The size and complexity of the oat genomes (Avena L., x = 7) have made genetic studies, including the discovery of molecular markers, difficult. Recent attention to these species has resulted in the development of many DArT -based markers in the tetraploid A. magna Murphy et Terrill (2n = 28, CCDD genomes), along with numerous RFLP's, SSR's, DArT's, and EST-based SNPs in hexaploid A. sativa L. (2n = 42, AACCDD). Here we report the first SNP markers for tetraploid oat based on genome reduction and high-throughput pyrosequencing in two inbred lines of A. magna: A-169 (wild) and Ba 13-13 (domesticated). Initially, the genomes were reduced using restriction digests with EcoRI and BfaI and sequenced to produce 706,426 reads for both genotypes that were subsequently assembled into 57,048 contigs with an average read length of 345 bp. Comparisons of the contigs between the two lines resulted in the detection of 31,304 in silico SNPs. High Resolution Melt (HRM) and KASPar assays were used to validate 1,108 of these in silico SNPs across a panel of diploid, tetraploid, and hexaploid oats. Of the assays, 119 were validated using HRM and 384 using KASPar genotyping in the Fluidigm EP1 system. Both sets of assays were then mapped on a population of 117 F2:8 recombinant inbred lines (RILs) developed from the A-169 x Ba 13-13 cross. A map of the A. magna genome was then constructed. The markers and map provide a new set of genomic tools for tetraploid and hexaploid oat breeding and allow for tracking of genes controlling traits of economic importance and other interesting genes through the evolution of Avena.
College and Department
Life Sciences; Plant and Wildlife Sciences
BYU ScholarsArchive Citation
Redman, Rachel Rebecca, "Oat SNP Marker Discovery and Mapping Based on 454 Pyrosequencing of Genome-Reduced Avena magna Murphy et Terrell" (2011). All Theses and Dissertations. 3068.
SNP, pyrosequencing, Bio-Rad, Fluidigm, Avena, oat, genetic map, genome reduction