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

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

doi:10.1186/s13059-018-1475-4

Abstract

BackgroundNumerous 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.ResultsUsing 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.ConclusionsSufficient 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.

Highlights

Numerous scaffold-level sequences for wheat are 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
The assembly combined a range of data sources including a 755 Megabase pairs (Mb) physical map comprising 732 bacterial artificial chromosome (BAC) contigs, represented by 11,451 BACs in 732 minimum tiling path (MTP) BAC sets, as well as mate-pair sequencing of genome-wide and chromosome-arm-specific libraries and chromosome-arm-specific Bionano optical maps
The islands are the combined result of scaffolding the individual BAC pool assemblies using both Bionano maps (546 maps covering 746 Mb) and sequence alignments

Summary

Introduction

Numerous scaffold-level sequences for wheat are 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. Other trait components contributing to grain yield such as grains per spike and vernalization requirements, as discussed in [5, 10], are located in the same region on chromosome 7A, and together they define an important candidate target region for finishing. Another region contributing to grain quality (grain fructan content [16]) provides a second target region. Manual annotation was performed based on the automated annotations [1] (RefSeq annotation v1.1), using alignments of available RNA-seq data [3, 18] to ensure gene models were consistent with transcriptome evidence

Methods

Results

Discussion

Conclusion