New DArT markers for oat provide enhanced map coverage and global germplasm characterization

Authors: TINKER, NICHOLAS; KILIAN, ANDRZEJ; Rines, Howard; BJORNSTAD, ASMUND; HOWARTH, CATHERINE; Jannink, Jean-Luc; Anderson, Joseph; ROSSNAGEL, BRIAN; WIGHT, CHARLENE; STUTHMAN, DEON; SORRELLS, MARK; SCOLES, GRAHAM; ECKSTEIN, PETER; OHM, HERBERT; Jackson, Eric; TUVESSON, STINE; KOLB, FREDERIC; MOLNAR, STEPHEN; OLSSON, OLOF; Carson, Martin; CEPLITIS, ALF; Bonman, John; FEDERIZZI, LUIZ CARLOS; LANGDON, TIM

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/16/2008
Publication Date: 1/21/2009
Citation: Tinker, N.A., Kilian, A., Rines, H.W., Bjornstad, A., Howarth, C.J., Jannink, J., Anderson, J.M., Rossnagel, B.G., Wight, C.P., Stuthman, D.D., Sorrells, M.E., Scoles, G.J., Eckstein, P.E., Ohm, H.W., Jackson, E.W., Tuvesson, S., Kolb, F.L., Molnar, S.J., Olsson, O., Carson, M.L., Ceplitis, A., Bonman, J.M., Federizzi, L., Langdon, T. 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. Biomed Central (BMC) Genomics. 10(39):1471-2164.

Interpretive Summary: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of common markers on different genetic maps, and by the difficulty of conducting whole-genome analysis using high throughput markers. In this study we developed, characterized, and applied a large set oat genetic markers based on Diversity Array Technology (DArT). The study resulted in the discovery of over 2000 markers that were variable among the oat lines used. Using the Kanota x Ogle recombinant inbred line population, 1010 new markers were mapped, improving coverage relative to the previous map. DNA sequence was obtained for 2600 marker probes. Based on probe sequence and marker scores, some markers were found to be redundant. A set of 1295 non-redundant markers was used to analyze genetic diversity in 182 cultivated oat lines of world-wide origin. The results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to major geographical regions where oat breeding has occurred. Minor clusters revealed groups that were often related to known pedigree structure. These results, together with future genetic discoveries enabled by DArT markers, will allow greater precision in directed breeding of superior oat cultivars, and maintenance of oat genetic diversity.

Technical Abstract: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of common markers on different genetic maps, and by the difficulty of conducting whole-genome analysis using high throughput markers. In this study we developed, characterized, and applied a large set oat genetic markers based on Diversity Array Technology (DArT). 19,000 genomic clones were isolated from pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays to identify over 2000 polymorphic markers for use in this study, and 2700 potentially polymorphic markers for use in future studies. DNA sequence was obtained for 2573 clones, and was assembled into a non-redundant set of 1770 contigs and singletons. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the previous Kanota x Ogle map. A set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of world-wide origin. The results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to major geographical regions where oat breeding had been active. Secondary clusters revealed groups that were often related to known pedigree structure. These results, together with future genetic discoveries enabled by DArT markers, will allow greater precision in directed breeding of superior oat cultivars, and maintenance of oat genetic diversity.