Development of Sequence-characterized Amplified Region Markers for the Identification of Grapevine Cultivars

Abstract

<jats:p>Grapevine cultivars have traditionally been identified based on the morphological characteristics, but the identification of closely related cultivars has been difficult because of their similar pedigree backgrounds. In this study, we developed DNA markers for genetic fingerprinting in 37 grapevine cultivars, including 20 cultivars bred in Korea. A total of 180 randomly amplified polymorphic DNA (RAPD) markers were obtained using 30 different primers. The number of polymorphic bands ranged from three (OPG-08 and OPU-19) to nine (OPV-01 and UBC116), with an average of six. RAPD markers were used in cluster analysis performed with the unweighted pair-group method of arithmetic averages (UPGMA). The average similarity value was 0.69 and the dendrogram clustered the 37 grapevine cultivars into five clusters. The relationships among the grapevine cultivars were consistent with the known pedigrees of the cultivars. The 50 RAPD fragments selected were sequenced for the development of sequence-characterized amplified region (SCAR) markers. As a result, 16 of 50 fragments were successfully converted into SCAR markers. A single polymorphic band, the same size as the RAPD fragments or smaller, was amplified depending on the primer combinations in the 14 SCAR markers, and codominant polymorphisms were detected using the SCAR markers G119_412 and GB17_732. Among these markers, combination of 11 SCAR markers, GG05_281, G116_319, G146_365, G119_412, GW04_463, G169_515, G116_539, GV04_618, GV01_678, GG05_689, and GB17_732, provided sufficient polymorphisms to distinguish the grapevine cultivars investigated in this study. These newly developed markers could be a fast and reliable tool for identifying grapevine cultivars.</jats:p>

Development of two elite water chestnut genotypes (Trapa spp.) and their molecular characterization using RAPD and ISSR markers

“…The improved varieties, IRS and IGS are also distinct from each other.and are the rst improved varieties of water chestnut developed at the Research Centre of Makhana, ICAR, India. The future aim would be to convert the polymorphic fragments of RAPD and ISSR markers into SCAR markers (Cho et al 2015) for the e cient utilization of these markers in the identi cation for the varieties as they are more reproducible than RAPD and ISSR markers.…”

Biotechnologies and Strategies for Grapevine Improvement

“…Although efficient for the assessment of qualitative traits, the application of morphological markers is limited in the evaluation of quantitative traits. Moreover, this method is time-consuming, requiring extensive field trials and the identification of closely related cultivars is difficult [38].…”

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

“…Nonetheless, the likelihood is there for SCARs to exhibit dominance in some instances where at a section of sequence variation, one or both PCR primers partially overlap. Cho et al (2015) described briefly the procedure for converting RAPDs into SCARs. Firstly, RAPD PCR is performed and polymorphisms associated with length variation are detected by electrophoresis using stained agarose gel, followed by visualization of DNA bands under UV light illumination.…”

“…The obtained sequence data of the polymorphic DNA fragments is analyzed by comparing the sequences with known DNA sequences that are available at the NCBI (National Center for Biotechnology Information) database for sequence uniqueness. Next, the obtained nucleotide sequences of the polymorphic DNAs are used to guide the design and synthesis of specific pairs of internal SCAR primers ( Cho et al., 2015 ). Apart from RAPDs, the usefulness of AFLP and ISSR markers in genetic applications has been greatly expanded by similarly converting polymorphic fragments of these markers to SCARs.…”