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

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 runnering associated locus uncovered by genome-wide association studies among diverse clonal genetic resources and progeny from narrow and wide crosses (1,537 individuals). We found that PF explained 22% of the genetic variance for runnering and was beneficial but insufficient for predicting runnering phenotypes. 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. DataThe phenotypic and genotypic data and supplemental material for these studies are available in the online supplements associated with this article. Supplemental File S1. Origin years, species, pedigrees, flowering habit classifications, runner score phenotypic means, and AX-184947290 SNP genotypes for $n = 932$ octoploid strawberry diversity panel (SDP) individuals. The SDP included 15 F. chiloensis, 24 F. virginiana, and 893 F. x ananassa clonally propagated individuals. SDP individuals were classified as short-day (SD = 0) or day-neutral (DN = 1). The runner scores of SDP individuals were recorded on clonally propagated plants in Winters, CA using an ordinal scale, where 1 = runnerless, 2 = weak runnering, 3 = intermediate runnering, 4 = strong runnering, and 5 = extreme runnering. The runner score estimated marginal means (EMMs) of SDP individuals were estimated from r = 1.92 observations, where r is the harmonic mean number of observations per individual (the data were unbalanced and some individuals were observed only once). Supplemental File S2. The physical positions of 50K and 850K Axiom array SNPs corroborated by genetic mapping. SNPs were physically anchored to the 'Camarosa' (FaCA1; \cite{edger2019origin}; https://phytozome-next.jgi.doe.gov/info/Fxananassa_v1_0_a1) and ‘UCD Royal Royce’ (FaRR1; https://phytozome-next.jgi.doe.gov/info/FxananassaRoyalRoyce_v1_0) genomes in silico. Chromosomes were numbered using the nomenclature of \cite{hardigan2020genome} and cross-referenced to the nomenclature of \cite{edger2019origin}. This database includes the physical positions of SNPs identified by BLAST in the 'Camarosa' and 'Royal Royce' genomes, DNA sequences of the SNP probes, chromosome assignments and physical positions of SNPs corroborated by genetic mapping, and associated information. Supplemental File S3. A Rosetta stone for cross-referencing linkage group and chromosome nomenclatures in octoploid strawberry. This database includes several previously published chromosome nomenclatures \citep{tennessen2014evolutionary, edger2019origin, hardigan2020genome} and the chromosome nomenclature proposed by \cite{session2023transposon}. Supplemental File S4. Pedigrees, runner count phenotypes, and AX-184947290 SNP genotypes for n = 87 seed-propagated 17C321P015 x 55C032P001 F2 and n = 183 seed-propagated 17C321P015 x 'UCD Royal Royce’ F2 progeny observed 26 March, 9 April, 22 April, 6 May, 20 May, 3 June, and 6 July 2023 in Davis, CA (the respective photoperiods on those dates were 12.3, 13.0, 13.3, 14.1, 14.3, 14.1, and 14.5 hr). Four F2 families (21S950, 21S951, 21S952, and 21S953) were developed by self-pollinating runnerless to near-runnerless F1 individuals (19A907P022, 19A907P024, 19A908P012, and 19A908P053) originating in 17C321P015 x 55C032P001 and 17C321P015 x 'UCD Royal Royce’ full-sib families (Table \ref{tab: parents}). Supplemental File S5. Pedigrees, runner count, runner score, and inflorescence count phenotypes, and AX-184947290 SNP genotypes for 372 seed-propagated full-sib progeny observed 1 May, 1 June, and 1 July 2024 in Winters, CA (the respective photoperiods on those dates were 13.5, 14.4, and 14.5 hr). The population included nine full-sib families developed from crosses among 13 elite UC parents. Supplemental File S6. Haplotypes for 51 phased SNPs among 808 SDP individuals. This database includes 1,606 0,1-coded haplotypes among 808 SDP individuals classified as either short-day (SD = 0) or day-neutral (DN = 1). Supplemental File S7. Graphical genotypes for 50K Axiom array-genotyped SNPs segregating between Mb 25.0 and 30.4 on chromosome 4B in 17C321P015 x55C032P001 and 17C321P015 x 'UCD Royal Royce’ F2 families. This database includes runnering phenotypes, SNP genotypes, and the ordered physical positions for 140 SNP loci among 279 individuals within four F2 families (21S950, 21S951, 21S952, and 21S953). Colors in file represent putative PF genotypes/haplotypes (green) and putative SD genotypes/haplotypes (orange). Supplemental File S8. Genotypes and haplotypes for 15 SNPs associated with the \textit{PF} locus on chromosome 4B among selected samples of three individuals each from an 17C321P015 x 'UCD Royal Royce’ F2 family (21S950) and two 17C321P015 x 55C032P001 F2 families (21S952 and 21S953). The SNPs spanned bp 26,389,744 (AX-184068183) to bp 27,597,497 (AX-184160850). Colors in file represent putative PF genotypes/haplotypes (green) and putative SD genotypes/haplotypes (orange). Supplemental File S9. The predicted functions of 173 annotated genes spanning bp 27,597,497 to 27,418,663 on chromosome 4B in the 'UCD Royal Royce' reference genome (FaRR1; https://phytozome-next.jgi.doe.gov/info/FxananassaRoyalRoyce_v1_0). Figures Supplemental Figure S1. Manhattan plots depicting the photoperiod-dependent effect of the PF locus on runner count among 270 F_2 progeny phenotyped between 26 March and 6 July 2022 in Davis, CA. F\textsubscript{2} individuals were genotyped with an Axiom 50K SNP array. Manhattan plots are shown for genome-wide association studies of phenotypes observed (A) 26 March (12.3 hr), (B) 9 April (13.0 hr), (C) 22 April (13.3 hr), (D) 6 May (14.1 hr) (E) 20 May (14.3 hr), (F) 3 June (14.1 hr), and (G) 6 July (14.5 hr) among 17C321P015 x 'UCD Royal Royce' and 17C321P015 x 55C032P001 F_2 progeny. Supplemental Figure S2. Synteny of REPRESSOR OF GA1 (RGA1) homoeologs on chromosome 4 in the A, B, C, and D genomes of octoploid strawberry (F. x ananassa) and A genome of woodland strawberry (F. vesca). The ortholog identified in F. vesca (FveRGA1) by \cite{caruana2018suppressor} is shown below F. x ananassa chromosome 4 haplotypes. Homoelogs found in the octoploid are identified by the prefix Fxa. Homology was calculated using GENESPACE \cite{lovell2022genespace}, and the synteny plot was generated using JCVI \cite{tang2024jcvi}. The synteny plot was developed using genes annotated in the haplotype-phased assemblies of the 'UCD Royal Royce' genome, a day-neutral F. x ananassa cultivar (https://phytozome-next.jgi.doe.gov/info/FxananassaRoyalRoyce_v1_0.)