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Article

SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks

1
Research Group of Bioinformatics, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia
2
Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
3
Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
4
Research Group of Plant Genetics and Immunology, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia
5
Department of Genetics and Cytology, Yerevan State University, Yerevan 0025, Armenia
*
Author to whom correspondence should be addressed.
Contributed equally to this study.
Genes 2020, 11(7), 817; https://doi.org/10.3390/genes11070817
Received: 4 June 2020 / Revised: 26 June 2020 / Accepted: 15 July 2020 / Published: 17 July 2020
Background: Whole-genome studies of vine cultivars have brought novel knowledge about the diversity, geographical relatedness, historical origin and dissemination, phenotype associations and genetic markers. Method: We applied SOM (self-organizing maps) portrayal, a neural network-based machine learning method, to re-analyze the genome-wide Single Nucleotide Polymorphism (SNP) data of nearly eight hundred grapevine cultivars. The method generates genome-specific data landscapes. Their topology reflects the geographical distribution of cultivars, indicates paths of cultivar dissemination in history and genome-phenotype associations about grape utilization. Results: The landscape of vine genomes resembles the geographic map of the Mediterranean world, reflecting two major dissemination paths from South Caucasus along a northern route via Balkan towards Western Europe and along a southern route via Palestine and Maghreb towards Iberian Peninsula. The Mediterranean and Black Sea, as well as the Pyrenees, constitute barriers for genetic exchange. On the coarsest level of stratification, cultivars divide into three major groups: Western Europe and Italian grapes, Iberian grapes and vine cultivars from Near East and Maghreb regions. Genetic landmarks were associated with agronomic traits, referring to their utilization as table and wine grapes. Pseudotime analysis describes the dissemination of grapevines in an East to West direction in different waves of cultivation. Conclusion: In analogy to the tasks of the wine waiter in gastronomy, the sommelier, our ‘SOMmelier’-approach supports understanding the diversity of grapevine genomes in the context of their geographic and historical background, using SOM portrayal. It offers an option to supplement vine cultivar passports by genome fingerprint portraits. View Full-Text
Keywords: grapevine genomes; genetic diversity; dissemination of vine; genome passporting; self-organizing maps; genome portrayal grapevine genomes; genetic diversity; dissemination of vine; genome passporting; self-organizing maps; genome portrayal
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MDPI and ACS Style

Nikoghosyan, M.; Schmidt, M.; Margaryan, K.; Loeffler-Wirth, H.; Arakelyan, A.; Binder, H. SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes 2020, 11, 817. https://doi.org/10.3390/genes11070817

AMA Style

Nikoghosyan M, Schmidt M, Margaryan K, Loeffler-Wirth H, Arakelyan A, Binder H. SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes. 2020; 11(7):817. https://doi.org/10.3390/genes11070817

Chicago/Turabian Style

Nikoghosyan, Maria, Maria Schmidt, Kristina Margaryan, Henry Loeffler-Wirth, Arsen Arakelyan, and Hans Binder. 2020. "SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks" Genes 11, no. 7: 817. https://doi.org/10.3390/genes11070817

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