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

Authors: OLIVER, REBEKAH - General Mills, Inc; TINKER, NICHOLAS - Agriculture And Agri-Food Canada; Lazo, Gerard; Chao, Shiaoman; JELLEN, ERIC - Brigham Young University; Carson, Martin; RINES, HOWARD - University Of Minnesota; OBERT, DONALD - Limagrain Cereal Seeds; LUTZ, JOSEPH - General Mills, Inc; Shackelford, Irene; KOROL, ABRAHAM - University Of Haifa; WIGHT, CHARLENE - Agriculture And Agri-Food Canada; GARDNER, KYLE - Agriculture And Agri-Food Canada; HATTORI, JIRO - Agriculture And Agri-Food Canada; BEATTIE, AARON - University Of Saskatchewan; BJORNSTAD, ASMUND - Norwegian University; Bonman, John; Jannink, Jean-Luc; MITCHELL FETCH, JENNIFER - Agriculture And Agri-Food Canada; HARRISON, STEPHEN - Louisana State University; HOWARTH, CATHERINE - Aberystwyth University; IBRAHIM, AMIR - Texas A&M University; KOLB, FREDERIC - University Of Illinois; MC MULLEN, MICHAEL - North Dakota State University; MURPHY, J - North Carolina State University; OHM, HERBERT - Purdue University; ROSSNAGEL, BRIAN - University Of Saskatchewan; YAN, WEIKAI - Agriculture And Agri-Food Canada; MICLAUS, KELCI - Sas Institute, Inc; HILLER, JORDAN - Sas Institute, Inc; MAUGHAN, PETER - Brigham Young University; REDMAN-HULSE, RACHEL - Brigham Young University; ANDERSON, JOSEPH - Purdue University; Islamovic, Emir; JACKSON, ERIC - General Mills, Inc

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2013
Publication Date: 3/22/2013
Citation: Oliver, R.E., Tinker, N.A., Lazo, G.R., Chao, S., Jellen, E.N., Carson, M.L., Rines, H.W., Obert, D., Lutz, J.D., Shackelford, I., Korol, A.B., Wight, C., Gardner, K.M., Hattori, J., Beattie, A., Bjornstad, A., Bonman, J.M., Jannink, J., Mitchell Fetch, J.W., Harrison, S., Howarth, C.J., Ibrahim, A., Kolb, F.L., McMullen, M.S., Murphy, J.P., Ohm, H., Rossnagel, B.G., Yan, W., Miclaus, K.J., Hiller, J., Maughan, P.J., Redman-Hulse, R.R., Anderson, J.M., Islamovic, E., Jackson, E.W. 2013. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One. 8:e58068.

Interpretive Summary: 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.

Technical Abstract: For the first time in many years a comprehensive genome map for cultivated oat has been constructed using a combination of single nucleotide polymorphism (SNP) markers and validated with a collection of cytogenetically defined germplasm lines. The markers were able to help distinguish the three genomes (A, C, and D) found in this hexaploid oat species, Avena sativa. This genome does not currently have a completed genome sequence; however the SNP candidates were able to be ascertained from sequencing twenty different oat cultivars with high-throughput sequencing methods covering over 9 million sequences. Six mapping populations were tested with the SNP markers and each was able to resolve the 21 chromosomes associated with this 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.