A chromosome conformation capture ordered sequence of the barley genome

Martin Mascher; Heidrun Gundlach; Axel Himmelbach; Sebastian Beier; Sven O Twardziok; Thomas Wicker; Volodymyr Radchuk; Christoph Dockter; Pete E. Hedley; Joanne Russell; Micha Bayer; Luke Ramsay; Hui Liu; Georg Haberer; Xiao-Qi Zhang; Qisen Zhang; Roberto A Barrero; Lin Li; Stefan Taudien; Marco Groth; Marius Felder; Alex Hastie; Hana Šimková; Helena Staňková; Jan Vrána; Saki Chan; María Muñoz-Amatriaín; Rachid Ounit; Steve Wanamaker; Daniel Bolser; Christian Colmsee; Thomas Schmutzer; Lala Aliyeva-Schnorr; Stefano Grasso; Jaakko Tanskanen; Anna Chailyan; Dharanya Sampath; Darren Heavens; Leah Clissold; Sujie Cao; Brett Chapman; Fei Dai; Yong Han; Hua Li; Xuan Li; Chongyun Lin; John K McCooke; Cong Tan; Penghao Wang; Songbo Wang; Shuya Yin; Gaofeng Zhou; Jesse A. Poland; Matthew I Bellgard; Ljudmilla Borisjuk; Andreas Houben; Jaroslav Doležel; Sarah Ayling; Stefano Lonardi; Paul Kersey; Peter Langridge; Gary J. Muehlbauer; Matthew D. Clark; Mario Caccamo; Alan H. Schulman; Klaus F. X. Mayer; Matthias Platzer; Timothy J. Close; Uwe Scholz; Mats Hansson; Guoping Zhang; Ilka Braumann; Manuel Spannagl; Chengdao Li; Robbie Waugh; Nils Stein

doi:10.1038/nature22043

A chromosome conformation capture ordered sequence of the barley genome

Martin Mascher, Heidrun Gundlach, Axel Himmelbach, Sebastian Beier, Sven O Twardziok, Thomas Wicker, Volodymyr Radchuk, Christoph Dockter, Pete E. Hedley, Joanne Russell, Micha Bayer, Luke Ramsay, Hui Liu, Georg Haberer, Xiao-Qi Zhang, Qisen Zhang, Roberto A Barrero, Lin Li, Stefan Taudien, Marco GrothMarius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz-Amatriaín, Rachid Ounit, Steve Wanamaker, Daniel Bolser, Christian Colmsee, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Anna Chailyan, Dharanya Sampath, Darren Heavens, Leah Clissold, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K McCooke, Cong Tan, Penghao Wang, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse A. Poland, Matthew I Bellgard, Ljudmilla Borisjuk, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Paul Kersey, Peter Langridge, Gary J. Muehlbauer, Matthew D. Clark, Mario Caccamo, Alan H. Schulman, Klaus F. X. Mayer, Matthias Platzer, Timothy J. Close, Uwe Scholz, Mats Hansson, Guoping Zhang (Lead / Corresponding author), Ilka Braumann (Lead / Corresponding author), Manuel Spannagl (Lead / Corresponding author), Chengdao Li (Lead / Corresponding author), Robbie Waugh (Lead / Corresponding author), Nils Stein (Lead / Corresponding author)

Plant Sciences

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Abstract

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Original language	English
Pages (from-to)	427-433
Number of pages	7
Journal	Nature
Volume	544
Issue number	7651
Early online date	26 Apr 2017
DOIs	https://doi.org/10.1038/nature22043
Publication status	Published - 27 Apr 2017

Keywords

Genome
Plant genetics
DNA sequencing
Natural variation in plants
Agricultural genetics

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10.1038/nature22043Licence: CC BY

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Final published version, 10.8 MBLicence: CC BY

Exploiting Synergies in Barley Research (Partnering Award)
Brown, J. (Investigator), Halpin, C. (Investigator) & Waugh, R. (Investigator)
Biotechnology and Biological Sciences Research Council
26/06/14 → 25/12/18
Project: Research

