Oat genome browser and 3D multimodal image analysis of oat seeds

SNIC 2017/4-57


SNAC Small

Principal Investigator:

Nick Sirijovski


Lunds universitet

Start Date:


End Date:


Primary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)



Relative to other cereals such as rice, barley and wheat, very little is know about the genetics of oat. Cultivated oat (Avena sativa) is a hexaploid comprised of three diploid genomes (AACCDD). It has a 1C genome of 21 chromosomes with a total size estimated to 13Gb. The large genome size and polyploidy has meant that deciphering the genetics of cultivated oat has lagged behind other cereals. Recently, oat has received much attention due to well documented health benefits of consuming this ‘super food’, which in turn has lead to increased production of oat-based novel foods and ingredients e.g. dairy alternatives, beta-glucan extracts, and even meat substitutes. With the fast paced development of next generation sequencing technologies, it has now become possible and affordable to undertake genome sequencing of hexaploid oat using short read technology. As a part of the newly inaugurated ScanOats research center in Lund, we have sequenced the hexaploid oat genome to 260X redundancy, and the raw data will be assembled into mega-scaffolds and then psuedochromosomes. The assembled genome needs to be visualised in a user friendly manner, which will make complex characterisation/annotations more easily visualisable and subsequent human-curation possible. In addition to the oat genome we are imaging oat seeds using X-rays and neutrons to allow for complementary non-destructive analysis of structure and chemical composition, which we can inturn link with genotypic data. Contrast differences between the modes arise due to the differences in interaction with seed matter. Due to the high sensitivity to hydrogen, neutrons are useful for separating liquid water or hydrogenous phases from the underlying structure while X-rays resolve the solid structure. We have generated a large dataset on 8 genetically different seeds using simultaneous X-ray and neutron tomography. The 8 seeds were selected for their extreme differences in relative amounts (and ratios) of starch, oil, β-glucan, and protein. We also plan on generating a complementary set of NMR data for the exact same set of 8 seeds.