The Development of a Dense SNP-Based Consensus Map and QTL Detection for Black Spot Resistance in Five Diploid Rose Populations

Black spot (BS) disease (Diplocarpon rosae (Lib.) Wolf) of rose is the most important leaf disease of garden roses in warm humid areas. Although the partial (horizontal) resistance to black spot has been shown to be moderately heritable, the responsible quantitative trait loci (QTL) remain unidentified. Because of the interspecific nature and high heterozygosity in commercial roses the genetic information available on rose is limited. We utilized genotyping by sequencing (GBS) technology to create abundant SNP markers. This was done with the use of a methylation sensitive restriction enzyme NgoMIV (G˅CCGCC) to construct the DNA template for three diploid rose populations segregating for resistance (derived from Rosa wichuriana) to the black spot fungus. The DNA fragments were sequenced using the Illumina Hiseq2500 platform and then aligned to the strawberry genome sequence to identify SNPs. Filtering the potential SNPs for informative polymorphism resulted in about 3500 SNPs to use in the consensus map construction. The consensus map was created by first developing individual maps for three populations, each with about 1,500 markers. Then the 677 SNPs and 14 SSRs bridge markers were used to link three individual populations. The anchor SSRs were used to determine the pseudo-chromosomes as defined in the current consensus map. In this diploid consensus map, the seven linkage groups (LGs) were covered with 3,527 markers resulting in a total length of 892.2cM for the diploid rose genome. The average distance between markers was 0.25cM. This is the first report of a high-density integrated consensus map for diploid roses (ICD). The high level of synteny between strawberry and diploid rose genome was revealed in this study. The analysis of the partial (horizontal) resistance to black spot as measured in a detached leaf assay among five diploid populations identified important QTLs for black spot resistance on various chromosomes.