Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology.

ABSTRACT:

Background

Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat.

Results

Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subg

SUBMITTER: Oliver RE 

PROVIDER: S-EPMC3041746 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature