Genetic Analysis of Tetraploid F1 Populations Using SNP Markers

Many ornamentals are polyploid. Genetic analysis using molecular markers is well established for diploid crops but until recently the tools for mapping and QTL analysis in tetraploids were not readily available. However, this is rapidly changing: next-generation sequencing enables the identification of large numbers of SNPs; array hybridisation generates large SNP marker data sets; and software for dosage scoring (fitTetra, Voorrips et al.,BMC Bioinform 12:172, 2011) allows efficient assignment of the tetraploid SNP genotypes of individuals.

We are generating a SNP data set for two F1 populations of rose and performing dosage scoring of the SNPs. Using the tetraploid dosage scores we will develop linkage maps, and subsequently work on QTL mapping of traits including frost tolerance for garden roses and flower colour, production traits and powdery mildew resistance for cut roses. In preparation for this work we developed software (PedigreeSim, Voorrips and Maliepaard,BMC Bioinform 13:248, 2012) for simulating marker data in a tetraploid crop, which models both bivalent and quadrivalent formation during meiosis and therefore also simulates double reduction (the situation where a gamete receives two copies of the same chromosome segment, which is only possible in polyploids). We present here the tetraploid meiosis and simulation process and the approach we developed for linkage mapping.