Loss-of-function mutations in the fruit softening gene <i>POLYGALACTURONASE1</i> doubled fruit firmness in strawberry

Wildtype fruit of cultivated strawberry (<i>Fragaria</i> [Formula: see text] <i>ananassa</i>) are typically soft and highly perishable when fully ripe. The development of firm-fruited cultivars by phenotypic selection has greatly increased shelf-life, decreased postharvest perishability, and driven the expansion of strawberry production worldwide. Hypotheses for the firm-fruited phenotype include mutations affecting the expression of genes encoding polygalacturonases (PGs) that soften fruit by degrading cell wall pectins. Here we show that loss-of-function mutations in the fruit softening gene <i>POLYGALACTURONASE1</i> (<i>FaPG1</i>; <i>PG1-6A1</i>) double fruit firmness in strawberry. <i>PG1-6A1</i> was one of three tandemly duplicated PG genes found to be in linkage disequilibrium (LD) with a quantitative trait locus (QTL) affecting fruit firmness on chromosome 6A. <i>PG1-6A1</i> 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 LD with <i>PG1-6A1</i> that were positively correlated with fruit firmness and negatively correlated with <i>PG1-6A1</i> expression. An <i>Enhancer/Suppressor-mutator</i> (<i>En/Spm</i>) transposable element insertion was discovered upstream of <i>PG1-6A1</i> in mutant homozygotes that we hypothesize transcriptionally downegulates the expression of <i>PG1-6A1</i>. The <i>PG1-6A1</i> 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 <i>En/Spm</i> insertion and single nucleotide polymorphisms associated with the <i>PG1-6A1</i> locus.