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

IWGSC

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number112
JournalGenome Biology
Volume19
Issue number1
DOIs
StatePublished - 17 Aug 2018

Bibliographical note

Funding Information:
Australian Government Department of Industry, Innovation, Science, Research and Tertiary Education (funding agreement ACSRF00542), BioPlatforms Australia (BPA) and Grains Research Development Corporation (agreement UMU00037) are thanked for funding the chromosome 7A project. CSIRO Plant Industry, Australia, funded the establishment of the MAGIC molecular genetic map. Agriculture Victoria Research funded bioinformatics capacity and infrastructure. The CENH3 antibody/cytological studies were supported by National Science Foundation (NSF) grant contract 1338897. The work of FC was supported by the INB (“Instituto National de Bioinformatica”) Project PT13/0001/0021 (ISCIII -FEDER). Chromosome flow-sorting, construction of BAC libraries and Bionano maps were partially supported by Czech Ministry of Education Youth and Sports (award LO1204 from the National Program of Sustainability).

Funding Information:
The authors are grateful to DM Appels for her dedication in establishing the early molecular genetic maps for chromosome 7A. Bernd Friebe is acknowledged for his guidance in the cytological studies of 7AS and 7AL. Etienne Paux is acknowledged for his guidance with the genetic and physical map alignments. Part of this work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. The authors are grateful to Professor Jia Jizeng for discussion in relation to the genome assembly of Aikang 58.

Publisher Copyright:
© 2018 The Author(s).

Keywords

  • Megabase-scale integration
  • Optical/physical maps Grain quality
  • Wheat sequence finishing
  • Yield

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Fingerprint

Dive into the research topics of 'Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome'. Together they form a unique fingerprint.

Cite this