Population-level whole genome sequencing ofAscochyta rabieiidentifies genomic loci associated with isolate aggressiveness

Abstract

AbstractAscochyta blight caused by the ascomyceteAscochyta rabieiis the major biotic threat to chickpea (Cicer arietinum) industries worldwide and incurs substantial costs to the Australian multimillion-dollar chickpea industry both in disease control and yield loss. The fungus was introduced to Australia in the 1970s from an unknown source population, and within a few decades, successfully established in all Australian agroecological chickpea growing regions. Although genetically highly clonal, a broad range of phenotypic variation in terms of aggressiveness exists among the AustralianA. rabieiisolates. More recently, highly aggressive isolates capable of causing severe disease on moderate to highly resistant chickpea cultivars have increased in frequency. To identify genetic loci potentially associated withA. rabieiaggressiveness on Australian chickpea cultivars, we performed deep genome sequencing of 230 isolates collected from a range of agroecological chickpea growing regions between 2013 and 2020. Population genetic analyses using genome-wide single nucleotide polymorphism data identified three main clusters of genetically closely related isolates in Australia. Phylogenetic analyses showed that highly aggressive phenotypes developed multiple times independently throughout the phylogeny. Results point to minor contribution of multiple genetic regions and most likely epigenomic variations to aggressiveness ofA. rabieiisolates on Australian chickpea cultivars.DATA SUMMARYAn online dataset containing the data and code required to reproduce the results found in this publication is available as supplementary material. Isolate aggressiveness and collection metadata are available in the Ascochyta dashboard athttp://bit.ly/asco-dashboard.