Wheat research and breeding in the new era of a high-quality reference genome
Rudi APPELS
Wheat research and breeding in the new era of a high-quality reference genome
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.
assembly technology / molecular markers / polyploidy / transcript networks / wheat genome
[1] |
The International Wheat Genorne Sequencing Consortium (IWGSC), Appels R, Eversole K, Stein N, Feuillet C, Keller B, Rogers J, Pozniak C J, Choulet F, Distelfeld A, Eversole K, Poland J, Ronen G, Sharpe A G, Barad O, Baruch K, Keeble-Gagnère G, Mascher M, Ben-Zvi G, Josselin A A, Himmelbach A, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Koh C, Muehlbauer G, Pasam R K, Paux E, Rigault P, Tibbits J, Tiwari V, Spannagl M, Lang D, Gundlach H, Haberer G, Mayer K F X, Ormanbekova D, Prade V, Šimková H, Wicker T, Swarbreck D, Rimbert H, Felder M, Guilhot N, Kaithakottil G, Keilwagen J, Leroy P, Lux T, Twardziok S, Venturini L, Juhász A, Abrouk M, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez R H, Arnaud D, Chalabi S, Chalhoub B, Cory A, Datla R, Davey M W, Jacobs J, Robinson S J, Steuernagel B, van Ex F, Wulff B B H, Benhamed M, Bendahmane A, Concia L, Latrasse D, Bartoš J, Bellec A, Berges H, Doležel J, Frenkel Z, Gill B, Korol A, Letellier T, Olsen O A, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S, Fahima T, Glikson V, Raats D, Číhalíková J, Toegelová H, Vrána J, Sourdille P, Darrier B, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Jones J D G, Witek K, Yu G, Small I, Melonek J, Zhou R, Belova T, Kanyuka K, King R, Nilsen K, Walkowiak S, Cuthbert R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Čížková J, Akpinar B A, Biyiklioglu S, Gao L, N’Daiye A, Kubaláková M, Šafář J, Alfama F, Adam-Blondon A F, Flores R, Guerche C, Loaec M, Quesneville H, Condie J, Ens J, Maclachlan R, Tan Y, Alberti A, Aury J M, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Kaur G, Luo M, Sehgal S, Chhuneja P, Gupta O P, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh N K, Khurana J P, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar R S, Holušová K, Plíhal O, Clark M D, Heavens D, Kettleborough G, Wright J, Balcárková B, Hu Y, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Cattonaro F, Jiumeng M, Kugler K, Pfeifer M, Sandve S, Xun X, Zhan B, Batley J, Bayer P E, Edwards D, Hayashi S, Tulpová Z, Visendi P, Cui L, Du X, Feng K, Nie X, Tong W, Wang L. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 2018, 361(6403): 361–374
Pubmed
|
[2] |
Ramírez-González R H, Borrill P, Lang D, Harrington S A, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson S J, Cory A T, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout C J, Chalhoub B, Mayer K F X, Benhamed M, Latrasse D, Bendahmane A, International Wheat Genome Sequencing Consortium, Wulff B B H, Appels R, Tiwari V, Datla R, Choulet F, Pozniak C J, Provart N J, Sharpe A G, Paux E, Spannagl M, Bräutigam A, Uauy C. The transcriptional landscape of polyploid wheat. Science, 2018, 361(6403): eaar6089
|
[3] |
Juhász A, Belova T, Florides C G, Maulis C, Fischer I, Gell G, Birinyi Z, Ong J, Keeble-Gagnère G, Maharajan A, Ma W, Gibson P, Jia J, Lang D, Mayer K F X, Spannagl M, Tye-Din J A, Appels R, Olsen O A. Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat. Science Advances, 2018, 4(8): eaar8602
CrossRef
Pubmed
Google scholar
|
[4] |
Keeble-Gagnère G, Rigault P, Tibbits J, Pasam R, Hayden M, Forrest K, Frenkel Z, Korol A, Huang B E, Cavanagh C, Taylor J, Abrouk M, Sharpe A, Konkin D, Sourdille P, Darrier B, Choulet F, Bernard A, Rochfort S, Dimech A, Watson-Haigh N, Baumann U, Eckermann P, Fleury D, Juhasz A, Boisvert S, Nolin M A, Doležel J, Šimková H, Toegelová H, Šafář J, Luo M C, Câmara F, Pfeifer M, Isdale D, Nyström-Persson J, Iwgsc, Koo D H, Tinning M, Cui D, Ru Z, Appels R. 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
