Tree Genetics & Genomes

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Simple DNA marker system reveals genetic diversity of MYB genotypes that determine skin color in grape genetic resources

  • Akifumi AzumaEmail author
  • Atsushi Kono
  • Akihiko Sato
Original Article
Part of the following topical collections:
  1. Breeding


Grape skin color is determined mainly by the quantity and composition of anthocyanins, and the MYB genotype at the color locus on chromosome 2 is the major genetic determinant of anthocyanin biosynthesis. Recently, poor coloration of grape berry skin has become a common problem caused mainly by high temperatures during maturation. In the present study, we developed a simple DNA marker system for predicting the MYB genotype at the color locus. Our sample preparation method for PCR and efficient DNA markers can distinguish many MYB genotypes derived from V. vinifera and interspecific hybrid grapes simultaneously. Furthermore, we constructed a database of the relationship between MYB genotype at the color locus and the “Skin color”, “Species”, “Region of origin”, and “Utilization” categories in more than 700 grape genetic resources. We found a significant association between MYB genotypes and each of the four categories. This novel DNA marker system and the database of MYB genotypes will contribute to the development of new grape varieties with well-pigmented berries despite global atmospheric warming. This study may also contribute to elucidation of the evolutionary differentiation of MYB genotypes at the color locus in Vitis species.


DNA marker Genetic diversity Grape Haplotype Skin color 



We thank Tamami Nakasumi, Fujie Umeda, Maki Nishimura, and Miho Kohata for technical assistance. We are also grateful to the members of the Technical Support Center at our institute for preparation of plant materials.

Authors’ contributions

All authors were involved in carrying out the research and in writing and/or reviewing the manuscript.

Funding information

This work was supported in part by the Cabinet Office, Government of Japan, Cross-ministerial Strategic Innovation Promotion Program (SIP) “Technologies for Smart Bio-industry and Agriculture” (funding agency: Bio-oriented Technology Research Advancement Institution, NARO).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

MYB genotypes at the color locus in grape genetic resources can be found in the supplementary information (Table S1).

Supplementary material

11295_2020_1421_MOESM1_ESM.xlsx (106 kb)
Table S1 (XLSX 105 kb).
11295_2020_1421_MOESM2_ESM.xlsx (22 kb)
Table S2 (XLSX 21 kb).
11295_2020_1421_MOESM3_ESM.pptx (693 kb)
Fig. S1 Sample preparation and MYB genotyping. a Grape seeds are germinated in trays in a greenhouse at a constant temperature of 24 °C. b Between 20 and 80% of seeds germinate within 2 weeks. c The seed trays are brought into the laboratory. d Filter paper is prepared before pricking the leaves. e Each leaf sample is pricked 20 times with a toothpick. f The material (including DNA) is transferred into 20 μL of TE buffer. g The samples are heated for 10 min at 75 °C and then cooled to 4 °C. h Aliquots of the crude DNA extracts (0.5 μL) are used for PCR. i PCR was performed and the fragment sizes were analyzed (PPTX 692 kb).
11295_2020_1421_MOESM4_ESM.pptx (307 kb)
Fig. S2 Nucleotide sequences of VvMYBA1a, VvMYBA1c, VlMYBA1-3a, and VlMYBA1-3b. Gret1, grapevine retrotransposon 1; LTR, long terminal repeat (PPTX 307 kb).


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea ScienceNational Agriculture and Food Research Organization (NARO)HigashihiroshimaJapan
  2. 2.Department of Intellectual PropertyNational Agriculture and Food Research Organization (NARO)TsukubaJapan

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