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Strain-specific hypersensitive (HR) and extreme resistance (ER) phenotypes elicited in potato plants by three Potato virus Y (PVY) isolates in strain groups PVY O (BL and DEL3) and PVY D (KIP1) were studied. PVY O and PVY D isolates elicit HR genes Ny or putative Nd, respectively, and all three isolates elicit ER gene Ry. They were inoculated to 39 Australasian, European, or North American potato cultivars released over a 117-year period and harvested tubers were replanted. Both primary and secondary symptoms were recorded. Two European cultivars always developed ER following sap and graft inoculation and, thus, carried comprehensive PVY resistance gene Ry. One Australasian and two European cultivars always developed susceptible phenotypes and, thus, lacked genes Ry, Ny, and putative Nd. Sap inoculation with isolate KIP1 elicited localized HR (LHR) in 31 cultivars and both LHR and systemic HR (SHR) in three others; thus, all carried putative Nd. Isolates BL and DEL3 both elicited susceptible phenotypes in 11 of these 34 cultivars but LHR alone, SHR alone, or both LHR and SHR in the other 23 which, therefore, all carry Ny. With these two isolates, SHR expression ranged from very severe to very weak, with the greatest numbers of isolate-cultivar combinations occurring in the severe category with BL (n = 11) and moderate category (n = 12) with DEL3. Within the same isolate-cultivar combination, overall, SHR symptom expression was weaker with secondary than primary infection. With both primary and secondary infection, SHR expression was most severe with KIP1 and weakest with DEL3. Genes Ny and putative Nd were present in cultivars released between 1939 and 2010 or 1893 and 2010, respectively, occurring in cultivars from all three world regions. These findings have important implications concerning breeding new PVY-resistant potato cultivars, especially for countries lacking healthy seed potato stocks, or where subsistence farmers cannot afford them. An alternative to including gene Ry is incorporating as many strain-specific PVY resistance genes as possible.

Potato virus Y (PVY) is an important plant pathogen, whose host range includes economically important crops such as potato, tobacco, tomato, and pepper. PVY presents three main strains (PVY(O), PVY(N) and PVY(C)) and several recombinant forms. PVY has a worldwide distribution, yet the mechanisms that promote and maintain its population structure and genetic diversity are still unclear. In this study, we used a pool of 77 complete PVY genomes from isolates collected worldwide. After removing the effect of recombination in our data set, we used bayesian techniques to study the influence of geography and host species in both PVY population structure and dynamics. We have also performed selection and covariation analyses to identify evolutionarily relevant amino acid residues. Our results show that both geographic and host-driven adaptations explain PVY diversification. Furthermore, purifying selection is the main force driving PVY evolution, although some indications of positive selection accounted for the diversification of the different strains. Interestingly, the analysis of P3N-PIPO, a recently described gene in potyviruses, seems to show a variable length among the isolates analyzed, and this variability is explained, in part, by host-driven adaptation.

Potato virus Y (PVY) strains were originally defined by interactions with different resistance genes in standard potato cultivars. Five distinct strain groups are defined that cause local or systemic hypersensitive responses (HRs) in genetic background with a corresponding N gene: PVY(O), PVY(N), PVY(C), PVY(Z), and PVY(E). The nucleotide sequences of multiple isolates of PVY(O) and PVY(N) differ from each other by ≈8% along their genomes. Additionally, complete genome sequences of multiple recombinant isolates are composed of segments of parental PVY(O) and PVY(N) sequences. Here, we report that recombinant isolate PVY-L26 induces an HR in potato 'Maris Bard' carrying the putative Nz gene, and is not recognized by two other resistance genes, Nc and Ny(tbr). These genetic responses in potato, combined with the inability of PVY-L26 to induce vein necrosis in tobacco, clearly define it as an isolate from the PVY(Z) strain group and provide the first information on genome structure and sequence of PVY(Z). The genome of PVY-L26 displays typical features of European NTN-type isolates with three recombinant junctions (PVY(EU-NTN)), and the PVY-L26 is named PVY(Z)-NTN. Three typical PVY(NTN) isolates and two PVY(N) isolates, all inducing vein necrosis in tobacco, were compared with PVY-L26. One PVY(NTN) isolate elicited HR reactions in Maris Bard, similar to PVY-L26, while two induced a severe systemic HR-like reaction quite different from the quasi-symptomless reaction induced by two PVY(N) isolates. 'Yukon Gold' potato from North America produced HR against several PVY(NTN) isolates, including PVY-L26, but only late and limited systemic necrosis against one PVY(N) isolate. Consequently, according to symptoms in potato indicators, both PVY(Z) and PVY(NTN) isolates appeared biologically very close and clearly distinct from PVY(O) and PVY(N) strain groups.

