A dense genetic map of tetraploid rose on the basis of the WagRhSNP AXIOM SNP array and build using a pipeline for genetic analyses in polyploids

Rose, as many other ornamental, vegetable and field crops, is tetraploid. This poses constraints in genetic analyses, due to the occurrence of multiple alleles at marker and trait loci and the existence of multiple allele dosages. Developments in marker discovery (next generation sequencing), genotyping (SNP arrays) and analysis (software for dosage scoring) now make it feasible to develop high-density molecular marker maps for the homologous chromosomes in tetraploids separately, and perform QTL analysis. We developed the WagRhSNP Axiom array based on sequences from tetraploid garden roses and cut roses, to be used for inheritance studies and genetic mapping. The array design can be used by all researchers working in rose. We have also developed a general strategy for mapping in polyploid crops including stringent error filtering, which we will also apply to other ornamentals, including tetraploid Alstroemeria and hexaploid Chrysanthemum. Using this strategy we have build genetics maps for cut and garden roses. They are based on the simplex:nulliplex, simplex:simplex and duplex:nulliplex segregating SNPs. The cut rose map contains a total of 2515 (parent P514) and 2762 (P867) SNP markers. Each linkage group has between 127 and 705 SNP markers. Twenty six of the 28 haplogroups (homologous chromosomes) are represented with 30-246 SNPs per haplogroup. Both maps enabled establishing that the predominant mode of inheritance is tetrasomic with a possible disomic inheritance in one chromosome. Furthermore, occurrence and distribution of double reduction is calculated, and a detailed overview of the synteny with the Fragaria vesca genome sequence is produced.