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

Maria Nikoghosyan,Arsen Arakelyan,Maria Schmidt,Henry Loeffler-Wirth,Hans Binder,Kristina Margaryan

doi:10.3390/genes11070817

Maria Nikoghosyan, Arsen Arakelyan + Show 4 more

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https://doi.org/10.3390/genes11070817

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Abstract

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.

Highlights

Grapes are tasty, and one of the most economically and culturally important crops.They are used for both winemaking and fresh (‘table’) consumption
The Single Nucleotide Polymorphism (SNP)-portraits were stratified into nine geographic regions, ranging from Middle and Far East (MFEA), Eastern Mediterranean and Caucasus (EMCA) over Russia and Ukraine (RUUK), Balkan (BALK), Western and Central Europe (WCEU), Italian Peninsula (ITAP) to Maghreb (MAGH) and Iberia (IBER) in the ‘Old World’ (Figure 1A)
The mean SNP-portrait of each region reveals specific patterns of red spot-like areas which visualizes the respective genotype in terms of the ‘meta-SNP’ score landscape, where red/blue areas refer to positive/negative excess minor allele frequencies (eMAF) values, meaning that the mean minor allele frequency (MAF) of the SNPs in this spot from this region exceeds/falls below their mean MAF value averaged over all cultivars studied of all geographic regions (Figure 1B)

Summary

Introduction

Grapes are tasty, and one of the most economically and culturally important crops.They are used for both winemaking and fresh (‘table’) consumption. Archaeological and historical studies suggested that the cultivation of the domesticated grape Whole-genome studies of vine cultivars have brought novel knowledge about the diversity, geographical relatedness, historical origin and dissemination, phenotype associations and genetic markers. 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. On the coarsest level of stratification, cultivars divide into three major groups: Western Europe and Italian grapes, Iberian grapes and vine cultivars from Near

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