Waugh, Robbie
- Plant Sciences - Professor of Crop Genomics
Person: Academic

Cite this

Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., Bayer, M., Ramsay, L., Liu, H., Haberer, G., Zhang, X.-Q., Zhang, Q., Barrero, R. A., Li, L., Taudien, S., ... Stein, N. (2017). A chromosome conformation capture ordered sequence of the barley genome. Nature, 544(7651), 427-433. https://doi.org/10.1038/nature22043

@article{234b5e54a477494d9c2a56591f559d77,

title = "A chromosome conformation capture ordered sequence of the barley genome",

abstract = "Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.",

keywords = "Genome, Plant genetics, DNA sequencing, Natural variation in plants, Agricultural genetics",

author = "Martin Mascher and Heidrun Gundlach and Axel Himmelbach and Sebastian Beier and Twardziok, {Sven O} and Thomas Wicker and Volodymyr Radchuk and Christoph Dockter and Hedley, {Pete E.} and Joanne Russell and Micha Bayer and Luke Ramsay and Hui Liu and Georg Haberer and Xiao-Qi Zhang and Qisen Zhang and Barrero, {Roberto A} and Lin Li and Stefan Taudien and Marco Groth and Marius Felder and Alex Hastie and Hana {\v S}imkov{\'a} and Helena Sta{\v n}kov{\'a} and Jan Vr{\'a}na and Saki Chan and Mar{\'i}a Mu{\~n}oz-Amatria{\'i}n and Rachid Ounit and Steve Wanamaker and Daniel Bolser and Christian Colmsee and Thomas Schmutzer and Lala Aliyeva-Schnorr and Stefano Grasso and Jaakko Tanskanen and Anna Chailyan and Dharanya Sampath and Darren Heavens and Leah Clissold and Sujie Cao and Brett Chapman and Fei Dai and Yong Han and Hua Li and Xuan Li and Chongyun Lin and McCooke, {John K} and Cong Tan and Penghao Wang and Songbo Wang and Shuya Yin and Gaofeng Zhou and Poland, {Jesse A.} and Bellgard, {Matthew I} and Ljudmilla Borisjuk and Andreas Houben and Jaroslav Dole{\v z}el and Sarah Ayling and Stefano Lonardi and Paul Kersey and Peter Langridge and Muehlbauer, {Gary J.} and Clark, {Matthew D.} and Mario Caccamo and Schulman, {Alan H.} and Mayer, {Klaus F. X.} and Matthias Platzer and Close, {Timothy J.} and Uwe Scholz and Mats Hansson and Guoping Zhang and Ilka Braumann and Manuel Spannagl and Chengdao Li and Robbie Waugh and Nils Stein",

note = "This work was performed in the frame of the International Barley Genome Sequencing Consortium and was supported by German Ministry of Education and Research grants 0314000 and 0315954 to K.F.X.M., M.P., U.S. and N.S., and 031A536 to U.S. and K.F.X.M.; Leibniz {\textquoteleft}Pakt f. Forschung und Innovation{\textquoteright} grant {\textquoteleft}sequencing barley chromosome 3H{\textquoteright} to N.S. and U.S.; Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 to R.W., P.E.H. and J.R.; BBSRC grants BB/I008357/1 to M.D.C. and M.C., and BB/I008071/1 to P.K.; Finland grant 266430 and a BioNano grant to A.H.S.; Carlsberg Foundation grant 2012_01_0461 to the Carlsberg Research Laboratory; Grains Research and Development Corporation (GRDC) grant DAW00233 to C.L. and P.L.; Department of Agricultural and Food, Government of Western Australia grant 681 to C.L.; National Natural Science Foundation of China (NSFC) grant 31129005 to C.L. and G. Zhang; NSFC grant 31330055 to G. Zhang.; Czech Ministry of Education, Youth and Sports grant LO1204 to J.D.; US National Science Foundation (NSF) grant DBI 0321756 to T.J.C. and S.L.; US Department of Agriculture–Cooperative State Research, Education, and Extension Service–National Institute of Food and Agriculture (USDA–CSREES–NIFA) grants 2009-65300-05645 and 2011-68002-30029 to T.J.C., S.L. and G.J.M.; NSF Advances in Biological Informatics grant DBI-1062301 to T.J.C. and S.L.; University of California grant CA-R-BPS-5306-H to T.J.C. and S.L.; NSF grant DBI 0321756 to S.L. BBSRC National Capability in Genomics (BB/J010375/1) and BBSRC Institute Strategic Programme funding for Bioinformatics (BB/J004669/1) to M.D.C., S.A. and M.C.; winter and spring barley accessions were a subset of genotypes selected from BBSRC and Agriculture and Horticulture Development Board projects AGOUEB and IMPROMALT (RD-2012-3776).",

