Abstract: 【Objective】 Alternaria alternata f.sp. mali is a main disease occurring in Chinese apple orchard, which seriously threatens the yield and quality of apples. The aim of this research is to identify apple cultivars and genes with high resistance to Alternaria alternata f.sp. mali, thus providing basis for disease resistance breeding of apples.【Methods】 In this study, the isolated Alternaria alternata f.sp. mali strain was used to inoculate leaf of 84 apple cultivars. To evaluate the resistance of apple cultivars to leaf spots, cluster analysis was carried out from two aspects of lesion area and lesion area growth rate. Genome-wide association study was performed based on the lesion area.【Results】Statistical analysis of lesion area showed significant diversity of 84 apple cultivars in resistance to Alternaria alternata f.sp. mali. Most apple cultivars were susceptible or resistant to Alternaria alternata f.sp. mali, while only a few cultivars were highly resistant and highly susceptible. A total of 1243071 high-quality SNP loci were finally obtained, among which 6 SNP loci showed significant aboriginality level (P ≤ 0.0000001).【Conclusion】We identified seven highly resistant cultivars and two susceptible varieties from 84 apple cultivars. In addition, six loci and seven key candidate genes significantly associated with the disease resistance were identified, among which the SNP located on chromosome 5 at 9336893 bp was the most significantly associated locus. The seven candidate genes included Integrin-linked protein kinase (MD05G1054300), FMN-linked oxidoreductase superfamily protein (MD05G1054400), GATA transcription factor (MD05G1048600), and B-box zinc finger family protein (MD00G1039900).

Key words: apple cultivars, , Alternaria alternata f.sp. mali, disease resistance, genome-wide association study