Loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 doubled fruit firmness in strawberry

Authors: JIMÉNEZ, NICOLÁS - University Of California, Davis; BJORNSON, MARTA - University Of California, Davis; FAMULA, RANDI - University Of California, Davis; PINCOT, DOMINIQUE - University Of California, Davis; Hardigan, Michael; MADERA, MARY - University Of California, Davis; LOPEZ RAMIREZ, 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: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/6/2024
Publication Date: 11/19/2024
Citation: Jiménez, N.P., Bjornson, M., Famula, R.A., Pincot, D.D., Hardigan, M.A., Madera, M.A., Lopez Ramirez, C.M., Cole, G.S., Feldmann, M.J., Knapp, S.J. 2024. Loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 doubled fruit firmness in strawberry. Horticulture Research. 12(2). Article uhae315. https://doi.org/10.1093/hr/uhae315.
DOI: https://doi.org/10.1093/hr/uhae315

Interpretive Summary: Fruit firmness was an essential trait that had to be genetically improved through breeding in order to transform strawberry from a locally harvested and consumed berry without meaningful shelf life to a modern commercial horticultural crop. The University of California Davis pioneered the development of commercially improved strawberries with high firmness that could be shipped over long distances and stored for longer periods of time. This study successfully mapped the causal mutation in a polygalacturonase gene that was responsible for the shift in strawberry firmness and shelf life, tracked its movement through strawberry breeding lines through time, and provides an important resource for selectively incorporating high fruit firmness into genetically diverse strawberry germplasm.

Technical Abstract: Wildtype fruit of cultivated strawberry (Fragaria × 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/Suppresor-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.