year = "2017",

month = apr,

day = "27",

doi = "10.1038/nature22043",

language = "English",

volume = "544",

pages = "427--433",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7651",

}

Mascher, M, Gundlach, H, Himmelbach, A, Beier, S, Twardziok, SO, Wicker, T, Radchuk, V, Dockter, C, Hedley, PE, Russell, J, Bayer, M, Ramsay, L, Liu, H, Haberer, G, Zhang, X-Q, Zhang, Q, Barrero, RA, Li, L, Taudien, S, Groth, M, Felder, M, Hastie, A, Šimková, H, Staňková, H, Vrána, J, Chan, S, Muñoz-Amatriaín, M, Ounit, R, Wanamaker, S, Bolser, D, Colmsee, C, Schmutzer, T, Aliyeva-Schnorr, L, Grasso, S, Tanskanen, J, Chailyan, A, Sampath, D, Heavens, D, Clissold, L, Cao, S, Chapman, B, Dai, F, Han, Y, Li, H, Li, X, Lin, C, McCooke, JK, Tan, C, Wang, P, Wang, S, Yin, S, Zhou, G, Poland, JA, Bellgard, MI, Borisjuk, L, Houben, A, Doležel, J, Ayling, S, Lonardi, S, Kersey, P, Langridge, P, Muehlbauer, GJ, Clark, MD, Caccamo, M, Schulman, AH, Mayer, KFX, Platzer, M, Close, TJ, Scholz, U, Hansson, M, Zhang, G, Braumann, I, Spannagl, M, Li, C, Waugh, R & Stein, N 2017, 'A chromosome conformation capture ordered sequence of the barley genome', Nature, vol. 544, no. 7651, pp. 427-433. https://doi.org/10.1038/nature22043

TY - JOUR

T1 - A chromosome conformation capture ordered sequence of the barley genome

AU - Mascher, Martin

AU - Gundlach, Heidrun

AU - Himmelbach, Axel

AU - Beier, Sebastian

AU - Twardziok, Sven O

AU - Wicker, Thomas

AU - Radchuk, Volodymyr

AU - Dockter, Christoph

AU - Hedley, Pete E.

AU - Russell, Joanne

AU - Bayer, Micha

AU - Ramsay, Luke

AU - Liu, Hui

AU - Haberer, Georg

AU - Zhang, Xiao-Qi

AU - Zhang, Qisen

AU - Barrero, Roberto A

AU - Li, Lin

AU - Taudien, Stefan

AU - Groth, Marco

AU - Felder, Marius

AU - Hastie, Alex

AU - Šimková, Hana

AU - Staňková, Helena

AU - Vrána, Jan

AU - Chan, Saki

AU - Muñoz-Amatriaín, María

AU - Ounit, Rachid

AU - Wanamaker, Steve

AU - Bolser, Daniel

AU - Colmsee, Christian

AU - Schmutzer, Thomas

AU - Aliyeva-Schnorr, Lala

AU - Grasso, Stefano

AU - Tanskanen, Jaakko

AU - Chailyan, Anna

AU - Sampath, Dharanya

AU - Heavens, Darren

AU - Clissold, Leah

AU - Cao, Sujie

AU - Chapman, Brett

AU - Dai, Fei

AU - Han, Yong

AU - Li, Hua

AU - Li, Xuan

AU - Lin, Chongyun

AU - McCooke, John K

AU - Tan, Cong

AU - Wang, Penghao

AU - Wang, Songbo

AU - Yin, Shuya

AU - Zhou, Gaofeng

AU - Poland, Jesse A.

