Genome sequencing and assembly of CDC Fraser malting barley variety

Posted on 22.02.2021 | Last Modified 10.01.2022
Lead Researcher (PI): Aaron Beattie
Institution: University of Saskatchewan
Total WGRF Funding: $118,962
Co-Funders: None
Start Date: 2020
Project Length: 1 Year

To fully sequence and assemble the genome of barley variety CDC Fraser in order to enable breeders to better understand the genes impacting traits relevant to western Canadian barley production to allow for the identification of the unique and relevant presence/absence variation that is key to trait variability and improvement.

Project Summary:

Barley is a significant Canadian crop that provided approximately $3.6 billion in revenue to producers, maltsters and exporters in 2020, with a total contribution of $13.6 billion to the Canadian GDP. A high-quality genome sequence assembly for barley germplasm that is relevant to Canadian producers and end-users is important for downstream activities such as gene discovery, gene/allele diversity investigation and marker development, and complements breeding applications like marker-assisted and genomic selection. Ultimately, this leads to better varieties for the entire barley value chain. ‘CDC Fraser’ is representative of the distinct combination of malt quality, disease resistance and agronomic performance of Canadian barley. The purpose of this project was to obtain a fully sequenced and assembled genome of CDC Fraser.
Three different sequencing strategies were used to obtain over 781 billion base pairs of sequence data on CDC Fraser, representing 153x coverage of the 5.1 billion base pair barley genome. The sequence data was assembled into 47,000 scaffolds comprising over 4.2 billion base pairs with N50 and N90 sizes of 87 and 12 million base pairs, respectively. Assembly quality was very high based on identifying 96% complete sequences associated with a set of genes that are highly conserved across genera, with 94% of the genes being single copy. Assembly of the scaffolds into pseudo-chromosomes was accomplished by anchoring the scaffolds to the reference genome of the two-row variety Golden Promise. Excellent alignment across the seven barley chromosomes was achieved, with a larger amount of assembled sequence data incorporated and fewer gaps observed in the CDC Fraser genome assembly. The aligned genomes of CDC Fraser and ‘Golden Promise’ have been uploaded into the NRGene Interactive Genome Viewer and will be annotated with currently available, public gene transcript data.
The genome assembly of CDC Fraser is a resource that will be useful for several other projects including: 1) aiding the assembly of four other Canadian barley genomes under the current TUGBOAT project lead by AAFC, 2) confirmation of the presence and location of the Un8 loose smut resistance gene and cloning of sequence upstream from the Un8 gene containing the promoter region. This was useful for transgenic studies in which the Un8 gene was placed, along with its native promoter, into the susceptible variety Golden Promise, thus creating a resistant transgenic line, 3) a platform on which to annotate gene transcripts relevant to spot blotch resistance that will be identified under an on-going project, 4) a platform on which to annotate SNPs that were identified within Canadian germplasm under the CropSNP project led by Laval University, and which will be used to create a genotyping platform useful for genetic mapping studies and genomic selection work.
Ultimately, the assembly of the CDC Fraser genome is a resource that would enable breeders to better understand the genes impacting agronomic, disease and quality traits relevant to western Canadian barley production and will allow identification of the unique and relevant presence/absence variation that is key to trait variability (and improvement) in barley. This in turn permits more relevant genotyping to be done for use in marker-assisted and genomic selection that will accelerate variety improvement.