DOI: 10.5061/dryad.k3j9kd5hk
title: Data from: Loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 doubled fruit firmness in strawberry

description: Wildtype fruit of cultivated strawberry (Fragaria x ananassa) are
 typically soft and highly perishable when fully ripe.  The
 development of firm-fruited cultivars by phenotypic selection has greatly
 increased shelf life, decreased post-harvest perishability, and driven the
 expansion of strawberry production worldwide.  Hypotheses for the
 firm-fruited phenotype include mutations affecting the expression of genes
 encoding polygalacturonases that soften fruit by degrading cell wall
 pectins.  Here we show that loss-of-function mutations in the
 fruit softening gene POLYGALACTURONASE1 (PG1-6A1) double fruit firmness in
 strawberry.  PG1-6A1 was one of three tandemly duplicated
 polygalacturonase genes found to be in linkage disequilibrium with a
 quantitative trait locus affecting fruit firmness on chromosome 6A.
 PG1-6A1 was strongly expressed in soft-fruited (wildtype) homozygotes and
 weakly expressed in firm-fruited (mutant) homozygotes.
  Genome-wide association, quantitative trait transcript, DNA
 sequence, and expression-QTL analyses identified genetic variants in
 linkage disequilibrium with PG1-6A1 that were positively correlated with
 fruit firmness and negatively correlated with PG1-6A1 expression.
  An Enhancer/Suppressor-mutator (En/Spm) transposable element
 insertion was discovered upstream of PG1-6A1 in mutant homozygotes that we
 hypothesize transcriptionally downegulates the expression of PG1-6A1.
  The PG1-6A1 locus was incompletely dominant and explained 26-76%
 of the genetic variance for fruit firmness among phenotypically diverse
 individuals.  Additional loci are hypothesized to underlie the
 missing heritability.  Highly accurate, codominant genotyping
 assays were developed for modifying fruit firmness by marker-assisted
 selection of the En/Spm insertion and SNPs associated with the PG1-6A1
 locus.
description: # Loss-of-function mutations in the fruit softening gene
 *POLYGALACTURONASE1* doubled fruit firmness in strawberry
 [https://doi.org/10.5061/dryad.k3j9kd5hk](https://doi.org/10.5061/dryad.k3j9kd5hk) ## Description of the data and file structure **Supplemental Data S1:** Phenotypic data was collected from 85 individuals during two harvests in separate years at field sites in Santa Maria (SM) and Oxnard (OX), California. **Supplemental Data S2.** Phenotypic data from 460 individuals evaluated across two harvest periods under commercial field conditions in Ventura, California. **Supplemental Data S3.** Phenotypic observations from a greenhouse experiment involving 43 individuals over six separate harvests. **Supplemental Data S4.** Phenotypic measurements for 87 individuals from the UC Davis Strawberry Germplasm Collection were collected at the Wolfskill Experiment Orchard (WEO) in Winters, California, over two years and six harvest dates. **Supplemental Data S5**. Data on 152 one-year-old seed-propagated plants collected from the UC Davis Strawberry Germplasm Collection at the Wolfskill Experiment Orchard (WEO) were assessed during two harvest periods. **Supplemental Data S6.** Genotypic information for 49,483 SNP markers evaluated across 562 individuals, with genotypes encoded as -1, 0, or 1, representing AA, AB, and BB, respectively. **Supplemental Table S1.** A compilation of genotypes (Axiom® 50K array, GBS, and KASP markers), phenotypic averages, pedigrees, and passport data for 574 octoploid strawberry entries. **Supplemental Table S2**. GWAS results for fruit firmness in 85 individuals genotyped with an Axiom® 50K array, including SNP allele frequencies, regression coefficients, standard errors, and p-values. SNP positions are mapped to the Royal Royce reference genome. **Supplemental Table S3.**  Annotated genes within chromosome 6A (Mb 27,253,733-27,849,333) linked to *PG1-6A1* and a GWAS QTL for fruit firmness. Key SNPs from the Axiom® 50K array are AX-184953741, AX-184023221, AX-184726882, and AX-184210676. Gene functions and ontology annotations, based on the Royal Royce reference genome (FaRR V1) and TAIR, are included. **Supplemental Table S4.**  Details of 39 genes identified by quantitative trait transcript (QTT) analysis for fruit firmness, with statistical significance at p &lt; 0.005. **Supplemental Table S5.** Physical locations and functional annotations of 227 genes predicted to encode polygalacturonases (GO:0004650) in the octoploid strawberry genome, based on the Royal Royce reference genome. **Supplemental Table S6.**  Linkage disequilibrium (r) among variants linked to the *PG1-6A1* locus, analyzed in 43 individuals with long-read sequencing. \**Supplemental Table S7. **Results from genome-wide expression quantitative trait loci (eQTL) analysis of ripe fruit transcriptomes in 85 individuals genotyped with an Axiom® 50K array. The physical positions, regression coefficients, and false discovery rate (FDR)-adjusted *p*-values are tabulated for SNPs associated with statistically significant gene expression differences. **Supplemental Table S8.** Analysis of 37 SNPs in the *PG1-6A1* gene, including predicted effects based on nucleotide sequence comparisons and QTL statistics for fruit firmness in a population of 43 long-read sequenced individuals.  **Supplemental Table S9.**  DPrimer sequences for KASP markers targeting genetic variants in *PG1-6A1* and for qRT-PCR of *PG1-6A1*, PG1-6A2, and PG1-6D1. **Supplemental Table S10.** Genotypic data for 152 full-sibling individuals assessed for fruit firmness using four KASP markers in a field experiment conducted in Davis, California, in 2024. **Supplemental Fig. S1.**  Single nucleotide polymorphisms (SNPs) associated with fruit firmness variation in 460 genetically diverse individuals, visualized in a Manhattan plot based on the Royal Royce reference genome. **Supplemental Fig. S2.**  Heatmap showing log2-transformed expression levels of 17 polygalacturonase genes in ripe fruit of 85 individuals, including key paralogs and homoeologs related to a firmness QTL on chromosome 6A. **Supplemental Fig. S3.** Quantitative RT-PCR data comparing PG1-6A2 and PG1-6D1 expression across different fruit ripeness stages in cultivars with varying firmness phenotypes. **Supplemental Fig. S4.** (A)Visual representation of SNPs and INDELs associated with *PG1-6A1* in various cultivars, including (B) 'Royal Royce', (C) 'Mara des Bois', (D) Beaver Belle', and (E) 'ILE 02' . **Supplemental Fig. S5.** Fluorescence scatter plot illustrating allele discrimination for four KASP markers in a population of 92 octoploid strawberry individuals. **Supplemental Fig. S6.** Extended view of fruit firmness phenotypes across 500 strawberry accessions, including *F. chiloensis* and *F. virginiana* ecotypes, categorized by genotypic predictions of *PG1-6A1* alleles. **Supplemental Fig. S7.** qPCR efficiency analysis for DNA-binding protein and PG1 genes, showing optimal dilution thresholds for different fruit development stages.