ARS | Publication request: Genome-wide identification and characterization of simple sequence repeat loci in grape phylloxera, Daktulosphaira vitifoliae

Submitted to: Genetics and Molecular Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 3, 2012
Publication Date: May 15, 2012
Citation: Lin, H., Islam, M., Ramming, D.W. 2012. Genome-wide identification and characterization of simple sequence repeat loci in grape phylloxera, Daktulosphaira vitifoliae. Genetics and Molecular Research. 11(2):1409-1416.

Interpretive Summary: Grape phylloxera, Daktulosphaira vitifoliae Fitch (Homoptera: Phylloxeridae) is a viticultural pest that specializes in feeding on grapevine (Vitis spp.). Since the 18th century, this pest had been introduced to most of grape growing regions worldwide causing a great economic loss. To better understand genetic diversity and reproductive mode of grape phylloxera populations, a genome-wide sequence search was performed to identify simple sequence repeat (SSR) loci in phylloxera genome. Based on genome sequence analyses, 1,524 SSR loci containing mono, di-, tri-, tetra-, penta- and hexanucleotide motifs were identified. The abundance and inherent variations in SSRs provide valuable information for developing SSR markers. This marker system will facilitate assessment of the genetic diversity and structure of phylloxera in agricultural and natural populations.

Technical Abstract: A genome-wide sequence search was conducted to identify simple sequence repeat (SSR) loci in phylloxera, Daktulosphaira vitifoliae (Fitch), a key grape pest throughout the world. Collectively, 1,524 SSR loci containing mono, di-, tri-, tetra-, penta- and hexanucleotide motifs were identified. Among them, trinucleotide repeats represent most abundant (34.4%) followed by hexanucleotide (20.4%) and di- (19.6%) repeats in phylloxera genome. Mono, tetra- and pentanucleotide repeats occurred in an order of 1.3%, 11.2% and 12.9%, respectively. The abundance and inherent variations in SSRs provide valuable information for developing molecular markers. The high levels of allelic variation and codominant features of SSRs make this marker system a useful tool for genotyping, diversity assessment and population genetic studies of reproductive characteristics of phylloxera in agricultural and natural populations.