A genome-wide association study reveals that epistasis underlies the pathogenicity of Pectobacterium .

Abstract

Importance Plant diseases and pests are responsible for the loss of up to 40% of food crops, and annual economic losses caused by plant diseases reach more than $220 billion. Fighting against plant diseases requires an understanding of the pathogenic mechanisms of pathogens. This study adopted an advanced approach using population genomics integrated with virulence-related phenotype data to investigate the genetic basis of Pectobacterium spp., which causes serious crop losses worldwide. An automated software program based on artificial intelligence was developed to measure the virulence phenotype (lesion area), which greatly facilitated this research. The analysis predicted key genomic loci that were highly associated with virulence phenotypes, exhibited epistasis effects, and were further confirmed as critical for virulence with mutant gene deletion experiments. The present study provides new insights into the genetic determinants associated with Pectobacterium pathogenicity and provides a valuable new software resource that can be adapted to improve plant infection measurements.

Code and data availability

The paper's plant-phenotyping assets are publicly available: the authors' Lesionsurvey software (source code, test data, documentation) for automated lesion-area measurement on Chinese cabbage is on GitHub, and the supplemental material (Tables S1–S7) contains the virulence (lesion area) and cellulase activity phenotyp