A super-pangenome of the North American wild grape species

Authors: COCHETEL, NOE - University Of California, Davis; MINIO, ANDREA - University Of California, Davis; GUARACCINO, ANDREA - Human Technopole; GARCIA, JADRAN - University Of California, Davis; FIGUEROA-BALDERAS, ROSA - University Of California, Davis; MASSONNET, MELANIE - University Of California, Davis; Kasuga, Takao; LONDO, JASON - Cornell University; GARRISON, ERIK - University Of Tennessee; GAUT, BRANDON - University Of California Irvine; CANTU, DARIO - University Of California, Davis

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2023
Publication Date: 12/19/2023
Citation: Cochetel, N., Minio, A., Guaraccino, A., Garcia, J., Figueroa-Balderas, R., Massonnet, M., Kasuga, T., Londo, J., Garrison, E., Gaut, B., Cantu, D. 2023. A super-pangenome of the North American wild grape species. Genome Biology. 24. Article 290. https://doi.org/10.1186/s13059-023-03133-2.
DOI: https://doi.org/10.1186/s13059-023-03133-2

Interpretive Summary: Capturing the genetic diversity of wild relatives is crucial for improving crops, as it provides a valuable source of agronomical traits essential to enhance the sustainability and adaptability of domesticated cultivars. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes. Using the genome resources, we identified loci associated with salt tolerance in natural populations of grapes. This study highlights how genomes of grape species can expedite future research to improve the cultivated grapevine.

Technical Abstract: Capturing the genetic diversity of wild relatives is crucial for improving crops, as it provides a valuable source of agronomical traits essential to enhance the sustainability and adaptability of domesticated cultivars. Super-pangenomes serve as comprehensive frameworks to harness the full spectrum of genomic variations within a genus. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which were phased and scaffolded at chromosome scale. A super-pangenome graph was generated and revealed the genetic diversity among the wild grape species at sequence and gene level. The graph captured not only genomic variations between the haplotypes within a species but also across different species and accurately assessed the similarity of the parents with their hybrids. The careful selection of the species to build the pangenome ensured a comprehensive representation of the genus capturing known allelic variations illustrated by the sex-determining region and Pierce’s disease resistance loci. Using pangenome-wide association analysis (pan-GWAS) we identified loci associated with salt tolerance in natural populations of grapes. This study highlights how a super-pangenome of wild relative grape species can expedite future research to improve the cultivated grapevine.