RT Journal Article SR Electronic T1 QTL mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici JF bioRxiv FD Cold Spring Harbor Laboratory SP 051169 DO 10.1101/051169 A1 E. L. Stewart A1 D. Croll A1 M. H. Lendenmann A1 A. Sanchez Vallet A1 F. E. Hartmann A1 J Palma Guerrero A1 Z. Ma A1 B. A. McDonald YR 2016 UL http://biorxiv.org/content/early/2016/05/07/051169.abstract AB We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using QTL mapping. High throughput phenotyping based on automated image analysis allowed measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540,710 pycnidia were counted and their sizes and grey values were measured, yielding over 1.6 million phenotypes associated with pathogen reproduction. Large pycnidia were shown to produce more numerous and larger spores than small pycnidia. Precise measures of percent leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotype datasets with a dense panel of RADseq genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and components related to pathogen reproduction. We show that different components of virulence can be under separate genetic control. Large-and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence or absence of accessory chromosomes with several virulence traits, providing the first evidence for an important function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to identification of candidate genes having a large effect on virulence.