The pear (Pyrus spp.), a perennial fruit tree, is subjected to genetic alterations over decades or even centuries to adapt to complex climatic and cultivation conditions. Genome-wide studies of deleterious mutations remain limited in perennial fruit trees, particularly regarding the effects of domestication on deleterious mutations. In this study, 232 pear accessions were resequenced, and 9 909 773 single-nucleotide polymorphisms (SNPs), and 139 335 deleterious mutation sites, were identified genome wide. A higher proportion of deleterious mutations in coding regions (1.4%) were observed in the pear genome than annual crops. During domestication, a reduction in deleterious mutations in Pyrus pyrifolia/P. bretschneideri was found to be associated with their decreases in selective sweep regions. Conversely, an increase in the number of deleterious mutations in P. communis was observed, which may be related to a higher occurrence within selective sweep regions. In P. ussuriensis, an overall increasing trend in deleterious mutations was identified, which was determined to be unrelated to domestication or gene introgression but instead linked to its relatively high heterozygosity. Differential deleterious mutation genes were identified during the domestication process. Among these, the PyMYC2 gene, associated with stone cell synthesis, was identified through GWAS, overexpression of PyMYC2 in pear callus significantly promoter lignin biosynthesis, PyMYC2 contains three nonsynonymous deleterious mutations that were selected during the domestication of Asian pears. This research provides new insights into developing future breeding strategies aimed at improving agronomic traits and offers a framework for studying deleterious mutation patterns in the domestication of perennial fruit trees.

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