2018 ASHS Annual Conference

Although roses are the backbone of the ornamental plant industry, genetic studies in roses have been complicated by the lack of an available rose genome sequence. However, with the release of the Rosa chinensis sequence, new opportunities have arisen for rose genetics and breeding. Prior to the release of the diploid rose genome, we genotyped 15 inter-related diploid rose populations using genotype by sequencing (GBS) for single nucleotide polymorphisms (SNPs) using the Fragaria vesca genome as a reference and created an integrated consensus map for use in quantitative trait locus (QTL) discovery. This resulted in the discovery of 40-50,000 SNPs over the 15 populations with about 3,500 determined to be useful for the integrated consensus map created via JoinMap 4.1. To determine if the map could be improved after the release of the rose genome, the GBS reads were aligned with the rose genome and SNPs were called. This resulted in approximately 60-80,000 SNPs (depending on the family), which is significantly greater than the number of SNPs called when the Fragaria genome was used as a reference. These SNP calls were filtered and used to make a new integrated consensus map via JoinMap 5. The two maps were compared on the criteria of marker number, map length, mean distance between markers, and the largest distance between markers.