Late blight, caused by Phytophthora infestans, has emerged as the most destructive disease of potato and tomato in South India since 2008. One hundred and fifty‐seven isolates of Phytophthora infestans, 63 from potato and 94 from tomato, were collected from major potato and tomato production areas of South India between 2010 and 2012. Their phenotypic and genotypic characteristics were determined and compared with reference isolates. Isolates were characterized based on mating type, in vitro metalaxyl sensitivity, mitochondrial DNA haplotype, RG57 DNA fingerprinting patterns, SSR markers and aggressiveness on potato and tomato, in order to monitor population changes in P. infestans. All isolates were A2 mating type, metalaxyl resistant, mtDNA haplotype Ia and had RG57 and SSR fingerprints almost identical to the 13_A2 clonal lineage reported in Europe. Variation at the D13 and SSR4 loci allowed discrimination of minor variants, designated as 13_A2_3, 13_A2_3b, 13_A2_3c and 13_A2_1. A comparison of the lesion diameters caused by 157 isolates on detached leaflets of three potato and tomato cultivars showed all isolates to be equally aggressive, confirming that the same clonal population is infecting both hosts. This study demonstrates that the 13_A2 lineage was responsible for severe late blight outbreaks on potato and tomato in South India and has replaced the prior population represented by the US‐1 and other genotypes. Revised management strategies will be required to combat this destructive 13_A2 clonal lineage and monitoring of the population across other potato‐ and tomato‐growing regions of India is warranted.

Prior to 2007, late blight was not reported as a serious threat to tomato cultivation in India although the disease has been known on potato since 1953. During the July–December cropping season of 2009 and 2010, severe late blight epidemics were observed in Karnataka state of India, causing crop losses up to 100%. Nineteen Phytophthora isolates, recovered from late blight affected tomato tissues from different localities in Karnataka state between 2009 and 2010, were identified as Phytophthora infestans based on morphology, a similarity search of ITS sequences at GenBank and species‐specific PCR using PINF/ITS5 primer pair. The isolates were further assessed for metalaxyl sensitivity, mating type, mitochondrial DNA (mtDNA) haplotype, DNA fingerprinting patterns based on simple sequence repeats (SSR) and RFLPs using the RG57 probe and aggressiveness on tomato. All isolates were metalaxyl resistant, A2 mating type, mtDNA haplotype Ia and had identical SSR and RG57 fingerprints and highly aggressive on tomato. The phenotypic and genotypic characters of isolates examined in this study were found to be similar to that of 13_A2 genotype of P. infestans population reported in Europe. Thus, appearance of new population similar to 13_A2 genotype was responsible for severe late blight epidemics on tomato in South‐West India.

Prior to 2011, foliar blight was not reported as a serious threat to hot pepper cultivation in India. During the June-to-January cropping season of 2011 and 2012, severe foliar blight epidemics were observed in Karnataka and Tamil Nadu states of India. In all, 52 Phytophthora isolates, recovered from blight-affected leaf tissues of hot pepper from different localities in Karnataka and Tamil Nadu states between 2011 and 2012, were identified: 43 isolates as P. boehmeriae and 9 isolates as P. capsici, based on morphology, a similarity search of internal transcribed spacer sequences at GenBank, polymerase chain reaction (PCR) restriction fragment length polymorphism patterns, and species-specific PCR using PC1/PC2 and PB1/PB2 primer pairs. The isolates were further assessed for metalaxyl sensitivity and aggressiveness on hot pepper. All isolates of P. boehmeriae were metalaxyl sensitive while P. capsici isolates were intermediate in sensitivity. P. boehmeriae isolates were highly aggressive and produced significantly (P < 0.01) larger lesion than those of P. capsici isolates. Thus, emergence of P. boehmeriae was responsible for severe leaf blight epidemics on hot pepper in South India, although it is not serious pathogen on any crop in any part of the world. These results have epidemiological and management implications for the production of hot pepper in India.

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Severe outbreaks of Phytophthora fruit rot on brinjal, ridge gourd, and tomato have been observed since 2011 in Andhra Pradesh, Karnataka, Telangana, and Tamil Nadu states of India. Therefore, 76 Phytophthora nicotianae isolates, recovered from brinjal (17), ridge gourd (40), and tomato (19) from different localities in these states during the June to December cropping season of 2012 and 2013, were characterized based on phenotypic and genotypic analyses and aggressiveness on brinjal, tomato, and ridge gourd. All brinjal and ridge gourd isolates were A2, while tomato isolates were both A1 (13) and A2 (6). All isolates were metalaxyl sensitive. In addition, isolates were genotyped for three mitochondrial (ribosomal protein L5-small subunit ribosomal RNA [rpl5-rns], small subunit ribosomal RNA-cytochrome c oxidase subunit 2 [rns-cox2], and cox2+spacer) and three nuclear loci (hypothetical protein [hyp], scp-like extracellular protein [scp], and beta-tubulin [β-tub]). All regions were polymorphic but nuclear regions were more variable than mitochondrial regions. The network analysis of genotypes using the combined dataset of three nuclear regions revealed a host-specific association. However, the network generated using mitochondrial regions limited such host-specific groupings only to brinjal isolates. P. nicotianae isolates were highly aggressive and produced significantly (P ≤ 0.01) larger lesions on their respective host of origin than on other hosts. The results indicate significant genetic variation in the population of P. nicotianae, leading to identification of host-specific lineages responsible for severe outbreaks on brinjal, ridge gourd, and tomato.