AU - Bellgard, Matthew I

AU - Borisjuk, Ljudmilla

AU - Houben, Andreas

AU - Doležel, Jaroslav

AU - Ayling, Sarah

AU - Lonardi, Stefano

AU - Kersey, Paul

AU - Langridge, Peter

AU - Muehlbauer, Gary J.

AU - Clark, Matthew D.

AU - Caccamo, Mario

AU - Schulman, Alan H.

AU - Mayer, Klaus F. X.

AU - Platzer, Matthias

AU - Close, Timothy J.

AU - Scholz, Uwe

AU - Hansson, Mats

AU - Zhang, Guoping

AU - Braumann, Ilka

AU - Spannagl, Manuel

AU - Li, Chengdao

AU - Waugh, Robbie

AU - Stein, Nils

N1 - This work was performed in the frame of the International Barley Genome Sequencing Consortium and was supported by German Ministry of Education and Research grants 0314000 and 0315954 to K.F.X.M., M.P., U.S. and N.S., and 031A536 to U.S. and K.F.X.M.; Leibniz ‘Pakt f. Forschung und Innovation’ grant ‘sequencing barley chromosome 3H’ to N.S. and U.S.; Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 to R.W., P.E.H. and J.R.; BBSRC grants BB/I008357/1 to M.D.C. and M.C., and BB/I008071/1 to P.K.; Finland grant 266430 and a BioNano grant to A.H.S.; Carlsberg Foundation grant 2012_01_0461 to the Carlsberg Research Laboratory; Grains Research and Development Corporation (GRDC) grant DAW00233 to C.L. and P.L.; Department of Agricultural and Food, Government of Western Australia grant 681 to C.L.; National Natural Science Foundation of China (NSFC) grant 31129005 to C.L. and G. Zhang; NSFC grant 31330055 to G. Zhang.; Czech Ministry of Education, Youth and Sports grant LO1204 to J.D.; US National Science Foundation (NSF) grant DBI 0321756 to T.J.C. and S.L.; US Department of Agriculture–Cooperative State Research, Education, and Extension Service–National Institute of Food and Agriculture (USDA–CSREES–NIFA) grants 2009-65300-05645 and 2011-68002-30029 to T.J.C., S.L. and G.J.M.; NSF Advances in Biological Informatics grant DBI-1062301 to T.J.C. and S.L.; University of California grant CA-R-BPS-5306-H to T.J.C. and S.L.; NSF grant DBI 0321756 to S.L. BBSRC National Capability in Genomics (BB/J010375/1) and BBSRC Institute Strategic Programme funding for Bioinformatics (BB/J004669/1) to M.D.C., S.A. and M.C.; winter and spring barley accessions were a subset of genotypes selected from BBSRC and Agriculture and Horticulture Development Board projects AGOUEB and IMPROMALT (RD-2012-3776).

PY - 2017/4/27

Y1 - 2017/4/27

N2 - Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

AB - Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

KW - Genome

KW - Plant genetics

KW - DNA sequencing

KW - Natural variation in plants

KW - Agricultural genetics

U2 - 10.1038/nature22043

DO - 10.1038/nature22043

M3 - Article

C2 - 28447635

SN - 0028-0836

VL - 544

SP - 427

EP - 433

JO - Nature

JF - Nature

IS - 7651

ER -

A chromosome conformation capture ordered sequence of the barley genome

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Projects

Exploiting Synergies in Barley Research (Partnering Award)

Profiles

Waugh, Robbie

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