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Frontiers of Agricultural Science and Engineering

Front. Agr. Sci. Eng.    2019, Vol. 6 Issue (3) : 225-232     https://doi.org/10.15302/J-FASE-2019265
REVIEW
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.

Keywords assembly technology      molecular markers      polyploidy      transcript networks      wheat genome     
Corresponding Authors: Rudi APPELS   
Just Accepted Date: 15 May 2019   Online First Date: 25 June 2019    Issue Date: 26 July 2019
 Cite this article:   
Rudi APPELS. Wheat research and breeding in the new era of a high-quality reference genome[J]. Front. Agr. Sci. Eng. , 2019, 6(3): 225-232.
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http://journal.hep.com.cn/fase/EN/10.15302/J-FASE-2019265
http://journal.hep.com.cn/fase/EN/Y2019/V6/I3/225
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Rudi APPELS
Fig.1  A representative view of c. 200 kb of the wheat genome showing the gene islands (blue) and retrotransposable elements (pink). The scale near the top of the image is in the genome position scale base pairs. The image is a screen capture of IWGSC RefSeq v1.0 viewed in Apollo[19] as established in the Earlham Institute, Norwich Research Park, UK.
Fig.2  Detail of a 2.4-Mb region from chromosome 7AS (modified from Keeble-Gagnère et al.[4]). The matching regions from IWGSC RefSeq v1.0 (orange), TGAC (cyan) and PacBio (yellow) assemblies show the alignments of the genome sequences and the black bars indicate differences between genome sequences. The vertical pink bars indicate regions of the finished sequence not present in any other assembly.
Fig.3  Summary of overall diversity in gene numbers within the wheat genome: modified from IWGSC[1]. The ratio, 1:1:1, indicates homeologous genes present on the A, B and D genomes. The ratio, 1:1:N, indicates the respective homeologous gene on the D genome has multiple copies, similarly for 1:N:1 and N:1:1 designators as indicated in the table. The ratio, 1:1:0, indicates the respective homeologous gene on the D genome is absent, similarly for 1:0:1 and 0:1:1 designators as indicated in the table.
Fig.4  Synteny alignment of a well-known rice blast locus on rice chromosome 8 to a new location on the long arm of wheat chromosome 5A. The synteny based alignment was performed with Pretzel software[33].
1 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
2 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
3 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
4 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
5 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
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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