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Wheat research and breeding in the new era of a high-quality reference genome |
Rudi APPELS1,2() |
1. Centre for AgriBioscience/Department of Economic Development, LaTrobe University, Bundoora VIC 3083, Australia 2. Department of BioSciences, The University of Melbourne, Victoria 2052, Australia |
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Abstract The publications of the International Wheat Genome Sequencing Consortium (IWGSC) released in August 2018 are reviewed and placed into the context of developments arising from the availability of the high-quality wheat genome assembly.
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Keywords
assembly technology
molecular markers
polyploidy
transcript networks
wheat genome
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Corresponding Author(s):
Rudi APPELS
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Just Accepted Date: 15 May 2019
Online First Date: 25 June 2019
Issue Date: 26 July 2019
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The International Wheat Genorne Sequencing Consortium (IWGSC), R Appels, K Eversole, N Stein, C Feuillet, B Keller, J Rogers, C J Pozniak, F Choulet, A Distelfeld, K Eversole, J Poland, G Ronen, A G Sharpe, O Barad, K Baruch, G Keeble-Gagnère, M Mascher, G Ben-Zvi, A A Josselin, A Himmelbach, F Balfourier, J Gutierrez-Gonzalez, M Hayden, C Koh, G Muehlbauer, R K Pasam, E Paux, P Rigault, J Tibbits, V Tiwari, M Spannagl, D Lang, H Gundlach, G Haberer, K F X Mayer, D Ormanbekova, V Prade, H Šimková, T Wicker, D Swarbreck, H Rimbert, M Felder, N Guilhot, G Kaithakottil, J Keilwagen, P Leroy, T Lux, S Twardziok, L Venturini, A Juhász, M Abrouk, I Fischer, C Uauy, P Borrill, R H Ramirez-Gonzalez, D Arnaud, S Chalabi, B Chalhoub, A Cory, R Datla, M W Davey, J Jacobs, S J Robinson, B Steuernagel, F van Ex, B B H Wulff, M Benhamed, A Bendahmane, L Concia, D Latrasse, J Bartoš, A Bellec, H Berges, J Doležel, Z Frenkel, B Gill, A Korol, T Letellier, O A Olsen, K Singh, M Valárik, E van der Vossen, S Vautrin, S Weining, T Fahima, V Glikson, D Raats, J Číhalíková, H Toegelová, J Vrána, P Sourdille, B Darrier, D Barabaschi, L Cattivelli, P Hernandez, S Galvez, H Budak, J D G Jones, K Witek, G Yu, I Small, J Melonek, R Zhou, T Belova, K Kanyuka, R King, K Nilsen, S Walkowiak, R Cuthbert, R Knox, K Wiebe, D Xiang, A Rohde, T Golds, J Čížková, B A Akpinar, S Biyiklioglu, L Gao, A N’Daiye, M Kubaláková, J Šafář, F Alfama, A F Adam-Blondon, R Flores, C Guerche, M Loaec, H Quesneville, J Condie, J Ens, R Maclachlan, Y Tan, A Alberti, J M Aury, V Barbe, A Couloux, C Cruaud, K Labadie, S Mangenot, P Wincker, G Kaur, M Luo, S Sehgal, P Chhuneja, O P Gupta, S Jindal, P Kaur, P Malik, P Sharma, B Yadav, N K Singh, J P Khurana, C Chaudhary, P Khurana, V Kumar, A Mahato, S Mathur, A Sevanthi, N Sharma, R S Tomar, K Holušová, O Plíhal, M D Clark, D Heavens, G Kettleborough, J Wright, B Balcárková, Y Hu, E Salina, N Ravin, K Skryabin, A Beletsky, V Kadnikov, A Mardanov, M Nesterov, A Rakitin, E Sergeeva, H Handa, H Kanamori, S Katagiri, F Kobayashi, S Nasuda, T Tanaka, J Wu, F Cattonaro, M Jiumeng, K Kugler, M Pfeifer, S Sandve, X Xun, B Zhan, J Batley, P E Bayer, D Edwards, S Hayashi, Z Tulpová, P Visendi, L Cui, X Du, K Feng, X Nie, W Tong, L Wang. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 2018, 361(6403): 361–374
pmid: 30115783
