.1250091

Genome interplay in the grain transcriptome of hexaploid bread wheat

Matthias Pfeifer, Karl G. Kugler, Simen R. Sandve, Bujie Zhan, Heidi Rudi, Torgeir R. Hvidsten, Klaus F.X. Mayer, Odd Arne Olsen, Jane Rogers, Jaroslav Doležel, Curtis Pozniak, Kellye Eversole, Catherine Feuillet, Bikram Gill, Bernd Friebe, Adam J. Lukaszewski, Pierre Sourdille, Takashi R. Endo, Marie Kubaláková, Jarmila ČíhalíkováZdeňka Dubská, Jan Vrána, Romana Šperková, Hana Šimková, Melanie Febrer, Leah Clissold, Kirsten McLay, Kuldeep Singh, Parveen Chhuneja, Nagendra K. Singh, Jitendra Khurana, Eduard Akhunov, Frédéric Choulet, Adriana Alberti, Valérie Barbe, Patrick Wincker, Hiroyuki Kanamori, Fuminori Kobayashi, Takeshi Itoh, Takashi Matsumoto, Hiroaki Sakai, Tsuyoshi Tanaka, Jianzhong Wu, Yasunari Ogihara, Hirokazu Handa, P. Ron Maclachlan, Andrew Sharpe, Darrin Klassen, David Edwards, Jacqueline Batley, Simen Rød Sandve, Sigbjørn Lien, Burkhard Steuernagel, Brande Wulff, Mario Caccamo, Sarah Ayling, Ricardo H. Ramirez-Gonzalez, Bernardo J. Clavijo, Jonathan Wright, Manuel Spannagl, Mihaela M. Martis, Martin Mascher, Jarrod Chapman, Jesse A. Poland, Uwe Scholz, Kerrie Barry, Robbie Waugh, Daniel S. Rokhsar, Gary J. Muehlbauer, Nils Stein, Heidrun Gundlach, Matthias Zytnicki, Véronique Jamilloux, Hadi Quesneville, Thomas Wicker, Primetta Faccioli, Moreno Colaiacovo, Antonio Michele Stanca, Hikmet Budak, Luigi Cattivelli, Natasha Glover, Lise Pingault, Etienne Paux, Sapna Sharma, Rudi Appels, Matthew Bellgard, Brett Chapman, Thomas Nussbaumer, Kai Christian Bader, Hélène Rimbert, Shichen Wang, Ron Knox, Andrzej Kilian, Michael Alaux, Françoise Alfama, Loïc Couderc, Nicolas Guilhot, Claire Viseux, Mikaël Loaec, Beat Keller, Sebastien Praud

Research output: Contribution to journal › Article › peer-review

259 Scopus citations

Abstract

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.

Original language	English (US)
Journal	Science
Volume	345
Issue number	6194
DOIs	https://doi.org/10.1126/science.1250091
State	Published - Jan 1 2014
Externally published	Yes

Bibliographical note

Generated from Scopus record by KAUST IRTS on 2022-09-13

Access to Document

10.1126/science.1250091

Cite this

Pfeifer, M., Kugler, K. G., Sandve, S. R., Zhan, B., Rudi, H., Hvidsten, T. R., Mayer, K. F. X., Olsen, O. A., Rogers, J., Doležel, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A. J., Sourdille, P., Endo, T. R., Kubaláková, M., ... Praud, S. (2014). Genome interplay in the grain transcriptome of hexaploid bread wheat. Science, 345(6194). https://doi.org/10.1126/science.1250091

