Genome assembly and sequencing of Prunus dulcis and Prunus webbii provide insights into almond evolution and basis to harness wild genetic diversity

Chiara Delvento 
DIPARTIMENTO DI SCIENZE DEL SUOLO,DELLA PIANTA E DEGLI ALIMENTI - DISSPA (UNIBA) - Italy

March 04, 2026 (11:30-12:30)
Webinar Link: https://teams.microsoft.com/meet/38568513579385?p=kfG2MSylNbAz8ltqnn

Abstract: Cultivated almond (Prunus dulcis, Pd) is the leading tree nut species worldwide, yet genomic research on Pd and its wild relatives remains limited. Here, we present haplotype-resolved genomes for the Pd cultivar ’Tuono’ the primary source of self-compatibility in global almond breeding and the xerophytic wild almond species Prunus webbii (Pw), together with whole-genome resequencing data from 72 Pd, Pw, and Pd × Pw hybrid individuals. Phylogenomic inference indicated that the ancestral lineages leading to Pd and Pw diverged in the early Pleistocene and thereafter followed distinct evolutionary trajectories favoring energy production and stress adaptation, respectively. Selection scans revealed candidate genes for domestication-related traits in Pd, including seed size, tree architecture, and shell hardness, and for Pw drought tolerance. Population genomic analyses indicated that Pw did not contribute self-compatibility to Pd, challenging a long-standing hypothesis. Instead, allele-specific expression profiling highlighted convergent evolution of self-compatibility through transcriptional inactivation of the S-RNase and F-box determinants of Prunus self-incompatibility. Notably, Pd × Pw hybrids carrying the Sweet kernel allele displayed reduced accumulation of toxic amygdalin, highlighting a path toward neo-domestication of additional edible almond species from wild relatives. Overall, this study advances almond biology and provides actionable guidance to leverage wild almond diversity

Author's Info: https://scholar.google.com/citations?user=LneSW54AAAAJ&hl=en&oi=ao