Studies Using DNA Markers in Fragaria × ananassa: Genetic Analysis, Genome Structure, and Cultivar Identification

Abstract

The cultivated strawberry, Fragaria × ananassa (2n = 8x = 56), is an economically important crop in many regions of the world, and many breeding programs are competing to produce new, high-value cultivars. Despite this level of interest, marker-assisted selection of strawberry based on QTL analysis has lagged behind that of diploid crops because of its complex polyploidy and unclear genomic construction. During the past decade, great progress in the development of DNA markers has begun to overcome these difficulties, and the study of inheritance, mapping, and phylogeny is proceeding rapidly. Meanwhile, strawberry breeders have become much more aware of their rights with respect to the cultivars they have developed, as the volumes of harvested fruits that are transported globally have increased. To address the need to identify illegally grown strawberry fruits, genomics researchers have been required to develop simple and reproducible techniques for cultivar identification. This review summarizes the recent development of DNA marker studies in F. × ananassa, with a focus on the genome-specific markers we have developed.

Construction of an Integrated High Density Simple Sequence Repeat Linkage Map in Cultivated Strawberry (Fragaria x ananassa) and its Applicability

“…In addition, it is well known that PCR results can vary depending on experimental conditions such as the type of thermal cycler and Taq polymerase employed during PCR analysis. In a previous study, Kunihisa 44 investigated the stability of polymorphic analysis of CAPS markers by comparing the results obtained in 14 laboratories to verify the adequacy of the makers used for variety identification tests in F. × ananassa . Govan et al 50 also screened 32 SSRs that produced reliable PCR results for the identification of 60 varieties.…”

“…The thermal cycling conditions were as follows: 7 min denaturation at 95°C; 30 cycles of 30 s denaturation at 95°C, 30 s annealing at 57°C, and 1 min extension at 72°C, with a final 10 min extension at 72°C. A total of 100 markers showing high repeatability were screened, and the robustness of PCR was again confirmed for 129 F. × ananassa lines, 119 of which were previously investigated polymorphisms identified using CAPS markers 44 (Supplementary Table S2). The 45 best SSR markers were thereby selected to distinguish the varieties of 129 strawberry lines.…”

Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

“…Until now, three genome composition models, namely AABBBBCC, 4 AAA′A′BBBB, 5 and AAA′A′BBB′B′, 6 have been proposed based on cytological and genetic evidence. Of the three models, the most recently proposed model, AAA′A′BBB′B′, 6 is considered the most probable candidate, since several studies have reported the disomic inheritance of large numbers of DNA markers, 7–9 which suggests an allopolyploid genome composition in F. x ananassa .…”

Identification and Parentage Analysis of Citrus Cultivars Developed in Japan by CAPS Markers

“…), CAPS markers have contributed greatly to preventing infringement of breeders' rights (Kunihisa, 2011). Packed strawberry fruits imported from Korea that were labeled as 'Nyohou' were identified as a mix of 'Redpearl' and 'Sachinoka' by using CAPS markers (Kunihisa et al, 2005).…”