A SNP Genotyping Array for Hexaploid Oat

Nicholas A. Tinker, Shiaoman Chao, Gerard R. Lazo, Rebekah E. Oliver, Yung-Fen Huang, Jesse A. Poland, Eric N. Jellen, Peter J. Maughan, Andrzej Kilian, Eric W. Jackson
2014 The Plant Genome  
Recognizing a need in cultivated hexaploid oat (Avena sativa L.) for a reliable set of reference SNPs, we have developed a 6K BeadChip design containing 257 Infinium I and 5,486 Infinium II designs corresponding to 5,743 SNPs. Of those, 4,975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1,100 samples from six
more » ... RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3,500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party. Oat is an important cereal crop grown throughout most of the world. In cultivated hexaploid oat (Avena sativa L.), as in most other crop species, there has been considerable interest in developing efficient SNP genotyping methods to facilitate genomic discovery and molecular breeding. Discovery and application of SNPs in a hexaploid species is challenging due to the presence of homoeologous gene copies. Many putative SNPs are later found to be inter-locus variants (homeo-SNPs), and true intra-locus SNPs may be difficult to assay due to the confounding presence of homoeologous loci. Nevertheless, successful SNP assays in oat can be developed (Oliver et al., 2011) and a first-generation SNP array has been used to develop a physically anchored consensus map in oat (Oliver et al., 2013). The objectives of the present communication are to report the expansion of this SNP array, to evaluate its performance, and to formally announce its public availability. In addition, we report an annotation of the SNPs and the loci that they represent, we share lessons learned during the assay development, and we evaluate a new cluster-based method for calling SNP genotypes in a polyploid. Materials and Methods Plant materials Details of 20 oat lines used for cDNA sequencing and SNP discovery are described by Oliver et al. (2011) . Briefly, tissues from roots, shoots, pistillate structures, and mature embryos from 20 diverse oat varieties were pooled for cDNA library construction and sequencing. These 20 varieties were included within a set of 109 diverse varieties and a set of 390 recombinant inbred lines (RILs) from six mapping populations used by Oliver et al. (2013) for SNP validation
doi:10.3835/plantgenome2014.03.0010 fatcat:mfzftbs32racfjnft6fzgrjlfi