Resistant Evaluation of 84 Apple Cultivars to Alternaria alternata f. sp. mali and Genome-Wide Association Analysis

Alternaria alternata f. sp. mali is a main disease occurring in the apple orchards in China, which seriously threatens the yield and quality of apples. The aim of this research was to identify apple cultivars and genes responsible for high resistance to Alternaria alternata f. sp. mali, thus providing the basis for disease resistance breeding of apples.

In this study, the isolated Alternaria alternata f. sp. mali strain was used to inoculate leaves of 84 apple cultivars. To evaluate the resistance of apple cultivars to Alternaria alternata f. sp. mali, the cluster analysis was carried out from two aspects including lesion area and lesion area growth rate. The genome-wide association study was performed based on the lesion area. The disease spot area of the inoculated leaves was used as a phenotypic trait, and the 1243071 high-quality SNP loci obtained by whole genome deep resequencing were used as genetic markers. Genome wide association analysis was performed by EMMAX method.

The 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. The disease resistance of Alternaria alternata f. sp. mali has the characteristics of normal distribution, showing the genetic characteristics of quantitative characters. The genome-wide association trait analysis finally obtained 6 SNP loci with a significant level of P≤0.0000001 (-LgP≥7), and in-depth analysis linked them to 7 key candidate genes, including Integrin-linked protein kinase, FMN-linked oxidoreductase superfamily protein, B-box zinc finger family protein, GATA type transcription factor, etc. The biological function of Integrin-linked protein kinase in disease resistance was further verified.

After two years of comprehensive analysis of data, 7 stable resistant varieties and 2 stable susceptible varieties were identified from 84 apple cultivars. Through genome-wide association trait analysis, six SNP loci and seven genes significantly related to the disease resistance of apple leaf spot were identified, and function of one gene was verified.