The genetic basis of microbiome recruitment in grapevine and its association with fermentative and pathogenic taxa

While grapevine is an exceptional perennial model for studying host‐microbiome interactions, the host genome's role in microbiome assembly is often masked by environmental factors. This research provides a first insight into the genetic mechanisms shaping berry‐associated microbial communities.

Using QTL mapping in a newly established population of 140 F1‐progeny grapevine genotypes in a complete random block design, we were able to control abiotic effects and investigate how the host genome influences grape berry‐associated bacterial and fungal communities.

We identify significant associations between various microorganisms and the grape genome, including pathogenic fungi such as Botrytis spp. and fermentative yeasts such as Saccharomyces cerevisiae . Many of these taxa map to the same genetic loci associated with plant immune responses, suggesting that specific genetic loci broadly influence microbial community assembly in fruits.

Our findings demonstrate that grapevine genetics significantly shape the microbiome, even under varying environmental conditions; moreover, that broad, rather than known symbiont‐specific mechanisms control microbial colonization of fruit, revealing an emergent ‘domino’ effect with implications for plant‐fungal‐bacterial interactions. We provide a framework for understanding genotype‐microbiome interactions in perennial plants, enabling future targeted experiments to establish causal relationships in microbiome recruitment and offer a potential avenue for breeding programs advancing sustainable viticulture.