Identification of a RAPD Marker Closely Linked to Fruit Color in Muscadine Grapes (Vitis rotundifolia)

Abstract

The major fruit color phenotypes in grapes are either white (including green, yellow, bronze etc.) or red (including pink, reddish) and black (including purple). Like other fruits, anthocyanin (Acy) pigments in the berry skin contribute to the colors of grapes. These water-soluble pigments are phenolic compounds as secondary metabolite and accumulated essentially in the epidermal cells of fruits. Seedling screening can be performed if a genetic marker for the fruit color is available. A F1 population of 82 progenies derived from a cross of two muscadine grape (Vitis rotundifolia) cultivars, `Summit' × `Noble', was used for tagging the gene determining the fruit color. `Noble' is a red grape while `Summit' is white. Segregation of berry color in the F1 population indicated that the red color is controlled by a single dominant gene. RAPD (Random Amplified Polymorphic DNA) technique and Bulk Segregant Analysis (BSA) was used for tagging the fruit color trait. A total of 350 oligonucleotide 10-mers were screened for polymorphisms between the red- and white-colored DNA pools (each pool was consisted of seven individual DNA samples). Two RAPD fragments linked to the target gene were identified and one of them, a 650-bp fragment completely co-segregated with the 56 progenies of red berries, while the white fruit progenies were absent of the RAPD fragment. The cosegregation data clearly indicated that the 650-bp RAPD fragment is tightly linked to the red fruit trait. The marker DNA was isolated from the agarose gel, cloned, and sequenced. A pair of 18-mers and 20-mers flanking the RAPD fragment were designed based on the sequencing information. The RAPD marker was reamplified in red-fruited muscadine grapes with this pair of universal primers.