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R H Ramírez-González, P Borrill, D Lang, S A Harrington, J Brinton, L Venturini, M Davey, J Jacobs, F van Ex, A Pasha, Y Khedikar, S J Robinson, A T Cory, T Florio, L Concia, C Juery, H Schoonbeek, B Steuernagel, D Xiang, C J Ridout, B Chalhoub, K F X Mayer, M Benhamed, D Latrasse, A Bendahmane, International Wheat Genome Sequencing Consortium, B B H Wulff, R Appels, V Tiwari, R Datla, F Choulet, C J Pozniak, N J Provart, A G Sharpe, E Paux, M Spannagl, A Bräutigam, C Uauy. The transcriptional landscape of polyploid wheat. Science, 2018, 361(6403): eaar6089
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A Juhász, T Belova, C G Florides, C Maulis, I Fischer, G Gell, Z Birinyi, J Ong, G Keeble-Gagnère, A Maharajan, W Ma, P Gibson, J Jia, D Lang, K F X Mayer, M Spannagl, J A Tye-Din, R Appels, O A Olsen. Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat. Science Advances, 2018, 4(8): eaar8602
https://doi.org/10.1126/sciadv.aar8602
pmid: 30128352
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G Keeble-Gagnère, P Rigault, J Tibbits, R Pasam, M Hayden, K Forrest, Z Frenkel, A Korol, B E Huang, C Cavanagh, J Taylor, M Abrouk, A Sharpe, D Konkin, P Sourdille, B Darrier, F Choulet, A Bernard, S Rochfort, A Dimech, N Watson-Haigh, U Baumann, P Eckermann, D Fleury, A Juhasz, S Boisvert, M A Nolin, J Doležel, H Šimková, H Toegelová, J Šafář, M C Luo, F Câmara, M Pfeifer, D Isdale, J Nyström-Persson, D H Iwgsc, Koo, M Tinning, D Cui, Z Ru, R Appels. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biology, 2018, 19(1): 112
https://doi.org/10.1186/s13059-018-1475-4
pmid: 30115128
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A K Thind, T Wicker, T Müller, P M Ackermann, B Steuernagel, B B H Wulff, M Spannagl, S O Twardziok, M Felder, T Lux, K F X Mayer, B Keller, S G Krattinger. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biology, 2018, 19(1): 104
https://doi.org/10.1186/s13059-018-1477-2
pmid: 30115097
|
6 |
T Wicker, H Gundlach, M Spannagl, C Uauy, P Borrill, R H Ramírez-González, R de Oliveira, K F X Mayer, E Paux, F Choulet. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biology, 2018, 19(1): 103
https://doi.org/10.1186/s13059-018-1479-0
pmid: 30115100
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7 |
M Alaux, J Rogers, T Letellier, R Flores, F Alfama, C Pommier, N Mohellibi, S Durand, E Kimmel, C Michotey, C Guerche, M Loaec, M Lainé, D Steinbach, F Choulet, H Rimbert, P Leroy, N Guilhot, J Salse, C Feuillet, E Paux, K Eversole, A F Adam-Blondon, H Quesneville. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 2018, 19(1): 111
https://doi.org/10.1186/s13059-018-1491-4
pmid: 30115101
|
8 |
E R Sears. Misdivision of univalents in common wheat. Chromosoma, 1952, 4(6): 535–550
pmid: 14945063
|
9 |
E R Sears. Chromosome mapping with the aid of telocentrics. Hereditas, 1966, 2: 370–381
|
10 |
E R Sears, T Miller. The history of Chinese Spring wheat. Cereal Research Communications, 1985, 13: 261–263
|
11 |
D Liu, L Zhang, M Hao, S Ning, Z Yuan, S Shoufen Dai, L Huang, B Wu, Z Yan, X Lan, Y Zheng. Wheat breeding in the hometown of Chinese Spring. Crop Journal, 2018, 6(1): 82–90
https://doi.org/10.1016/j.cj.2017.08.009
|
12 |
B S Gill, R Appels, A M Botha-Oberholster, C R Buell, J L Bennetzen, B Chalhoub, F Chumley, J Dvorák, M Iwanaga, B Keller, W Li, W R McCombie, Y Ogihara, F Quetier, T Sasaki. A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics, 2004, 168(2): 1087–1096
https://doi.org/10.1534/genetics.104.034769
pmid: 15514080
|
13 |
