Developing a Genetic Map for Tetraploid Roses Using Genotyping-By-Sequencing

Roses are a popular ornamental plant found throughout the world.  Despite their popularity there are few genomics resources that have been developed for them.  This limitation, coupled with their complex auto-tetraploid genetics, makes the creation of genetic maps for marker assisted selection in breeding programs difficult.  Here, we detail a pilot experiment to generate genetic maps from 88 F1 siblings from parental material in Vineland’s landscape rose breeding program.  Genotyping-by-sequencing (GBS) is a low-cost technique to identify polymorphisms from a collection of individuals and genotype the population simultaneously using high-throughput short read sequencing technology.  We applied GBS to generate 70 million single-end sequencing reads from a PCR-reduced GBS library using an Illumina MiSeq instrument.  Over 1000 polymorphic positions were identified in the lines and used to construct genetic maps of rose.  Application of GBS to quantify allele dosages and construct consensus genetic maps of rose and the use of these maps to identify marker-trait associations will be discussed.