From Diploid Avena Sequence to Hexaploid Genomics and Allele Discovery: Triple the Fun?

An Avena reference genome was constructed, based on approximately 40-fold sequencing coverage of the wild diploid Avena atlantica with map information provided by survey sequencing of selected progeny of a population of A. atlantica x A. strigosa. Homology evidence and gene prediction were used to annotate the assembly with gene models. Transcriptome data from eleven A. atlantica tissues was used to further catalogue gene content and expression. This provides an overview of a typical wild Avena genome and gives some indication of the specific pathways and adaptations that distinguish oat from other cereals. We are currently using this information to guide assembly of genomic information from the hexaploid oat A. sativa, and to identify markers and candidate genes for agronomically important traits in the oat crop. A novel chromosome sorting method has greatly improved the efficiency of our hexaploid sequencing and is being applied to the common parent in our Nested Association Mapping (NAM) population. Genotyping-by-sequence and survey sequencing of NAM progeny will allow mapping of the hexaploid assemblies, and simplify association of traits and candidate genes in this population. Developing grain transcriptomes of the NAM parents are also being used to examine variation in expression in the hexaploid. The combined sequence and genotyping resources shed light on the processes of oat domestication and will help access useful genetic variation from historic and wild material.