Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity

Abstract

Summary An outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site‐associated DNA sequencing (RAD‐seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole‐genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD‐seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.

Mixed-Mating Model of Reproduction Revealed in European Phytophthora cactorum by ddRADseq and Effector Gene Sequence Data

“…Preferences of particular isolates to produce either antheridia or oogonia in heterothallic species have been recorded; however, bisexuality is hypothesised in homothallic species [ 29 ], therefore, the possibility of the mating of two isolates of homothallic species cannot be excluded. Outbreeding was documented in either heterothalic P. infestans [ 30 , 31 , 32 ] or P. ramorum [ 33 ], or in homothallic species such as P. sojae and P. porri . In homothallic Phytophthora spp., outbreeding was reported as a possible mechanism generating new pathotypes able to overcome host resistance [ 34 , 35 , 36 , 37 ].…”

Genome-Wide Association Mapping of Late Blight Tolerance Trait in Potato (Solanum tuberosum L.)

“…In traditional agriculture, late blight is primarily controlled using protective agents or systemic fungicides. However, pesticides pollute the environment and accelerate the development of tolerance and the mutation of Phytophthora infestans (Maurice et al, 2009). Risch and Merikangas (1996) and Hansen et al (2001) first reported genome-wide association analysis (GWAS).…”

Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans

“…Epigenetic reprogramming in plants also can be triggered by abiotic constrains (Wibowo et al, 2016;Lämke and Bäurle, 2017) and if applicable to P. infestans, such a function could generate increased opportunities to adapt to various changes in climate conditions. The extent of genetic variation in Scandinavian P. infestans populations has been debated (Maurice et al, 2019). Beside different marker systems employed for the analysis by different research groups, variation in the observations may as well reflect epigenetic influences driven by annual climate fluctuations.…”