Current diversity of Phytophthora infestans infecting cultivated potato in the Peruvian Andes

Late blight caused by P. infestans is the most devastating disease of potato worldwide. To understand the current P. infestans population structure in the Peruvian Andes, 701 single-lesion samples were collected from cultivated potato in different agroecological zones at 2016-2017. Genetic diversity was analyzed using the 12-plex SSR markers kit and mtADN. Phenotypic diversity was characterized for mating type, metalaxyl resistance and virulence. SSR analysis showed that population consists of EC-1 and PE-3 clonal lineages variants, that have the mtADN IIa and Ia, respectively. All isolates were A1 mating type. 94% of the EC-1 variant isolates were resistant to metalaxil, whereas the sensitive proportion (47%) in the PE-3 variants was bigger than the resistant (35%). Furthermore, virulence assays detected 41 complex physiological races from 142 selected isolates, the most frequent physiological race was 1,3,4,7,10,11 in both EC-1 and PE-3 variants. Phylogenetic analysis evidenced that isolates share identical SSR genotypes and physiological races in distant regions, that suggests that migration could have occurred. Additionally, no detection of A2 mating type indicate that population reproduction must be asexual. EC-1 clonal lineage continues to dominate across the Peruvian Andes, since 91% of the isolates were variants of this clonal lineage. The US-1 clonal lineage reported at 2001, appears to be displaced as it was no longer detected infecting cultivated potato

Protocol for assessing bacterial wilt resistance in greenhouse and field conditions. International cooperators’ guide

This protocol is an updated version of “Assessing potato clone field resistance to bacterial wilt” issued in The International Cooperators’ Guide (CIP 2007). The first edition of the protocol presented a standard procedure for field assessment of resistance to bacterial wilt for documenting levels of resistance of advanced potato germplasm. This second edition has included a standardized procedure for greenhouse screening of potato seedlings for bacterial wilt resistance useful for perform genetic studies, parental selection or identification of new sources of resistance in accessions of wild species propagated or maintained as true see

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

BACKGROUND: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. RESULTS: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. CONCLUSIONS: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes