Species hybridisation and clonal expansion as a new fungicide resistance evolutionary mechanism in Pyrenophora teres spp

Abstract

The barley net blotch diseases are caused by two fungal species of the Pyrenophora genus. Specifically, spot form net blotch is caused by P. teres f. sp. maculata (Ptm) whereas net form net blotch is caused by P. teres f. sp. teres (Ptt). Ptt and Ptm show high genetic diversity in the field due to intraspecific sexual recombination and hybridisation of the two species although the latter is considered rare. Here we present occurrence of a natural Ptt/Ptm hybrid with azole fungicides resistance and its implication to barley disease management in Australia. We collected and sequenced a hybrid, 3 Ptm and 10 Ptt isolates and performed recombination analyses in the intergenic and whole genome level. Eleven out of 12 chromosomes showed significant (P < 0.05) recombination events in the intergenic regions while variable recombination rate showed significant recombination across all the chromosomes. Locus specific analyses of Cyp51A1 gene showed at least four recombination breakpoints including a point mutation that alter target protein function. This point mutation did not found in Ptt and Ptm collected prior to 2013 and 2017, respectively. Further genotyping of fourteen Ptt, 48 HR Ptm, fifteen Ptm and two P. teres isolates from barley grass using Diversity Arrays Technology markers showed that all HR Ptm isolates were clonal and not clustered with Ptt or Ptm. The result confirms occurrence of natural recombination between Ptt and Ptm in Western Australia and the HR Ptm is likely acquired azole fungicide resistance through recombination and underwent recent rapid selective sweep likely within the last decade. The use of available fungicide resistance management tactics are essential to minimise and restrict further dissemination of these adaptive HR Ptm isolates.

Using a Hybrid Mapping Population to Identify Genomic Regions of Pyrenophora teres Associated With Virulence

“…However, most of the progeny isolates showed spot-like disease symptoms and only 13 of the progeny isolates could be clearly identified as having net-like symptoms. Similar observation was made for field collected hybrids which also all showed spot-like disease symptoms ( Campbell et al, 2002 ; Mclean et al, 2014 ; Turo et al, 2021 ). Spot- and net-form symptoms are impossible to differentiate at the lower infection rates and thus, some of these progeny isolates could have been miss-classified as spot-form instead of net-form.…”

“…To the author’s knowledge, this is the first study to use a hybrid population of Pyrenophora teres f. teres and Pyrenophora teres f. maculata in a QTL analysis study. Recent identification of an increasing number of hybrids in barley fields indicates the importance of understanding the virulence patterns of hybrid isolates ( Turo et al, 2021 ). The results of this study give an insight into the virulence profile of hybrid isolates with respect to their parental isolates and provide useful information about barley- P. teres pathosystem.…”

“…Molecular studies have shown that the two forms of P. teres are phylogenetically independent and divergent groups ( Mclean et al, 2009 ; Liu et al, 2011 ; Ellwood and Wallwork, 2018 ; Syme et al, 2018 ; Marin-Felix et al, 2019 ; Clare et al, 2020 ); hence, sexual reproduction between the two forms is suggested to be rare ( Serenius et al, 2005 ; Lehmensiek et al, 2010 ; Mclean et al, 2014 ; Akhavan et al, 2015 ). However, identification of Ptt / Ptm hybrids collected from barley fields ( Campbell et al, 2002 ; Leišova et al, 2005 ; Mclean et al, 2014 ; Dahanayaka et al, 2021b ; Turo et al, 2021 ) and successful establishment of laboratory-based hybrids ( Smedegård-Petersen, 1971 ; Crous et al, 1995 ; Louw et al, 1995 ; Campbell et al, 1999 ; Jalli, 2011 ) suggest that the two forms can overcome sexual reproduction barriers under certain environmental conditions ( Dahanayaka et al, 2021a ). Hybridisation between the two forms may result in hybrids harbouring both Ptt and Ptm virulence genes, which could result in devasting yield losses in the absence of barley cultivars resistant to both P. teres forms.…”

Widespread genetic heterogeneity and genotypic grouping associated with fungicide resistance among barley spot form net blotch isolates in Australia

“…The low number of clones in these MLGs (11) provides weak evidence for recent selection of beneficial genotypes, perhaps masked by susceptible popular cvs. For example, predominantly clonal Ptm isolates were previously found in cv Oxford in southern WA, associated with a virulent new pathotype in combination with demethylase inhibitor (DMI) fungicide resistance ( Turo et al . 2021 ).…”

Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen

“…Pyrenophora teres form teres (Ptt) produces net-like lesions while P. teres f. maculata (Ptm) causes brown spots surrounded by chlorosis, thus referred to as 'net form net blotch' and 'spot form net blotch' , respectively. Ptt and Ptm cross easily in lab conditions [34], their artificial hybrids are fertile [35], and they can produce clonal hybrid lineages in the field [36]. However, population genomic studies revealed neither pervasive admixture nor rampant gene flow [37][38][39][40], which suggests that ecologically-based reproductive barriers contribute to the maintenance of Ptt and Ptm in sympatry on the same host [41].…”