@article{b130f559fefc48c09d76319d692002bb,

title = "Genome interplay in the grain transcriptome of hexaploid bread wheat",

abstract = "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.",

author = "Matthias Pfeifer and Kugler, {Karl G.} and Sandve, {Simen R.} and Bujie Zhan and Heidi Rudi and Hvidsten, {Torgeir R.} and Mayer, {Klaus F.X.} and Olsen, {Odd Arne} and Jane Rogers and Jaroslav Dole{\v z}el and Curtis Pozniak and Kellye Eversole and Catherine Feuillet and Bikram Gill and Bernd Friebe and Lukaszewski, {Adam J.} and Pierre Sourdille and Endo, {Takashi R.} and Marie Kubal{\'a}kov{\'a} and Jarmila {\v C}{\'i}hal{\'i}kov{\'a} and Zde{\v n}ka Dubsk{\'a} and Jan Vr{\'a}na and Romana {\v S}perkov{\'a} and Hana {\v S}imkov{\'a} and Melanie Febrer and Leah Clissold and Kirsten McLay and Kuldeep Singh and Parveen Chhuneja and Singh, {Nagendra K.} and Jitendra Khurana and Eduard Akhunov and Fr{\'e}d{\'e}ric Choulet and Adriana Alberti and Val{\'e}rie Barbe and Patrick Wincker and Hiroyuki Kanamori and Fuminori Kobayashi and Takeshi Itoh and Takashi Matsumoto and Hiroaki Sakai and Tsuyoshi Tanaka and Jianzhong Wu and Yasunari Ogihara and Hirokazu Handa and Maclachlan, {P. Ron} and Andrew Sharpe and Darrin Klassen and David Edwards and Jacqueline Batley and Sandve, {Simen R{\o}d} and Sigbj{\o}rn Lien and Burkhard Steuernagel and Brande Wulff and Mario Caccamo and Sarah Ayling and Ramirez-Gonzalez, {Ricardo H.} and Clavijo, {Bernardo J.} and Jonathan Wright and Manuel Spannagl and Martis, {Mihaela M.} and Martin Mascher and Jarrod Chapman and Poland, {Jesse A.} and Uwe Scholz and Kerrie Barry and Robbie Waugh and Rokhsar, {Daniel S.} and Muehlbauer, {Gary J.} and Nils Stein and Heidrun Gundlach and Matthias Zytnicki and V{\'e}ronique Jamilloux and Hadi Quesneville and Thomas Wicker and Primetta Faccioli and Moreno Colaiacovo and Stanca, {Antonio Michele} and Hikmet Budak and Luigi Cattivelli and Natasha Glover and Lise Pingault and Etienne Paux and Sapna Sharma and Rudi Appels and Matthew Bellgard and Brett Chapman and Thomas Nussbaumer and Bader, {Kai Christian} and H{\'e}l{\`e}ne Rimbert and Shichen Wang and Ron Knox and Andrzej Kilian and Michael Alaux and Fran{\c c}oise Alfama and Lo{\"i}c Couderc and Nicolas Guilhot and Claire Viseux and Mika{\"e}l Loaec and Beat Keller and Sebastien Praud",

note = "Generated from Scopus record by KAUST IRTS on 2022-09-13",

year = "2014",

month = jan,

day = "1",

doi = "10.1126/science.1250091",

language = "English (US)",

volume = "345",

journal = "Science",

issn = "1095-9203",

publisher = "AMER ASSOC ADVANCEMENT SCIENCE",

number = "6194",

}

Pfeifer, M, Kugler, KG, Sandve, SR, Zhan, B, Rudi, H, Hvidsten, TR, Mayer, KFX, Olsen, OA, Rogers, J, Doležel, J, Pozniak, C, Eversole, K, Feuillet, C, Gill, B, Friebe, B, Lukaszewski, AJ, Sourdille, P, Endo, TR, Kubaláková, M, Číhalíková, J, Dubská, Z, Vrána, J, Šperková, R, Šimková, H, Febrer, M, Clissold, L, McLay, K, Singh, K, Chhuneja, P, Singh, NK, Khurana, J, Akhunov, E, Choulet, F, Alberti, A, Barbe, V, Wincker, P, Kanamori, H, Kobayashi, F, Itoh, T, Matsumoto, T, Sakai, H, Tanaka, T, Wu, J, Ogihara, Y, Handa, H, Maclachlan, PR, Sharpe, A, Klassen, D, Edwards, D, Batley, J, Sandve, SR, Lien, S, Steuernagel, B, Wulff, B, Caccamo, M, Ayling, S, Ramirez-Gonzalez, RH, Clavijo, BJ, Wright, J, Spannagl, M, Martis, MM, Mascher, M, Chapman, J, Poland, JA, Scholz, U, Barry, K, Waugh, R, Rokhsar, DS, Muehlbauer, GJ, Stein, N, Gundlach, H, Zytnicki, M, Jamilloux, V, Quesneville, H, Wicker, T, Faccioli, P, Colaiacovo, M, Stanca, AM, Budak, H, Cattivelli, L, Glover, N, Pingault, L, Paux, E, Sharma, S, Appels, R, Bellgard, M, Chapman, B, Nussbaumer, T, Bader, KC, Rimbert, H, Wang, S, Knox, R, Kilian, A, Alaux, M, Alfama, F, Couderc, L, Guilhot, N, Viseux, C, Loaec, M, Keller, B & Praud, S 2014, 'Genome interplay in the grain transcriptome of hexaploid bread wheat', Science, vol. 345, no. 6194. https://doi.org/10.1126/science.1250091

TY - JOUR

T1 - Genome interplay in the grain transcriptome of hexaploid bread wheat

AU - Pfeifer, Matthias

AU - Kugler, Karl G.

