The PERPETUAL FLOWERING Locus: Necessary But Insufficient for Genomic Prediction of Runnerless and Other Asexual Reproduction Phenotypes in Strawberry

Strawberry (Fragaria x ananassa) reproduces sexually through seeds and asexually through stolons. The ability to cost-effectively clonally propagate hybrid individuals on a large scale has profoundly 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, other than the photoperiod-dependent pleiotropic effects of PERPETUAL FLOWERING (PF), a dominant, yield-doubling gene introgressed from a wild relative that knocks out temperature-dependent photoperiod sensitivity and partially suppresses runnering. Herewe showthat runnering phenotypes are highly variable and heritable, ranging from runnerless to prolific and unrestrained in both short-day (pfpf) and day-neutral (PF_) plants. We physically mapped the PF locus to Mb 26.4-27.3 on chromosome 4B using high-density SNP haplotypes and historical recombination among 932 individuals. PF was the only runneringassociated locus uncovered by genome-wide association studies among diverse clonal genetic resources and progeny from narrow and wide crosses (1,537 individuals). However, PF explained only 22% of the genetic variance for runnering. Genomic-estimated breeding values for runnering were accurately estimated especially among runnerless to near-runnerless individuals. Genomic prediction accuracies were greater within than between populations, increased when corrected for PF, and are sufficient for implementing genomic selection. These results pave the way for enhancing the productivity of strawberry by creating runnerless cultivars for seed-propagation and near-runnerless and reduced runnering cultivars for clone-propagation through phenotypic or genomic selection. 1 CORE IDEASO_LIGenetic variation for runnering is substantial and heritable C_LIO_LIThe dominant PERPETUAL FLOWERING (PF) allele does not uniformly or ubiquitously suppress asexual reproduction C_LIO_LISubstantial wild donor DNA has persisted in day-neutral and summer-plant cultivars carrying the Wasatch PF allele C_LIO_LIThe accuracy of PF-corrected breeding values for runnering are sufficient for implementing genomic selection C_LIO_LIStrawberry productivity can be improved by introducing cultivars with runnerless or near-runnerless phenotypes C_LI