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Recent advances in high-throughput genome sequencing technologies are now making the genetic dissection of the complex genome of cultivated strawberry easier. We sequenced Maehyang (short-day cultivar) × Albion (day-neutral cultivar) crossing populations using double digest restriction-associated DNA (ddRAD) sequencing technique that yielded 978,968 reads, 80.2% of which were aligned to strawberry genome allowing the identification of 13,181 high quality single nucleotide polymorphisms (SNPs). Total 3051 SNPs showed Mendelian segregation in F 1 , of which 1268 were successfully mapped to 46 linkage groups (LG) spanning a total of 2581.57 cM with an average interval genetic distance of 2.22 cM. The LGs were assigned to the 28 chromosomes of  Fragaria  ×  ananassa  as determined by positioning the sequence tags on  F. vesca  genome. In addition, seven QTLs namely,  qRU-5D, qRU-3D1, qRU-1D2, qRU-4D, qRU-4C, qRU-5C  and  qRU-2D2  were identified for runner production with LOD value ranging from 3.5–7.24 that explained 22–38% of phenotypic variation. The key candidate genes having putative roles in meristem differentiation for runnering and flowering within these QTL regions were identified. These will enhance our understanding of the vegetative vs sexual reproductive behavior in strawberry and will aid in setting breeding targets for developing perpetual flowering and profuse runnering cultivar.

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High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria × ananassa based on ddRAD-seq derived SNPs