J, Doležel M Doleželová, P Suchánková,, J Šafář, P Kovářová, J Bartoš, J Číhalíková, H Šimková. Flow cytogenetic analysis of the wheat genome. Frontiers of Wheat Bioscience, 2005, Memorial Issue (Wheat Information Service No.100): 3–15
|
14 |
B J Clavijo, L Venturini, C Schudoma, G G Accinelli, G Kaithakottil, J Wright, P Borrill, G Kettleborough, D Heavens, H Chapman, J Lipscombe, T Barker, F H Lu, N McKenzie, D Raats, R H Ramirez-Gonzalez, A Coince, N Peel, L Percival-Alwyn, O Duncan, J Trösch, G Yu, D M Bolser, G Namaati, A Kerhornou, M Spannagl, H Gundlach, G Haberer, R P Davey, C Fosker, F D Palma, A L Phillips, A H Millar, P J Kersey, C Uauy, K V Krasileva, D Swarbreck, M W Bevan, M D Clark. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Research, 2017, 27(5): 885–896
https://doi.org/10.1101/gr.217117.116
pmid: 28420692
|
15 |
A V Zimin, D Puiu, R Hall, S Kingan, B J Clavijo, S L Salzberg. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. GigaScience, 2017, 6(11): 1–7
https://doi.org/10.1093/gigascience/gix097
pmid: 29069494
|
16 |
Y Ogihara. Genome science of polyploid wheat. Wheat Information Service, 2005, 100: 169–184
|
17 |
R Appels, J Nystrom-Persson, G Keeble-Gagnere. Advances in genome studies in plants and animals. Functional & Integrative Genomics, 2014, 14(1): 1–9
https://doi.org/10.1007/s10142-014-0364-5
pmid: 24626952
|
18 |
M Simonis, P Klous, E Splinter, Y Moshkin, R Willemsen, E de Wit, B van Steensel, W de Laat. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genetics, 2006, 38(11): 1348–1354
https://doi.org/10.1038/ng1896
pmid: 17033623
|
19 |
E Lee, G A Helt, J T Reese, M C Munoz-Torres, C P Childers, R M Buels, L Stein, I H Holmes, C G Elsik, S E Lewis. Web Apollo: a web-based genomic annotation editing platform. Genome Biology, 2013, 14(8): R93
https://doi.org/10.1186/gb-2013-14-8-r93
pmid: 24000942
|
20 |
The International Wheat Genome Sequencing Consortium (IWGSC), K F X Mayer, J Rogers, J Doležel, C Pozniak, K Eversole, C Feuillet, B Gill, B Friebe, A J Lukaszewski, P Sourdille, T R Endo, M Kubaláková, J Cíhalíková, Z Dubská, J Vrána, R Sperková, H Simková, M Febrer, L Clissold, K McLay, K Singh, P Chhuneja, N K Singh, J Khurana, E Akhunov, F Choulet, A Alberti, V Barbe, P Wincker, H Kanamori, F Kobayashi, T Itoh, T Matsumoto, H Sakai, T Tanaka, J Wu, Y Ogihara, H Handa, P R Maclachlan, A Sharpe, D Klassen, D Edwards, J Batley, O A Olsen, S R Sandve, S Lien, B Steuernagel, B Wulff, M Caccamo, S Ayling, R H Ramirez-Gonzalez, B J Clavijo, J Wright, M Pfeifer, M Spannagl, M M Martis, M Mascher, J Chapman, J A Poland, U Scholz, K Barry, R Waugh, D S Rokhsar, G J Muehlbauer, N Stein, H Gundlach, M Zytnicki, V Jamilloux, H Quesneville, T Wicker, P Faccioli, M Colaiacovo, A M Stanca, H Budak, L Cattivelli, N Glover, L Pingault, E Paux, S Sharma, R Appels, M Bellgard, B Chapman, T Nussbaumer, K C Bader, H Rimbert, S Wang, R Knox, A Kilian, M Alaux, F Alfama, L Couderc, N Guilhot, C Viseux, M Loaec, B Keller, S Praud. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 2014, 345(6194): 1251788
https://doi.org/10.1126/science.1251788
pmid: 25035500
|
21 |
F C Ogbonnaya, G M Halloran, E S Lagudah. D genome of wheat: 60 years on from Kihara, Sears and McFadden. Wheat Information Service, 2005, 100: 205–220
|
22 |
S Bromilow, L A Gethings, M Buckley, M Bromley, P R Shewry, J I Langridge, E N Clare Mills. A curated gluten protein sequence database to support development of proteomics methods for determination of gluten in gluten-free foods. Journal of Proteomics, 2017, 163: 67–75
