15 trillion base pairs of beet DNA sequencing enables a genomic retrospective of 8 decades of breeding progress.

Abstract

The post-genomics era of sugar beet trait discovery and breeding is upon us, with the deployment of multiple high quality reference genome assemblies for sugar beet, other beet crop types, and crop wild relatives. Reference genomes like EL10 and RefBeet provide a scaffold on which to build a genomic understanding of the history of sugar beet domestication and improvement. In this study, we present population level whole genome resequencing of a broad panel of 196 beet germplasm spanning an 86 year history of public improvement efforts. The germplasm panel represents early public sugar beet cultivars, USDA-ARS pre-breeding lines, as well as accessions from table beet, fodder beet, and chard. DNA samples of 25 individual plants per accession were pooled together and sequenced to a target of 80 fold genomic coverage (average 75.9 gigabases per sample, minimum = 49.3 gigabases, maximum = 157 gigabases). Utilizing the new, highly contiguous and well-annotated reference genome EL10.2.2, various clustering statistics based on allele frequency datasets from the mapped pools help characterize the genomic history according to crop type and breeding location. Using sliding windows across the genome, diversity statistics such as Fst and Pi identify regions of the genome that differentiate crop types, disease resistance breeding targets, and breeding locations. Collectively, these genome resequencing resources represent a component of a tractable rare allele discovery pipeline for genes of interest. We envision that the integration of these resequencing datasets into BeetBase will provide the beet genetics community a new tool for mining germplasm for useful genetic diversity.