Development of molecular markers for the early detection of scion roots in Shiranuhi Mandarin hybrid and other citrus cultivars

Abstract Recently, scion rooting at the grafted region of Poncirus trifoliata rootstocks has been found to decrease fruit setting and quality. Under cultivation conditions, the identification of scion-rooted Shiranuhi mandarin hybrid [( Citrus unshiu Marcov. × C. sinensis Osbeck) × C. reticulata Blanco] trees is difficult. Therefore, we aimed to develop a novel method for rapid and accurate identification of scion roots based on sequence-related amplified polymorphism (SRAP) in combination with a sequence-characterized amplified region (SCAR) marker. The genomic DNA was extracted from the normal rootstocks of P. trifoliata and scion roots of Shiranuhi. The sequence of amplified DNA fragments from scion root samples was analyzed using SRAP F4 and R15 primer combination, and was used to construct nine combinations of SCAR primers. Five markers (P1, P2, P3, P4, and P6) were obtained, of which SCAR-P3 presented the best results. We also efficiently screened the scion roots in Kiyomi and Settokka. These SCAR markers accurately identified scion rooting in Shiranuhi mandarin hybrid and other citrus cultivars, thus allowing the implementation of improved cultivation techniques to ensure normal fruit setting. The proposed method can also be applied to control the damage caused by scion rooting in other Citrus cultivars.