https://doi.org/10.1016/j.jprot.2017.03.026
pmid: 28385663
|
23 |
S B Altenbach, H C Chang, A Simon-Buss, Y R Jang, S Denery-Papini, F Pineau, Y Q Gu, N Huo, S H Lim, C S Kang, J Y Lee. Towards reducing the immunogenic potential of wheat flour: omega gliadins encoded by the D genome of hexaploid wheat may also harbor epitopes for the serious food allergy WDEIA. BMC Plant Biology, 2018, 18(1): 291
https://doi.org/10.1186/s12870-018-1506-z
pmid: 30463509
|
24 |
K Kawaura, M Miura, Y Kamei, T M Ikeda, Y Ogihara. Molecular characterization of gliadins of Chinese Spring wheat in relation to celiac disease elicitors. Genes & Genetic Systems, 2018, 93(1): 9– 20
https://doi.org/10.1266/ggs.17-00034
pmid: 29343665
|
25 |
X C Zhao, I L Batey, P J Sharp, G Crosbie, I Barclay, R Wilson, M K Morell, R Appels. A single genetic locus associated with starch granule and noodle quality in wheat. Journal of Cereal Science, 1998, 27(1): 7–13
https://doi.org/10.1006/jcrs.1997.0145
|
26 |
T Wicker, H Gundlach, M Spannagl, C Uauy, P Borrill, R H Ramírez-González, R de Oliveira, K F X Mayer, E Paux, F Choulet. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biology, 2018, 19(1): 103
https://doi.org/10.1186/s13059-018-1479-0
pmid: 30115100
|
27 |
A K Thind, T Wicker, T Müller, P M Ackermann, B Steuernagel, B B H Wulff, M Spannagl, S O Twardziok, M Felder, T Lux, K F X Mayer, B Keller, S G Krattinger. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biology, 2018, 19(1): 104
https://doi.org/10.1186/s13059-018-1477-2
pmid: 30115097
|
28 |
Y. Mukai Perspectives in molecular cytogenetics of wheat. Wheat Information Service, 2005, 100: 17–32
|
29 |
A Rasheed, Y Hao, X Xia, A Khan, Y Xu, R K Varshney, Z He. Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Molecular Plant, 2017, 10(8): 1047–1064
https://doi.org/10.1016/j.molp.2017.06.008
pmid: 28669791
|
30 |
J Poland, J Endelman, J Dawson, J Rutkoski, S Wu, Y Manes, S Dreisigacker, J Crossa, H Sánchez-Villeda, M Sorrells, J L Jannink. Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome, 2012, 5(3): 103–113
https://doi.org/10.3835/plantgenome2012.06.0006
|
31 |
P M Manosalva, R M Davidson, B Liu, X Zhu, S H Hulbert, H Leung, J E Leach. A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice. Plant Physiology, 2009, 149(1): 286–296
https://doi.org/10.1104/pp.108.128348
pmid: 19011003
|
32 |
R Mago, L Tabe, S Vautrin, H Šimková, M Kubaláková, N Upadhyaya, H Berges, X Kong, J Breen, J Doležel, R Appels, J G Ellis, W Spielmeyer, W Spielmeyer. Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biology, 2014, 14(1): 379
https://doi.org/10.1186/s12870-014-0379-z
pmid: 25547135
|
33 |
G Keeble-Gagnere, D Isdale, R Suchecki, A Kruger, K Lomas, D Carroll, S Li, A Whan, M Hayden, J Tibbits. Integrating past, present and future wheat research with Pretzel. bioRix, 2019 (preprint). doi:10.1101/517953
|
34 |
N Sharma, P Ruelens, M D’hauw, T Maggen, N Dochy, S Torfs, K Kaufmann, A Rohde, K Geuten. A flowering locus C homolog is a vernalization-regulated repressor in Brachypodium and is cold regulated in wheat. Plant Physiology, 2017, 173(2): 1301–1315
https://doi.org/10.1104/pp.16.01161
pmid: 28034954
|
35 |
L M Shaw, B Lyu, R Turner, C Li, F Chen, X Han, D Fu, J Dubcovsky. FLOWERING LOCUS T2 regulates spike development and fertility in temperate cereals. Journal of Experimental Botany, 2019, 70(1): 193–204
https://doi.org/10.1093/jxb/ery350
pmid: 30295847
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