SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. Academic Article uri icon


  • A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n=6x=42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

published proceedings

  • PLoS One

altmetric score

  • 1.75

author list (cited authors)

  • Oliver, R. E., Tinker, N. A., Lazo, G. R., Chao, S., Jellen, E. N., Carson, M. L., ... Jackson, E. W.

citation count

  • 64

complete list of authors

  • Oliver, Rebekah E||Tinker, Nicholas A||Lazo, Gerard R||Chao, Shiaoman||Jellen, Eric N||Carson, Martin L||Rines, Howard W||Obert, Donald E||Lutz, Joseph D||Shackelford, Irene||Korol, Abraham B||Wight, Charlene P||Gardner, Kyle M||Hattori, Jiro||Beattie, Aaron D||Bjørnstad, Åsmund||Bonman, J Michael||Jannink, Jean-Luc||Sorrells, Mark E||Brown-Guedira, Gina L||Mitchell Fetch, Jennifer W||Harrison, Stephen A||Howarth, Catherine J||Ibrahim, Amir||Kolb, Frederic L||McMullen, Michael S||Murphy, J Paul||Ohm, Herbert W||Rossnagel, Brian G||Yan, Weikai||Miclaus, Kelci J||Hiller, Jordan||Maughan, Peter J||Redman Hulse, Rachel R||Anderson, Joseph M||Islamovic, Emir||Jackson, Eric W

editor list (cited editors)

  • Xu, M.

publication date

  • March 2013