Haplotype-resolved assembly and resequencing of wild and cultivated genomes shed light on the almond evolutionary history and the genetic basis of self-compatibility.

Almond (Prunus amygdalus Batsch) is a major nut crop worldwide and one of the oldest domesticated trees; however, its evolutionary history and phenotypic diversification still require thorough investigation. Moreover, there is limited genomic, genetic and phenotypic information on wild almond relatives, which hinders studies on almond domestication, and restricts the use of the extensive wild almond gene pool in breeding. Herein, we present haplotype-resolved assemblies of the almond cv. Tuono, dominating global breeding programs as a source of self-compatibility, and the self-compatible wild almond species Prunus webbii, together with a genetic variation map obtained by P. amygdalus and P. webbii whole-genome resequencing. Population genomic analyses indicated that P. webbii did not contribute to the evolution of self-compatible P. amygdalus cultivars, in contrast with a previous assumption. Rather, haplotype profiling revealed that the self-compatibility alleles of Tuono and P. webbii arose from parallel evolution, as they originated from independent losses of the stylar RNAse gene involved in the Prunus self-incompatibility system. The analysis of nutritional components in genetically homogeneous samples of P. amygdalus and P. webbii revealed significant differences in volatile compounds and amygdalin content. Genome-wide scan for selective sweeps resulted in the detection of several loci and genes putatively associated with P. amygdalus domestication and breeding. Overall, our study highlights the potential of haplotype-resolved genomic information for the genetic analysis of highly heterozygous species and provides information of broad interest for plant biologists and breeders.