Abstract

Strawberry (Fragaria ananassa) reproduces sexually through seeds and asexually through stolons. The ability to cost-effectively clonally propagate hybrid individuals on a large scale has shaped strawberry breeding and production practices. Despite the technical and economic importance of clonal propagation, little is known about the genetic regulation of runnering in strawberry, apart from the pleiotropic effects of PERPETUAL FLOWERING (PF), a dominant gene introgressed from a wild relative that abolishes temperature-dependent photoperiod sensitivity and incompletely and variably suppresses runnering. Here, we show that runnering phenotypes are heritable and highly variable in strawberry, ranging from runnerless to prolific in short-day (pfpf) and day-neutral (PF_) plants. The PF locus was physically mapped to Mb 26.4-27.3 on chromosome 4B and found to explain 22% of the genetic variance for runnering (78% of the heritability was missing). PF was the only runnering-associated locus identified by genome-wide association studies among diverse clonal genetic resources and progeny from narrow and wide crosses (1537 individuals). The pleotropic effect of PF on runnering was temporal, variable, and incompletely dominant. Genomic selection was found to be a viable strategy for modifying runnering phenotypes in strawberry. Genomic prediction accuracies ranged from 0.53 to 0.79 for runnering, were greater within than between populations, and increased when corrected for PF. Our study builds the foundation for improving the productivity of strawberry by developing runnerless cultivars for seed-propagation or reduced runnering cultivars for clonal-propagation through phenotypic or genomic selection.