Pervasive hybridization with local wild relatives in Western European grapevine varieties

Abstract

Hybridization footprint suggests introgression with local wild relatives in Western European grape varieties.

Alternative Modes of Introgression-Mediated Selection Shaped Crop Adaptation to Novel Climates

“…Previous studies showed that the genetic basis of crops was produced through domestication events followed by adaptive gene flow from relatives encountered during postdomestication expansion processes ( Janzen et al 2019 ). New genomic data reveal that introgressed loci of large effect that are target of directional selection explain a small proportion of the full phenotypic variance in traits associated with altitudinal, latitudinal, and longitudinal climatic gradients in different crop species (phenotypic variance associated with cold stress [maize; Crow et al 2020 ], drought stress [wheat, grapevine, and ryegrass; He et al 2019 ; Blanco-Pastor et al 2021 ; Freitas et al 2021 ] and day length [potato] differences [ Hardigan et al 2017 ]). These studies also show that the evolutionary consequences of introgression from wild relatives are also far more diverse than previously identified ( Martin and Jiggins 2017 ; Warburton et al 2017 ; Suarez-Gonzalez, Lexer, et al 2018 ; Janzen et al 2019 ).…”

“…Environmental adaptation played a key role in both the evolution of wild genotypes and the outcome of introgression with cultivated varieties. Freitas et al (2021) found significantly enriched climate- and pathogenesis-associated loci in introgressed genomic regions of Iberian cultivated grapevines. The proportion of introgressed regions ranged from 25% to 50% of the grapevine genome, in a set of related Iberian varieties.…”

“…It was initially thought that grapevine domestication included two separate domestication events, one derived from wild Caucasian grapevines and the other from wild Western European grapevines ( Grassi et al 2003 ; Arroyo-García et al 2006 ). However, recent genomic data have confirmed a single origin in West Asia with a strong introgression signal from the subspecies sylvestris as it moved toward the western Mediterranean ( Terral et al 2010 ; Myles et al 2011 ; Bouby et al 2013 ; Freitas et al 2021 ), which lead to a reduction in its genetic load ( Zhou et al 2017 ; Freitas et al 2021 ). One of the first and strongest evidence of introgression was the increase in genetic diversity toward the west, contrary to expectations given the east-to-west direction of domestication.…”

“…The proportion of introgressed regions ranged from 25% to 50% of the grapevine genome, in a set of related Iberian varieties. These introgressed genomic regions were significantly enriched in genes under directional selection in both Iberian cultivars and Iberian wild populations and were enriched in genes associated with abiotic and biotic stress stimuli, including genes associated with flowering time and light perception, hormone signaling, abiotic stress responses to cold and drought, sugar content regulation, and pathogen perception ( Freitas et al 2021 ). Also including some large-effect genes such as abscisic acid ( ABA ) signaling genes, a key hormone in plant adaptation to abiotic stress stimuli ( Kuromori et al 2018 ), and pathogenesis-related proteins ( Fernandes et al 2013 ).…”

“…Genetic structure analyses and genome-wide introgressions: Genetic clusters should be used as operational units to identify gene flow at the intraspecific level, but neutral and putative adaptive genetic structure usually differ. These differences can be observed at the chromosome level with different signature of selection in different individuals from the same gene pool or genetic cluster (e.g., Freitas et al 2021 ; Lovell et al 2021 ). Local ancestry blocks across the different chromosomes can be inferred using sophisticated probabilistic hidden Markov models such as those implemented in HAPMIX ( Price et al 2009 ) or Ancestry_HMM ( Corbett-Detig and Nielsen 2017 ).…”