September 22, 2019  |  

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome.

Authors: Keeble-Gagnère, Gabriel and Rigault, Philippe and Tibbits, Josquin and Pasam, Raj and Hayden, Matthew and Forrest, Kerrie and Frenkel, Zeev and Korol, Abraham and Huang, B Emma and Cavanagh, Colin and Taylor, Jen and Abrouk, Michael and Sharpe, Andrew and Konkin, David and Sourdille, Pierre and Darrier, Benoît and Choulet, Frédéric and Bernard, Aurélien and Rochfort, Simone and Dimech, Adam and Watson-Haigh, Nathan and Baumann, Ute and Eckermann, Paul and Fleury, Delphine and Juhasz, Angela and Boisvert, Sébastien and Nolin, Marc-Alexandre and Doležel, Jaroslav and Šimková, Hana and Toegelová, Helena and Šafár, Jan and Luo, Ming-Cheng and Câmara, Francisco and Pfeifer, Matthias and Isdale, Don and Nyström-Persson, Johan and Iwgsc and Koo, Dal-Hoe and Tinning, Matthew and Cui, Dangqun and Ru, Zhengang and Appels, Rudi

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.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.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.

Journal: Genome biology
DOI: 10.1186/s13059-018-1475-4
Year: 2018

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