Genome-wide identification and expression analysis revealed cinnamyl alcohol dehydrogenase genes correlated with fruit-firmness in strawberry

BACKGROUND: Strawberry fruits are perishable with a short post-harvest life. Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis strengthening plant cell wall. A systematic characterization of strawberry CAD family is absent and their involvement in fruit firmness is largely elusive. OBJECTIVE: Current work aims for a genome-wide identification of CAD family and its expression correlation with fruit firmness in strawberry varieties. METHODS: A genome-scale identification and molecular characterization for CADs were performed in the commercial strawberry (Fragariaxananassa) and woodland strawberry (F. vesca). qPCR analysis of CAD homoeologs in three cultivars varying with fruit firmness revealed candidate CAD members positively correlated with lignin content and fruit firmness. RESULTS: A total of 14 and 24 CAD loci were identified in the genomes of F.vesca var. Hawaii4 and F. xananassa cv. Camarosa, respectively. Phylogenetic analysis supported a division of this family into three classes. Class I FvCAD each has four homoeologs in commercial strawberry, while those of Class II and Class III have only one or two homoeologs. Except for FvCAD2 and -6, there exits at least one pair of CADs sharing similar to 97% or above amino acid identity between F. vesca and F. xananassa. The flesh firmness and lignin content varied greatly among strawberry germplasm. Distinct dynamic changes in fruit lignin content were observed before the large green stage, but fruit firmness displayed a similar decrease profile during fruit development in three varieties. Of the eight genes detected in F.xananassa, FvCAD3 and -12 did not display a F. vesca-biased expression pattern during fruit development. FvCAD4 of Class I was expressed at levels positively correlated with variation in fruit lignin content at white stage. Transcript abundance of five Class II genes including FvCAD3, -8, -10, -11, and -12 was positively correlated with lignin content and fruit firmness, with FvCAD10 and -11 (FaCAD in previous publication) reaching an extremely significant correlation with the genetic variation in fruit firmness across three varieties. CONCLUSION: Strawberry Class II CADs were significantly correlated with the genetic variation in fruit firmness, which might expand the potential choices for improving strawberry shelf life.

Automated summary

This study identified CAD family in strawberries at the genome scale and found that Class II CADs were significantly correlated with the genetic variation in fruit firmness, potentially expanding options for improving strawberry shelf life.