A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.

ABSTRACT:

Background

High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < approximately 300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript hybridization to expression arrays has been used for genotyping. Although rice is a fully sequenced model plant of medium genome size (approximately 400 Mb), there are a few examples of the use of rice oligonucleotide array as a genotyping tool.

Results

We compared the single feature polymorphism (SFP) detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip Rice Genome Array, using the rice cultivars with full genome sequence, japonica

SUBMITTER: Horiuchi Y 

PROVIDER: S-EPMC2885369 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature