Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/119029
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Type: Journal article
Title: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
Author: Keeble-Gagnère, G.
Rigault, P.
Tibbits, J.
Pasam, R.
Hayden, M.
Forrest, K.
Frenkel, Z.
Korol, A.
Huang, B.
Cavanagh, C.
Taylor, J.
Abrouk, M.
Sharpe, A.
Konkin, D.
Sourdille, P.
Darrier, B.
Choulet, F.
Bernard, A.
Rochfort, S.
Dimech, A.
et al.
Citation: Genome Biology, 2018; 19(1):112-1-112-18
Publisher: BMC
Issue Date: 2018
ISSN: 1474-7596
1474-760X
Statement of
Responsibility: 
Gabriel Keeble-Gagnère, Philippe Rigault ... Benoît Darrier ... Nathan Watson-Haigh ... Ute Baumann ... Delphine Fleury ... et al.
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.
Keywords: Wheat sequence finishing; megabase-scale integration; optical/physical maps Grain quality; Yield
Rights: © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
RMID: 0030096284
DOI: 10.1186/s13059-018-1475-4
Grant ID: http://purl.org/au-research/grants/arc/IH130200027
Appears in Collections:Agriculture, Food and Wine publications

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