CrossRef
Pubmed
Google scholar
|
[5] |
Thind A K, Wicker T, Müller T, Ackermann P M, Steuernagel B, Wulff B B H, Spannagl M, Twardziok S O, Felder M, Lux T, Mayer K F X, Keller B, Krattinger S G. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biology, 2018, 19(1): 104
CrossRef
Pubmed
Google scholar
|
[6] |
Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramírez-González R H, de Oliveira R, Mayer K F X, Paux E, Choulet F. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biology, 2018, 19(1): 103
CrossRef
Pubmed
Google scholar
|
[7] |
Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, Paux E, Eversole K, Adam-Blondon A F, Quesneville H. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 2018, 19(1): 111
CrossRef
Pubmed
Google scholar
|
[8] |
Sears E R. Misdivision of univalents in common wheat. Chromosoma, 1952, 4(6): 535–550
Pubmed
|
[9] |
Sears E R. Chromosome mapping with the aid of telocentrics. Hereditas, 1966, 2: 370–381
|
[10] |
Sears E R, Miller T. The history of Chinese Spring wheat. Cereal Research Communications, 1985, 13: 261–263
|
[11] |
Liu D, Zhang L, Hao M, Ning S, Yuan Z, Shoufen Dai S, Huang L, Wu B, Yan Z, Lan X, Zheng Y. Wheat breeding in the hometown of Chinese Spring. Crop Journal, 2018, 6(1): 82–90
CrossRef
Google scholar
|
[12] |
Gill B S, Appels R, Botha-Oberholster A M, Buell C R, Bennetzen J L, Chalhoub B, Chumley F, Dvorák J, Iwanaga M, Keller B, Li W, McCombie W R, Ogihara Y, Quetier F, Sasaki T. A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics, 2004, 168(2): 1087–1096
CrossRef
Pubmed
Google scholar
|
[13] |
Doležel J, Doleželová M, Suchánková, P, Šafář J, Kovářová P, Bartoš J, Číhalíková J, Šimková H. Flow cytogenetic analysis of the wheat genome. Frontiers of Wheat Bioscience, 2005, Memorial Issue (Wheat Information Service No.100): 3–15
|
[14] |
Clavijo B J, Venturini L, Schudoma C, Accinelli G G, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu F H, McKenzie N, Raats D, Ramirez-Gonzalez R H, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser D M, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey R P, Fosker C, Palma F D, Phillips A L, Millar A H, Kersey P J, Uauy C, Krasileva K V, Swarbreck D, Bevan M W, Clark M D. 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
CrossRef
Pubmed
Google scholar
|
[15] |
Zimin A V, Puiu D, Hall R, Kingan S, Clavijo B J, Salzberg S L. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. GigaScience, 2017, 6(11): 1–7
CrossRef
Pubmed
Google scholar
|
[16] |
Ogihara Y. Genome science of polyploid wheat. Wheat Information Service, 2005, 100: 169–184
|
[17] |
Appels R, Nystrom-Persson J, Keeble-Gagnere G. Advances in genome studies in plants and animals. Functional & Integrative Genomics, 2014, 14(1): 1–9
CrossRef
Pubmed
Google scholar
|
[18] |
Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genetics, 2006, 38(11): 1348–1354
CrossRef
Pubmed
Google scholar
|
[19] |
Lee E, Helt G A, Reese J T, Munoz-Torres M C, Childers C P, Buels R M, Stein L, Holmes I H, Elsik C G, Lewis S E. Web Apollo: a web-based genomic annotation editing platform. Genome Biology, 2013, 14(8): R93
CrossRef
Pubmed
Google scholar
|
[20] |