AU - Sandve, Simen R.

AU - Zhan, Bujie

AU - Rudi, Heidi

AU - Hvidsten, Torgeir R.

AU - Mayer, Klaus F.X.

AU - Olsen, Odd Arne

AU - Rogers, Jane

AU - Doležel, Jaroslav

AU - Pozniak, Curtis

AU - Eversole, Kellye

AU - Feuillet, Catherine

AU - Gill, Bikram

AU - Friebe, Bernd

AU - Lukaszewski, Adam J.

AU - Sourdille, Pierre

AU - Endo, Takashi R.

AU - Kubaláková, Marie

AU - Číhalíková, Jarmila

AU - Dubská, Zdeňka

AU - Vrána, Jan

AU - Šperková, Romana

AU - Šimková, Hana

AU - Febrer, Melanie

AU - Clissold, Leah

AU - McLay, Kirsten

AU - Singh, Kuldeep

AU - Chhuneja, Parveen

AU - Singh, Nagendra K.

AU - Khurana, Jitendra

AU - Akhunov, Eduard

AU - Choulet, Frédéric

AU - Alberti, Adriana

AU - Barbe, Valérie

AU - Wincker, Patrick

AU - Kanamori, Hiroyuki

AU - Kobayashi, Fuminori

AU - Itoh, Takeshi

AU - Matsumoto, Takashi

AU - Sakai, Hiroaki

AU - Tanaka, Tsuyoshi

AU - Wu, Jianzhong

AU - Ogihara, Yasunari

AU - Handa, Hirokazu

AU - Maclachlan, P. Ron

AU - Sharpe, Andrew

AU - Klassen, Darrin

AU - Edwards, David

AU - Batley, Jacqueline

AU - Sandve, Simen Rød

AU - Lien, Sigbjørn

AU - Steuernagel, Burkhard

AU - Wulff, Brande

AU - Caccamo, Mario

AU - Ayling, Sarah

AU - Ramirez-Gonzalez, Ricardo H.

AU - Clavijo, Bernardo J.

AU - Wright, Jonathan

AU - Spannagl, Manuel

AU - Martis, Mihaela M.

AU - Mascher, Martin

AU - Chapman, Jarrod

AU - Poland, Jesse A.

AU - Scholz, Uwe

AU - Barry, Kerrie

AU - Waugh, Robbie

AU - Rokhsar, Daniel S.

AU - Muehlbauer, Gary J.

AU - Stein, Nils

AU - Gundlach, Heidrun

AU - Zytnicki, Matthias

AU - Jamilloux, Véronique

AU - Quesneville, Hadi

AU - Wicker, Thomas

AU - Faccioli, Primetta

AU - Colaiacovo, Moreno

AU - Stanca, Antonio Michele

AU - Budak, Hikmet

AU - Cattivelli, Luigi

AU - Glover, Natasha

AU - Pingault, Lise

AU - Paux, Etienne

AU - Sharma, Sapna

AU - Appels, Rudi

AU - Bellgard, Matthew

AU - Chapman, Brett

AU - Nussbaumer, Thomas

AU - Bader, Kai Christian

AU - Rimbert, Hélène

AU - Wang, Shichen

AU - Knox, Ron

AU - Kilian, Andrzej

AU - Alaux, Michael

AU - Alfama, Françoise

AU - Couderc, Loïc

AU - Guilhot, Nicolas

AU - Viseux, Claire

AU - Loaec, Mikaël

AU - Keller, Beat

AU - Praud, Sebastien

N1 - Generated from Scopus record by KAUST IRTS on 2022-09-13

PY - 2014/1/1

Y1 - 2014/1/1

N2 - 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.

AB - 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.

UR - https://www.science.org/doi/10.1126/science.1250091

UR - http://www.scopus.com/inward/record.url?scp=85048671720&partnerID=8YFLogxK

U2 - 10.1126/science.1250091

DO - 10.1126/science.1250091

M3 - Article

SN - 1095-9203

VL - 345

JO - Science

JF - Science

IS - 6194

ER -

Genome interplay in the grain transcriptome of hexaploid bread wheat

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this