PLoS ONE (Jan 2013)

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

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

DOI
https://doi.org/10.1371/journal.pone.0058068
Journal volume & issue
Vol. 8, no. 3
p. e58068

Abstract

Read online

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.