The PERPETUAL FLOWERING locus: Necessary but insufficient for genomic prediction of runnerless and other asexual reproduction phenotypes in strawberry

Authors: BRUKENTAL, HILLEL - University Of California, Davis; BJORNSON, MARTA - University Of California, Davis; PINCOT, DOMINIQUE - University Of California, Davis; Hardigan, Michael; SHARMA, SADIKSHYA - University Of California, Davis; JIMENEZ, NICOLAS - University Of California, Davis; FAMULA, RANDI - University Of California, Davis; LOPEZ, CINDY - University Of California, Davis; COLE, GLENN - University Of California, Davis; FELDMANN, MITCHELL - University Of California, Davis; KNAPP, STEVEN - University Of California, Davis

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2025
Publication Date: 8/19/2025
Citation: Brukental, H., Bjornson, M.L., Pincot, D.D., Hardigan, M.A., Sharma, S., Jimenez, N.P., Famula, R.A., Lopez, C.M., Cole, G.S., Feldmann, M.J., Knapp, S.J. 2025. The PERPETUAL FLOWERING locus: Necessary but insufficient for genomic prediction of runnerless and other asexual reproduction phenotypes in strawberry. The Plant Genome. 18(3). Article e70086. https://doi.org/10.1002/tpg2.70086.
DOI: https://doi.org/10.1002/tpg2.70086

Interpretive Summary: Day neutral flowering, also referred to as perpetual flowing in strawberry, has revolutionized the global strawberry industry over the last 50 years by allowing year-round production outside of the normal short-day, photoperiod-dependent production season of traditional cultivars. The primary source of day neutral flowering was introgressed from a wild, high elevation ecotype discovered by UC Davis breeder Royce Bringhurst in the 1950s. This study genetically maps the underlying PFRU locus for day neutral flowering, tracks its progression the the strawberry pedigree from wild source to modern cultivars, and publishes a validated and predictive genetic marker that be used to select for day neutral floweing habit in breeding populations. This research will assist in breeding and development of improved day neutral strawberry cultivars, while providing both historic and genomic context to one of the most economically valuable genes found among modern small fruit crops.

Technical 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 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. Here we show that 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.