Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation

Abstract

Background Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. Results By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce’s disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. Conclusions Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.

Evaluating the persistence and utility of five wildVitisspecies in the context of climate change

“…For each species, 18 to 24 accessions were resequenced (Table 1). For our analyses, we employed SNPs determined previously (Morales-Cruz et al, 2021), but we focused on a subset of SNPs that had no missing data within each species. The resulting number of SNPs ranged from 3.6 million in V. girdiana to 5.6 million in V. riparia.…”

“…Aguirre-Gutiérrez, 2021). Here we included one biotic interaction, based on information about resistance to the bacterium X. fastidiosa (Morales-Cruz et al, 2021;Summaira Riaz, Tenscher, Heinitz, Huerta-Acosta, & Andrew Walker, 2020). Two previous studies categorized susceptibility to PD across all 105 accessions by evaluating the concentration of colonizing forming units (CFU) of X. fastidiosa after a period of experimental exposure to the bacterium.…”

“…The plant material used in this study consisted of 105 individuals from six American Vitis species (V. arizonica, n = 22; V. mustangensis, n = 24; V. berlandieri, n = 22; V. girdiana, n = 18 and V. riparia; n = 19), previously described in (Morales-Cruz et al, 2021). Samples were collected from the wild grape germplasm collection at Davis, California.…”

“…The germplasm reported in this study was collected from 1997 to 2016 as cuttings across the southwestern states and maintained at the Department of Viticulture and Enology, University of California, Davis, CA. A table of sampling locations is available from (Morales-Cruz et al, 2021). The 105 accessions were also assayed previously for X. fastidiosa resistance (or tolerance) (Morales-Cruz et al, 2021;S.…”

“…We determined the functional region (exonic, intronic, and intergenic) in which each mutation occurred using information from the V. arizonica B4014 genome annotations ((Morales-Cruz et al, 2021), https://doi.org/10.5281/zenodo.4977234 and www.grapegenomics.com/pages/Vari/). Exonic SNPs were annotated to be synonymous, nonsynonymous and frameshift using SnpEff version 5.0e (Cingolani et al, 2012).…”