Journal article
Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
Genome Biology, Vol.19(1), Article 112
2018
Abstract
Background: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.
Results: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.
Conclusions: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
Details
- Title
- Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
- Authors/Creators
- G. Keeble-Gagnère (Author/Creator) - Agriculture VictoriaP. Rigault (Author/Creator) - Heidelberg UniversityJ. Tibbits (Author/Creator) - Agriculture VictoriaR. Pasam (Author/Creator) - Agriculture VictoriaM. Hayden (Author/Creator) - Agriculture VictoriaK. Forrest (Author/Creator) - Agriculture VictoriaZ. Frenkel (Author/Creator) - University of HaifaA. Korol (Author/Creator) - University of HaifaB.E. Huang (Author/Creator) - Commonwealth Scientific and Industrial Research OrganisationC. Cavanagh (Author/Creator) - Commonwealth Scientific and Industrial Research OrganisationJ. Taylor (Author/Creator) - Commonwealth Scientific and Industrial Research OrganisationM. Abrouk (Author/Creator) - King Abdullah University of Science and TechnologyA. Sharpe (Author/Creator) - University of SaskatchewanD. Konkin (Author/Creator) - University of SaskatchewanP. Sourdille (Author/Creator) - Génétique, Diversité, Écophysiologie des CéréalesB. Darrier (Author/Creator) - Génétique, Diversité, Écophysiologie des CéréalesF. Choulet (Author/Creator) - Génétique, Diversité, Écophysiologie des CéréalesA. Bernard (Author/Creator) - Génétique, Diversité, Écophysiologie des CéréalesS. Rochfort (Author/Creator) - Agriculture VictoriaA. Dimech (Author/Creator) - Agriculture VictoriaN. Watson-Haigh (Author/Creator)U. Baumann (Author/Creator) - The University of AdelaideP. Eckermann (Author/Creator) - The University of AdelaideD. Fleury (Author/Creator) - The University of AdelaideA. Juhász (Author/Creator) - Murdoch UniversityS. Boisvert (Author/Creator) - GYDLE, Québec, CanadaM.-A. Nolin (Author/Creator) - GYDLE, Québec, CanadaJ. Doležel (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyH. Šimková (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyH. Toegelová (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyJ. Safar (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyM.-C. Luo (Author/Creator) - University of California, DavisF. Câmara (Author/Creator) - Universitat Pompeu FabraM. Pfeifer (Author/Creator) - Center for Systems Biology DresdenD. Isdale (Author/Creator) - Agriculture VictoriaJ. Nyström-Persson (Author/Creator) - Level (Czechia)D.-H. Koo (Author/Creator) - Kansas State UniversityM. Tinning (Author/Creator) - AGRF LtdD. Cui (Author/Creator) - Henan Agricultural UniversityZ. Ru (Author/Creator) - Henan Institute of Science and TechnologyR. Appels (Author/Creator) - Murdoch University
- Publication Details
- Genome Biology, Vol.19(1), Article 112
- Publisher
- BioMed Central Ltd
- Identifiers
- 991005540165507891
- Copyright
- © 2018 The Author(s)
- Murdoch Affiliation
- School of Veterinary and Life Sciences
- Language
- English
- Resource Type
- Journal article
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