The International Wheat Genome Sequencing Consortium (IWGSC), Mayer K F X, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski A J, Sourdille P, Endo T R, Kubaláková M, Cíhalíková J, Dubská Z, Vrána J, Sperková R, Simková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh N K, 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 P R, Sharpe A, Klassen D, Edwards D, Batley J, Olsen O A, Sandve S R, Lien S, Steuernagel B, Wulff B, Caccamo M, Ayling S, Ramirez-Gonzalez R H, Clavijo B J, Wright J, Pfeifer M, Spannagl M, Martis M M, Mascher M, Chapman J, Poland J A, Scholz U, Barry K, Waugh R, Rokhsar D S, Muehlbauer G J, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca A M, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader K C, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 2014, 345(6194): 1251788
CrossRef
Pubmed
Google scholar
|
[21] |
Ogbonnaya F C, Halloran G M, Lagudah E S. D genome of wheat: 60 years on from Kihara, Sears and McFadden. Wheat Information Service, 2005, 100: 205–220
|
[22] |
Bromilow S, Gethings L A, Buckley M, Bromley M, Shewry P R, Langridge J I, Clare Mills E N. 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
CrossRef
Pubmed
Google scholar
|
[23] |
Altenbach S B, Chang H C, Simon-Buss A, Jang Y R, Denery-Papini S, Pineau F, Gu Y Q, Huo N, Lim S H, Kang C S, Lee J Y. 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
CrossRef
Pubmed
Google scholar
|
[24] |
Kawaura K, Miura M, Kamei Y, Ikeda T M, Ogihara Y. Molecular characterization of gliadins of Chinese Spring wheat in relation to celiac disease elicitors. Genes & Genetic Systems, 2018, 93(1): 9– 20
CrossRef
Pubmed
Google scholar
|
[25] |
Zhao X C, Batey I L, Sharp P J, Crosbie G, Barclay I, Wilson R, Morell M K, Appels R. A single genetic locus associated with starch granule and noodle quality in wheat. Journal of Cereal Science, 1998, 27(1): 7–13
CrossRef
Google scholar
|
[26] |
Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramírez-González R H, de Oliveira R, Mayer K F X, Paux E, Choulet F. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biology, 2018, 19(1): 103
CrossRef
Pubmed
Google scholar
|
[27] |
Thind A K, Wicker T, Müller T, Ackermann P M, Steuernagel B, Wulff B B H, Spannagl M, Twardziok S O, Felder M, Lux T, Mayer K F X, Keller B, Krattinger S G. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biology, 2018, 19(1): 104
CrossRef
Pubmed
Google scholar
|
[28] |
Mukai Y. Perspectives in molecular cytogenetics of wheat. Wheat Information Service, 2005, 100: 17–32
|
[29] |
Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney R K, He Z. Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Molecular Plant, 2017, 10(8): 1047–1064
CrossRef
Pubmed
Google scholar
|
[30] |
Poland J, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y, Dreisigacker S, Crossa J, Sánchez-Villeda H, Sorrells M, Jannink J L. Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome, 2012, 5(3): 103–113
CrossRef
Google scholar
|
[31] |
Manosalva P M, Davidson R M, Liu B, Zhu X, Hulbert S H, Leung H, Leach J E. 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
CrossRef
Pubmed
Google scholar
|
[32] |
Mago R, Tabe L, Vautrin S, Šimková H, Kubaláková M, Upadhyaya N, Berges H, Kong X, Breen J, Doležel J, Appels R, Ellis J G, Spielmeyer W, Spielmeyer W. 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
CrossRef
Pubmed
Google scholar
|
[33] |
Keeble-Gagnere G, Isdale D, Suchecki R, Kruger A, Lomas K, Carroll D, Li S, Whan A, Hayden M, Tibbits J. Integrating past, present and future wheat research with Pretzel. bioRix, 2019 (preprint). doi:10.1101/517953
|
[34] |
Sharma N, Ruelens P, D’hauw M, Maggen T, Dochy N, Torfs S, Kaufmann K, Rohde A, Geuten K. 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
CrossRef
Pubmed
Google scholar
|
[35] |
Shaw L M, Lyu B, Turner R, Li C, Chen F, Han X, Fu D, Dubcovsky J. FLOWERING LOCUS T2 regulates spike development and fertility in temperate cereals. Journal of Experimental Botany, 2019, 70(1): 193–204
CrossRef
Pubmed
Google scholar
|
/
〈 | 〉 |