Haplotag: New GBS Software Facilitates Haplotype-Based GWAS in Hexaploid Oat

Genotyping-by-sequencing (GBS) is becoming an integral part of many plant genotyping projects. Haplotag is a population based GBS software that determines the proportion of sequence-tag-level haplotypes and selects the best model that fits the expectations of the population under investigation. In sequence tags that contain multiple SNPs, Haplotag can alternately report data either as haplotype calls or as individual SNP calls. Since multiple SNPs are often located on the same tag, and since only a subset of possible haplotypes are usually present in a population, the haplotype-based data represents the same genetic information using fewer degrees of freedom in a global association analysis. It is also possible that haplotype-based GWAS analysis may identify cryptic associations where an adapted allele is uniquely associated with an intermediate haplotype. The aim of this study was to compare GWAS using haplotype markers vs SNP markers. Results of this comparison suggest that haplotype-based GWAS analysis is more powerful than SNP-based GWAS, especially when error control is based on the stringent Bonferroni correction. An example of haplotype-based GWAS in flowering time and its hypothetical use in applied oat breeding will be illustrated.