SINGLE NUCLEOTIDE POLYMORPHISMS AND SIMPLE SEQUENCE REPEATS FOR ONION CULTIVAR IDENTIFICATION

Michael J. Havey, William Martin and Jernej Jakse

USDA-ARS and University of Wisconsin, Department of Horticulture, 1575 Linden Drive, University of Wisconsin, Madison, WI 53706. Phone: 608-262-1830; Fax: 608-262-4743; Email: mjhavey@wisc.edu.

Commercial onion production is based on open-pollinated and hybrid cultivars. Occasional mistakes at field planting and harvest or mislabeling of seed lots require grow outs in the appropriate environments to identify specific seed lots. These grow-outs are costly because they can significantly delay the movement of seed to market. The onion industry would benefit from a robust set of codominant, easily scorable molecular markers for cultivar identification. Large-scale sequencing of expressed sequences revealed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) are relatively abundant classes of codominant DNA markers in onion. SNPs exist as different individual nucleotides at specific places in the genome. SSRs exist as different numbers of short di or trinucleotide repeats. We evaluated elite commercial and public inbreds and populations for a set of SNPs and SSRs to establish the level at which these onion populations could be confidently discriminated.

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