Map Construction and Black Spot Resistance QTL Detection in Diploid Rose

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 (QTL) 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 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 thousands of informative 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. Fifteen 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’, ‘Sweet Chariot’ and ‘Little Chief’) were used for SNP detection. Their genomic DNA was digested using a methylation sensitive enzyme and the resulting fragments were sequenced using the Illumina Hiseq2500 platform. The sequencing reads were aligned to the strawberry V1.1 genome since the genomic sequence of rose is not yet available. The identified SNP markers were utilized to create individual genetic maps of each population and SNPs common to each population along with SSR (simple sequence repeat) markers were used to construct a diploid consensus map and identify markers associated with partial black spot resistance trait.

 

Keywords: Rosa, genotyping by sequencing, SNP marker, QTL, black spot resistance, Diplocarpon