Applying Genotyping by Sequencing Technology on Rosa spp

Black spot 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 (QTLs) remain unidentified. Because of the interspecific nature and high heterozygosity in commercial roses the genetic information available on rose is limited. To effectively identify markers associated with the QTL(s) controlling black spot resistance, one needs abundant markers along the genome and careful phenotyping. The objective of this study is to utilize genotyping by sequencing technology to generate abundant single nucleotide polymorphism (SNP) markers for genetic linkage and QTL mapping. Thus far, rose seedlings and parents have been phenotyped for partial black spot resistance in the lab and the field, and an efficient protocol to extract high quality DNA for sequencing from rose leaves has been developed. Four diploid rose populations created from the crosses of black spot resistant breeding lines derived from R. wichuriana 'Basye's Thornless' with susceptible commercial cultivars ('Vineyard Song', 'Red Fairy', and 'Little Chief') were used for SNP detection. Their genomic DNA was digested using methylation sensitive enzymes and the resulting fragments were sequenced using the Illumina Hiseq 2500 platform. Based on preliminary data, about 89% to 91% of the sequencing reads were aligned to the rose contigs and around 50% of the reads were mapped to the strawberry genome, respectively. This SNP data along with SSR (simple sequence repeat) data will be further utilized to create a diploid consensus map and identify markers associated with the partial black spot resistance trait.