Integrated transcriptomic and metabolomic analyses reveal a novel mechanism of resistance to Colletotrichum fructicola in pear

• Lipid metabolism is critically associated with anthracnose resistance in ‘Seli’ pear. • Dysregulated biosynthesis of amino acids and abnormal metabolism of proanthocyanidins contribute to anthracnose susceptibility in ‘Cuiguan’ pear. • Lipids and amino acids may serve as key resistance-regulating metabolites. Pear anthracnose, caused by Colletotrichum fructicola , is a devastating disease that seriously affects most pear varieties, compromising their yield and quality. However, effective control of this pathogen is lacking. Moreover, the critical resistance responses to C . fructicola in pear are unknown. To investigate these resistance mechanisms of pear against C . fructicola , transcriptomic and metabolomic analyses were performed on the anthracnose-resistant variety ‘Seli’ and susceptible variety ‘Cuiguan’ after C . fructicola infection. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were mainly involved in metabolism and secondary metabolite synthetic pathways, including α-linoleic acid metabolism, phenylalanine biosynthesis metabolism, unsaturated fatty acids biosynthesis, and biosynthesis of amino acids and their derivatives. In particular, the accumulation of unsaturated fatty acids (UFAs), amino acids, and their derivatives, such as linoleic acid and its derivatives, lauric acid, N-acetyl-L-glutamic acid, and L-proline, was significantly increased in ‘Seli’ after infection, while the amino acids of oxiglutatione and N-acetyl-L-glutamic acid, as well as the proanthocyanidins, were significantly decreased in ‘Cuiguan’. These findings suggest that these metabolites may contribute to the differential anthracnose resistance between ‘Seli’ and ‘Cuiguan’. Overall, our results provid new insights into the regulation of pear anthracnose resistance, which may assist in developing new control strategies and breeding anthracnose-resistant varieties.