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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #340406
Title: Genome differentiation among Beta vulgaris crop type populations and its application in dissecting economically important phenotypes

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

Submitted to: Annual Beet Sugar Development Foundation Research Report
Publication Type: Research Notes
Publication Acceptance Date: 3/31/2017
Publication Date: 4/1/2017
Citation: Galewski, P., McGrath, J.M. 2017. Genome differentiation among Beta vulgaris crop type populations and its application in dissecting economically important phenotypes. Annual Beet Sugar Development Foundation Research Report. Denver, Colorado: Beet Sugar Development Foundation. [CD-ROM].

Interpretive Summary:

Technical Abstract: Four main crop types are recognized with Beta vulgaris: sugar, table, fodder, and leafy chard. Twenty-three populations composed of 25 individuals each were selected to represent the four recognized crop types and capture a wide range of phenotypic crop diversity. Allele frequencies for each population were used to calculate Global Pairwise FST. On average 61.84 +/- 12.22 GB of sequence data was produced per accession with an average coverage was 81.5X. Approximately 20% of the bases were discarded due to trimming low quality bases and adapters. A total of 14,654,485 variants were detected across all populations, 12,933,966 were classified as a single nucleotide variant (SNP) and of these 10,215,761 we bi-allelic. INDELs accounted for 1,720,519 or 11.7% of the variants detected. 2,718,205 were multi-allelic variants. Lineage specific/ crop type private variation showed the sugar beet crop type as having accumulated the most private variation, with 4,018 lineage specific variants. The distribution of private/ lineage specific variation in regards to local genome differentiation along Chromosome 3 appears to correlate with highly differentiated regions.