Rapid trait mapping and characterization with purpose-built genome assemblies.

Abstract

Genomics has revolutionized plant breeding in the past decade and continues to rapidly shift the definition of state-of-the-art of the field. The adoption of genomics-assisted methods in both public and private sugar beet breeding efforts has been substantially bolstered by the release and continued updates of both the RefBeet and EL10 sugar beet genome assemblies. These two foundational reference genomes for sugar beet have enabled wide-scale adoption of high throughput genotyping and whole genome sequencing to study population genetics, resistance trait discovery and characterization, and domestication. The rapid advancement of sequencing technology, coupled with plummeting sequencing costs, have democratized plant de novo genome assembly. In this talk, I present examples of how three new beet genome assemblies that were built to mine specific traits of interest from specific genotypic backgrounds to specifically avoid reference genome bias. These examples each represent a new, tractable and affordable approach for the rapid mapping of traits of interest from any line of sugar beet or crop wild relative. Each of the three genome assemblies, two from Beta vulgaris and one from Patellifolia procumbens, are chromosome scale and fully phased. All three assemblies are the most complete and contiguous assemblies to date, and are enabling the beginnings of pan-genome analyses in beet, as well as shedding light on the genome biology and evolutionary history of the Betoideae subfamily.