A progress report for the oat genome project in ScanOats
We have now entered the genome era, where reference quality genomes from many different plant species are becoming readily available. Until recent years, large and complex genomes, such as oat, were cast into the too difficult and too expensive category. However, in January 2018 we achieved what seemed impossible only a few years earlier and assembled the first hexaploid oat genome using the short-read Illumina technology. Since then, ScanOats and international collaborators have strived to characterize the 21 chromosome DNA sequence in order to ultimately share a well-annotated reference quality oat genome with the international community in the form of full data access accompanied by a novel and enlightening research article.
The first step in any genome project is to assemble DNA sequences into complete chromosomes. After this, the meticulous annotation and down-stream analysis phase starts. A well-annotated oat genome is an absolute prerequisite to understanding what makes oat the healthy whole-grain cereal that we all know and love. Further, it is important to understand the genome landscape in terms of coding and non-coding regions, and how these regions influence the final grain quality in a specific oat variety. Such knowledge opens up for the development of molecular markers (specific DNA sequences) that greatly facilitate breeding of high-quality characters. On behalf of all the hard-working researchers involved in the oat genome project, we are pleased to announce that our upcoming research article about the first well-annotated hexaploid oat genome will be publically available in the very near future. This will be the first peer-reviewed publication ever on a well characterized hexaploid oat genome.
To our delight, PepsiCo recently announced the 21 chromosome DNA assembly of a North American oat variety (OT3098) using the long-read PacBio technology, and this was simultaneously made publically available via the Graingenes website. A direct comparison of the DNA sequence of our reference and OT3098 has revealed that both the Illumina and PacBio approaches have generated highly agreeable oat genome assemblies.
These achievements mark the beginning of a greater oat pangenome project (The international PanOat consortium) where upward of 20 carefully selected oat varieties will be assembled and compared to produce the Avena sativa pangenome. Clearly, this is an exiting time to be working on oats! Todays challenges faced by all oat breeders will be made easier by such a large collaborative project. Ultimately consumers stand to reap the benefits by gaining access to novel oat products derived from even better oat varieties developed via continued breakthroughs in the field of oat genomics.