TY - JOUR
AU - Jackson, Eric
AB - 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 subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, 
TI - Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology
JF - BMC Genomics
DO - 10.1186/1471-2164-12-77
DA - 2011-01-27
UR - https://www.deepdyve.com/lp/springer-journals/model-snp-development-for-complex-genomes-based-on-hexaploid-oat-using-5tam1ZjuNu
SP - 1
EP - 15
VL - 12
IS - 1
DP - DeepDyve
ER -