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

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Abstract

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.

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Acknowledgments

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.

Funding

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).

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  1. Atsushi Kono

    Present address: Department of Intellectual Property, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8517, Japan

Authors and Affiliations

  1. Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Higashihiroshima, Hiroshima, 739-2494, Japan

    Akifumi Azuma, Atsushi Kono & Akihiko Sato

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  1. Akifumi Azuma
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Correspondence to Akifumi Azuma.

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Data archiving statement

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

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Communicated by M. Troggio

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Table S1

(XLSX 105 kb).

Table S2

(XLSX 21 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).

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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Azuma, A., Kono, A. & Sato, A. Simple DNA marker system reveals genetic diversity of MYB genotypes that determine skin color in grape genetic resources. Tree Genetics & Genomes 16, 29 (2020). https://doi.org/10.1007/s11295-020-1421-y

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