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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #325305

Title: Beta vulgaris crop types: Genomic signatures of selection (GSS) using next generation sequencing of pooled samples

item GALEWSKI, PAUL - Michigan State University
item McGrath, Jon

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/8/2016
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: 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 and suggesting that selection directly affected many genes across the genome. Allele frequency variation 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 were aligned to the RefBeet1.1 genome assembly, used to evaluate nucleotide diversity (p), inbreeding coefficients (F), and population differentiation (Fst), and these measures were plotted against the RefBeet1.1 chromosomes. Positive and balancing selection was 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.