Beta vulgaris Crop Types: Genomic Signatures of Selection (GSS) Using Next Generation Sequencing of Pooled Samples

Beta vulgaris crop types represent highly diverged populations with distinct phenotypes resulting from long-term selection. Differential end use in the crop types includes: leaf quality (chard/leaf beet), root enlargement and biomass, (table beet, fodder beet, sugar beet), and secondary metabolite accumulation (sugar beet, table beet). Many of the defining features of the crop types are highly reproducible across environments suggesting that selection directly affected many genes across the genome. Variation in allele frequency among crop type populations provides a means to detect GSS and thus identify genic regions influencing some economically important traits. We sequenced six populations representing four of the B. vulgaris crop types by pooling 25 individuals per population, created PCR-free libraries, and sequenced each population to ~100X depth. Reads aligned to the RefBeet1.1 genome assembly were used to evaluate nucleotide diversity (π), inbreeding coefficients (F), and population differentiation (Fst). These measures were plotted against the RefBeet1.1 chromosomes and regions under positive selection were evaluated across each crop type genome and functional annotations for genes underlying the regions of interest were extracted. Understanding the function and ontology of genes under selection and their role in producing crop type variation is the primary impetus for this work.