Abstract
BackgroundGenomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT).ResultsApproximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure.ConclusionThese markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.
Highlights
Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers
Diversity Array Technology (DArT) marker development Before describing the results of the mapping and diversity analyses, we present a general account of DArT marker discovery in oat and a characterization of the clones on which these markers are based
Concerns regarding the stable inheritance of markers generated using PstI, a methylation sensitive enzyme, have been addressed in earlier work done on barley [25], where markers were stably inherited across developmental stages and environments
Summary
Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. As in other crop species, there is growing recognition of the need to identify patterns of global genetic diversity, and to use this information in concert with tools for genomic discovery and molecular breeding. Genetic diversity (and associated population structure) depends largely on historical patterns of deliberate and passive efforts to create improved crop varieties [3,4]. Patterns of diversity develop as a result of breeding objectives that are targeted toward specific adaptations and commercial uses. Both spring and winter forms of A. sativa exist, but the characteristics that define winter oat (requirement for vernalization and tolerance to freezing) are expressed to varying degrees, and many winter oat varieties can be grown as spring-seeded annuals. Most types of hexaploid oat are fully cross-fertile, and cross-hybridizations are made among different categories to varying degrees by different breeders
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
