Highlight PpYUC11 is a strong candidate gene for the control of the stony hard phenotype in peach.

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Mutation rates vary between species, between strains within species and between regions within a genome. What are the determinants of these forms of variation? Here, via parent–offspring sequencing of the peach we ask whether (i) woody perennials tend to have lower per unit time mutation rates compared to annuals, and (ii) hybrid strains have high mutation rates. Between a leaf from a low heterozygosity individual, derived from an intraspecific cross, to a leaf of its selfed progeny, the mutation rate is 7.77 × 10−9 point mutations per bp per generation, similar to Arabidopsis thaliana (7.0–7.4 × 10−9 point mutations per bp per generation). This suggests a low per unit time mutation rate as the generation time is much longer in peach. This is supported by our estimate of 9.48 × 10−9 point mutations per bp per generation from a 200-year-old low heterozygosity peach to its progeny. From a more highly heterozygous individual derived from an interspecific cross to its selfed progeny, the mutation rate is 1.38 × 10−8 mutations per site per generation, consistent with raised rates in hybrids. Our data thus suggest that (i) peach has an approximately order of magnitude lower mutation rate per unit time than Arabidopsis, consistent with reports of low evolutionary rates in woody perennials, and (ii) hybridization may, indeed, be associated with increased mutation rates as considered over a century ago.