Skip to main content
ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #431221
Research Project: Breeding Prunus and Vitis to Improve Disease Resistance, Fruit Quality, and Climate Change Adaptation

Location: Crop Diseases, Pests and Genetics Research

Title: Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce’s disease in Vitis arizonica and its hybrids

Author
item MASSONNET, MELANIE - University Of California, Davis
item ZACCHEO, MIRELLA - University Of California, Davis
item COCHETEL, NOE - University Of California, Davis
item FIGUERORA-BALDERAS, ROSA - University Of California, Davis
item Riaz, Summaira
item CANTU, DARIO - University Of California, Davis

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2026
Publication Date: 4/30/2026
Citation: Massonnet, M., Zaccheo, M., Cochetel, N., Figuerora-Balderas, R., Riaz, S., Cantu, D. 2026. Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce’s disease in Vitis arizonica and its hybrids. G3: Genes, Genomes, Genetics. 16(7). Article jkag115. https://doi.org/10.1093/g3journal/jkag115.
DOI: https://doi.org/10.1093/g3journal/jkag115

Interpretive Summary: Pierce's disease (PD) is an important grapevine disease in the USA. Previously, grapevine resistance to PD was identified in many native American grapevine species and associated with a genomic region known as Pierce’s disease Resistance 1 (PdR1). In this study, further analysis of PdR1 present in four Vitis arizonica accessions revealed extensive DNA sequence diversity, including major differences in gene composition. Analysis of DNA sequences contrasted with gene expression data revealed defense-related candidate genes, suggesting that multiple co-localized determinants within PdR1 contribute to resistance. These findings provide targets for functional gene validation and underscore opportunities for genetic improvement of PD resistance in grapevine.

Technical Abstract: Previous genetic mapping studies indicate that multiple haplotypes of the Pierce’s disease (PD) Resistance 1 (PdR1) locus occur in Vitis arizonica and its hybrids. To characterize sequence diversity at this locus, we assembled chromosome-scale diploid genomes for four PD-resistant (PD-R) accessions: b43-17 (PdR1a'/PdR1b'), the backcross 07744-094 (PdR1c'/PdR1'), b46-43 (PdR1e'/PdR1f'), and b42-26 (PdR1'/PdR1'), which displays quantitative PD resistance not associated with PdR1. Haplotype resolution of PdR1a, PdR1b, and PdR1c revealed substantial variation in intergenic repeat content and gene composition between PD-R and PD-susceptible (PD-S) haplotypes, as well as among PD-R haplotypes, demonstrating extensive sequence diversity at the PdR1 locus. Sequence graph analysis uncovered substantial structural divergence concentrated in approximately one quarter of the locus, together with smaller-scale variation across haplotypes. This analysis identified PdR1-specific graph nodes, showing that PdR1a and PdR1b share most PdR1-specific features, whereas PdR1c contains the highest number of private nodes, followed by PdR1e. Integration of sequence graph features with gene expression data further refined a set of defense-related candidate genes within PdR1c. Together, these results identify candidate genes for functional validation and indicate that multiple resistance determinants co-localized within the PdR1 locus may contribute to PD resistance, highlighting opportunities for targeted genetic improvement strategies.