A microarray‐based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence

• DOI: 10.1111/j.1365-313x.2009.03828.x
• Publication Date: 2009-02-10T18:03:46Z
• Authors: Derek R. Drost; Evandro Novaes; Carolina Boaventu...; Catherine I. Bene...; Ryan S. Brown; Tongming Yin; Gerald A. Tuskan; Matias Kirst
• Keywords: Populus trichocarpa

Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently also revolutionized the genetic analysis segregating populations by genotyping thousands loci in a single assay. Although microarray-based approaches been successfully applied yeast several inbred plant species, their has not proven an outcrossing species with extensive diversity. Here we developed methods high-throughput such using pseudo-backcross progeny 154 individuals Populus trichocarpa P. deltoides analyzed long-oligonucleotide situ-synthesized microarray probes. Our resulted high-confidence genotypes 719 single-feature polymorphism (SFP) 1014 expression marker (GEM) candidates. Using these established microsatellite (SSR) framework map, produced high-density map comprising over 600 SFPs, GEMs SSRs. The abundance gene-based markers allowed us to localize 35 million base pairs previously unplaced whole-genome shotgun (WGS) scaffold sequence putative locations genome trichocarpa. A high proportion sampled scaffolds could be verified placement independently mapped SSRs, demonstrating un-utilized that can provide context map-based WGS reassembly. results substantial contribution continued improvement assembly, while feasibility highly heterozygous population. strategies presented are applicable mapping efforts all similarly levels