A North American (NA) isolate of tobacco veinal necrotic strain of Potato virus Y (PVY(N)) (N-Jg) and a NA isolate of potato tuber necrotic strain of Potato virus Y (PVY(NTN) (Tu 660) were tested for their phenotypes by inoculation to potato plants of three potato cultivars. Upon inoculation with Tu 660, tubers of the cultivars 'Norchip' and 'Ranger Russet' developed potato tuber necrotic ringspot disease (PTNRD) but not the tubers of 'Russet Burbank'. N-Jg failed to induce PTNRD in the tested cultivars. The genomic RNAs of both strains were completely sequenced and analysed. High homology (98% and 99% identity on nucleotide and polyprotein, respectively) was found between Tu 660 and N-Jg. When polyproteins were compared with other isolates, high identity was observed between Tu 660 and an European (Eu) PVY(N)-605 (98%) and with an Eu-PVY(NTN)-H (96%). However, when individual mature proteins were compared, much lower identities (86.5-94%) were found between Tu 660 and PVY9(NTN))-H compared to 98-99.5% between Tu 660 and PVY(N)-605 in the P3, 6K1 and CI regions. Further sequence analysis indicated that the PVY(NTN)-H is a hybrid molecule of the genomic RNA recombination of PVY(O) and Eu-PVY(N) as shown by Glais et al. (Arch Virol 147, 363-378), whereas NA-PVY(NTN) Tu 660 is free of recombination points. Phylogenetic analysis confirmed this observation, and suggested that, in light of high homology, the Tu 660 might have evolved from NA-PVY(N) by mutations rather than the genome recombinations. The non-recombinant nature of NA-PVY(NTN) Tu 660 strongly suggests that the recombinant structure of genome is not a necessary prerequisite for the PTNRD phenotype.

An increasing number of countries in recent years have reported the occurrence of potato tuber necrotic ringspot disease (PTNRD), caused by tobacco veinal necrosis strain of Potato virus Y (PVY(N)), belonging to the sub-group tuber necrosis (PVY(NTN)). Methods for the differentiation of PVY(NTN), based on primer sequences often detect isolates of European (EU) type but not the North American (NA) type. To resolve this problem, the nucleotide sequence of 5'-untranslated region (5'-UTR) and the P1 gene of 11 isolates of PVY(N) and PVY(NTN) from the European Union and North America was determined. Sequence comparison and phylogenetic analysis of 5'-UTR and P1 region indicated that PVY(N) isolates from the European Union and North America formed their own separate groups. Intra-group sequence identity for all except one was over 98%, as opposed to the inter-group identity of 90%. Additionally, the PVY(NTN) isolates from the European Union and North America clustered with their respective PVY(N) isolates. This indicates a possible evolution of PVY(NTN) isolates from the PVY(N) isolates of a geographical region. With this information of regional relationships of PVY(NTN) and PVY(N) isolates, two approaches were developed based on a competitive RT-PCR and a restriction pattern, for the differentiation of NA-PVY(NTN) from the local PVY(N) and from EU-PVY(NTN). Thus sequencing of the P1 gene and use of competitive RT-PCR approach could be applicable for determining the possible origin of new occurrences of PVY(NTN) from other geographical regions.

The potato tuber ringspot necrosis isolate of potato virus Y (PVY(NTN)) is a recently recognized and highly aggressive isolate of the PVY(N) group of strains. In order to screen specifically sources of resistance to PVY(NTN) a method to separate PVY(NTN) from PVY(N) is needed. To achieve this, 61 isolates from 13 imported and locally developed potato cultivars in Slovenia were studied. On the basis of the reactions in indicator plants Nicotiana tabacum cv. Samsun and Solanum brachycarpum and with a PVY(N) specific monoclonal antibody (4E7), all Slovenian isolates (Sl-NTN) were identified as PVY(N). Using two primer pairs from the P1 gene of a Hungarian isolate of PVY(NTN) by a conventional single primer pair, reverse transcription polymerase chain reaction (RT-PCR) both PVY(NTN) and PVY(N) were amplified similarly. However, specific amplification of PVY(NTN) was achieved by a nested-PCR at an annealing temperature of 63 degrees C. A simplified form of the nested-PCR, termed 3-primer PCR was developed, which is applicable for large-scale testing of samples. Using the 3-primer PCR at annealing temperature of 63 degrees C, known mixtures of PVY(NTN) and PVY(N) were correctly separated. PVY(NTN) was detected in dormant tubers and leaves from all Sl-NTN isolates. The 3-primer PCR was specific to PVY(NTN) and did not react with nine isolates of PVY(N), 13 isolates of PVY(o), one isolate of PVY(C), six commonly occurring potato viruses and a viroid.