Novel Strawberry (Fragaria spp) Gene Sequences That Affect Important Traits

Genomic information has increased exponentially from valued crop plants, revealing orthologs of many genes with demonstrated functions in model systems.  However, many genes defy convenient classification, as they lack conspicuous sequence homology or functional motifs that may imply function. One critical challenge for science is to connect the extensive suite of unknown, hypothetical or predicted genes to their biological functions. With a sequenced strawberry (Fragaria vesca) genome in-hand and substantial coverage from transcriptome information, novel, expressed sequences have been identified and assessed for in planta function using transgenic technology.  Four novel sequences have been studied that directly affect traits relevant to horticultural characteristics.  The first sequence encodes a WD-repeat protein that upon RNAisuppression transforms the perennial strawberry into an annual growth habit.  Leaves are dark and prone to atypical shape. The plant dies shortly after flowering, yet runners remain viable to perpetuate the genotype.  The second sequence maintains a predicted lucine-zipper motif, and upon suppression with RNAi leads to plants with longer pedicles that bear additional fruit.  The third sequence possesses a homeodomain and vague similarity to a kiwi allergen.  When suppressed with RNAi, the resulting plant produces fruits that are significantly larger than vector-only controls.  The final sequence does not encode a protein.  Instead it appears to represent a transcript with no open reading frames or strong secondary structure, and at first glance seems to be an artifact of cloning. However, it is expressed, and RNAi suppression dramatically alters canopy architecture, leading to an open configuration desired by breeders and growers for effective fungicide application.  These four sequences, although uncharacterized in model systems, represent conspicuous examples of why it is important to perform in planta functional studies to discover the functions of novel regulators in systems important to agriculture.  Together these sequences affect plant attributes desired by industry and may simultaneously help define new molecular mechanisms that contribute to the quality of valuable plant products.