An SSR Haplotype Linked to Muscat Flavor on Linkage Group 5 in Grapevine

Abstract

Inheritance of muscat flavor, a typical grape berry flavor, is controlled by several loci. A QTL in linkage group (LG) 5 was identified by several previous QTL analyses as a major muscat QTL. A total of 36 cultivars and a selection including muscat cultivars released in Japan were genotyped using four SSR markers: Nifts5-50910, Nifts5-50929, Nifts5-50937, and VVII52, located near QTL. We found that an SSR haplotype (LG5-Hap1) was harbored by all cultivars with muscat flavor. This haplotype was inherited from ‘Muscat of Alexandria’ to ‘Neo Muscat’ to ‘Kaiji’ to ‘Hakunan,’ and then to ‘Shine Muscat.’ Cultivars harboring LG5-Hap1 were also genotyped as muscat-type by the previously reported CAPS marker linked to the muscat trait. Overall, 145 grapevine plants that were produced by 75 crosses at NARO were divided into a group with muscat flavor and a group without the flavor. The ratios of selections with LG5-Hap1 were compared between the two groups. The proportion harboring LG5-Hap1 in the muscat group was significantly larger than that in the non-muscat group. All individuals with berries that were constantly evaluated as muscat throughout the evaluated years harbored the haplotype. Although the genotypes at other QTLs need to be muscat-type to breed grapevine plants with muscat flavor, the SSR polymorphisms defined as LG5-Hap1 as well as the CAPS marker may be used as DNA markers for muscat grapevine breeding.