Genotyping by sequencing of a barley mapping population

Abstract We explored the use of genotyping by sequencing on a recombinant inbred line population (GPMx) derived from a cross between the 2-row barley cultivar Golden Promise (ari-e.GP/Vrs1) and six-rowed cv. Morex (Ari-e/vrs1) to map the dwarfing gene Ari.e to a small region on chromosome 5H using continuous height data as a quantitative trait. We also investigated a possible interaction between ari.e-GP and the spike architecture gene Vrs1 which has previously been shown to affect tillering. Background Barley cultivars in north western Europe largely contain either of two dwarfing genes; Denso on chromosome 3H, a presumed ortholog of the rice green revolution gene SD1, or Ari.e on chromosome 5H. A recessive mutant allele of the latter gene, ari.e-GP, was introduced into cultivation via the cv. Golden Promise that was a favourite of the Scottish malt whisky industry for many years and is still used in agriculture today. Results Using high density GBS mapping data and phenotypic data we show that alternative alleles of Vrs1 have no influence on plant height and that ari.e-GP maps to a small genetic interval on chromosome 5H. This location is supported by analysis of nearly isogenic lines containing the ari.e-GP allele. We use the GBS sequence tags to populate the region with sequence contigs from the recently released physically and genetically integrated genome sequence assembly as a step towards gene identification. Conclusions GBS was an effective approach to rapidly and relatively cheaply construct a genetic map of the GPMx population that was suitable for genetic analysis of row type and height traits, allowing us to precisely position ari.e-GP on chromosome 5H. In our hands, the GBS data was more complex to handle than other data types but did directly provide linked SNP markers for subsequent higher resolution genetic analysis.