Differential gene expression analysis of strawberry cultivars that differ in fruit-firmness

Firmness is an important selection criterium in the breeding of fruit, including strawberry (Fragaria x ananassa Duch.). Clear differences in fruit-firmness are observed between cultivars. In order to identify candidate genes which might be associated with such textural differences, gene expression levels were compared for a soft and a firm cultivar (cv. Gorella and cv. Holiday, respectively). DNA-microarrays representing 1701 strawberry cDNAs were used for simultaneous hybridization of two RNA populations derived from red ripe fruit of both cultivars. In total 61 clones (3.6% of the total cDNAs on the arrays) displayed differential expression, including 10 clones (8 different ones) which showed homology to cell wall related genes in the public databases. The results from the microarray experiments were further confirmed by RNA gel blots, which were also used to examine gene expression in a third cultivar, Elsanta, showing an intermediate texture phenotype (offspring of a cross between Gorella and Holiday). Interestingly, two genes encoding proteins catalysing successive reactions in lignin metabolism (cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase) showed the highest difference in expression level.