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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research Unit

Title: Genome-wide characterization of microsatellites in Cucumis hystrix and in silico identification of polymorphic SSR markers

Authors
item Yang, Luming -
item Weng, Yiqun

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2013
Publication Date: January 13, 2014
Citation: Yang, L., Weng, Y. 2014. Genome-wide characterization of microsatellites in Cucumis hystrix and in silico identification of polymorphic SSR markers [abstract]. Plant and Animal Genome Conference. Paper No. P689.

Technical Abstract: Cucumis hystrix (2n = 2x = 24, genome HH) is a wild relative of cucumber (C. sativus L., 2n = 2x = 14) that possesses multiple disease resistances and has a great potential for cucumber improvement. Despite its importance, there is no genomic resource currently available for C. hystrix. To expedite molecular marker-assisted introgression of C. hystrix chromatins into cucumber genetic background and construct a linkage map for C. hystrix, we performed low-coverage whole genome sequencing of two accessions (WI7001 and WI7002) of the C. hystrix genome by Illumina Hi-Seq2000. De novo assembly generated 1, 282, 234 contigs with an average size 232 bp for WI7001 and 1, 352, 133 contigs with an average size 231 bp for WI7002. Genome-wide survey of microsatellites identified 128, 257 and 117, 711 microsatellites from the WI7001 and WI7002 contig assemblies, respectively. While SSRs with tetra nucleotide motifs were the most frequent, those with dinucleotide motifs had the most repeat units. A subset of 284 SSRs with high number repeat motifs from WI7001 and WI7002 were selected and primers were designed for in silico PCR using contig assembly from both accessions as the templates and 215 (84%) of them were empirically validated in polyacrylamide gel electrophoresis. In contrast, among 89 randomly selected SSR, only 28 (33%) were empirically polymorphic, suggesting that our in silico PCR strategy was a cost-effective and efficient way to identify polymorphisms SSR in the NGS assembly for marker development and genetic map construction.

Last Modified: 11/28/2014
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