Unravelling the synergistic interaction of Thrips tabaci and newly recorded, Thrips parvispinus with Alternaria porri (Ellis.) Cif., inciting onion purple blotch.

Onion purple blotch is the most indispensable foliar disease of crop and has become a major concern for farmers and research fraternity. An attempt to investigate the role of injury in parasitism by Alternaria porri indicated that disease incidence and severity enhance considerably with injury. Thrips injured plants inoculated with A. porri presented 100% incidence and 52-72% severity while mechanically injured plants inoculated with A. porri showed 60-70% incidence and 28-34% severity. The uninjured plants showed considerably less disease incidence (30-40%) and severity (10-16%). Injured inoculated plants presented reduced leaf length and leaf area while the leaf diameter remained unaffected. The lesion number, lesion length and size was substantially enhanced with concomitant infestation of pest and pathogen. Thrips tabaci injury led to more pronounced symptoms of purple blotch compared to Thrips parvispinus injury. There was substantial decrease in photosynthetic rate and chlorophyll content with stress imposed on plant whilst the relative stress injury was enhanced. The induction of injury and inoculation of A. porri had an impact on the concentration of total phenolics, total soluble sugars, total proteins and hydrogen peroxide in onion leaves. A. porri combined with injury caused a more pronounced decrease in total soluble sugars and total protein content while enhancement in total phenolics and hydrogen peroxide content compared to uninjured plants. The dynamic nature of morpho-physiological and biochemical changes owing to stress conditions imposed on onion plant adds an extra layer of complexity in understanding the onion plant physiology and their ability to work out in response to challenging environment conditions.

Development of SNP markers linked to purple blotch resistance for marker-assisted selection in onion (Allium cepa L.) breeding.

Purple blotch (PB), caused by Alternaria porri (Ellis) Cifferi, is one of the most destructive diseases of onion worldwide. Rapid development and deployment of resistant onion varieties is the most effective approach to control this disease. A single dominant gene, ApR1 was previously linked to PB resistance in onion cultivar 'Arka Kalyan'. In this study, an advanced RIL population derived from a cross between the resistant (Arka Kalyan) and susceptible (Agrifound Rose) cultivar of onion was used to fine map the resistant locus with SNP markers. Twenty plants from the RIL population, ten each with disease resistance and susceptibility trait, were subjected to restriction site-associated DNA sequencing (RAD-Seq) and generated 7388 single nucleotide polymorphisms (SNPs). Correlation analysis between marker genotypes and PB disease phenotype on the 20 plants identified 27 SNPs as candidate markers linked to ApR1 gene for PB resistance. Six candidate SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers designated as ApRsnip5, ApRsnip8, ApRsnip14, ApRsnip21, ApRsnip23 and ApRsnip25. Marker-trait association based on disease phenotyping and KASP genotyping data on 153 RILs confirmed that all six KASP markers were tightly associated with ApR1 gene within the genetic distance of 1.3 CentiMorgan (cM). ApRsnip14 co-segregated with the ApR1 locus. Further, the six KASP markers were tested on 27 onion lines with different genetic backgrounds. ApRsnip14, ApRsnip21, ApRsnip5 and ApRsnip23 not only showed the correct resistance allele in 3 resistance genotypes, but also clustered together in the remaining 24 susceptible lines. Alternatively, ApRsnip8 and ApRsnip25 exhibited false positives in two onion lines which do not have the R-gene. Overall, our results suggest that ApRsnip14 and ApRsnip23 with their close linkage to ApR1 locus and greater applicability on breeding germplasm are recommended in marker-assisted selection for PB resistance in onion breeding program. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03562-7.

Comparative Transcriptome Analysis of Onion in Response to Infection by Alternaria porri (Ellis) Cifferi.

Purple blotch (PB) is one of the most destructive foliar diseases of onion and other alliums, caused by a necrotrophic fungal pathogen Alternaria porri. There are no reports on the molecular response of onion to PB infection. To elucidate the response of onion to A. porri infection, we consequently carried out an RNAseq analysis of the resistant (Arka Kalyan; AK) and susceptible (Agrifound rose; AFR) genotype after an artificial infection. Through differential expression analyses between control and pathogen-treated plants, we identified 8,064 upregulated and 248 downregulated genes in AFR, while 832 upregulated and 564 downregulated genes were identified in AK. A further significant reprogramming in the gene expression profile was also demonstrated by a functional annotation analysis. Gene ontology (GO) terms, which are particularly involved in defense responses and signaling, are overrepresented in current analyses such as "oxidoreductase activity," "chitin catabolic processes," and "defense response." Several key plant defense genes were differentially expressed on A. porri infection, which includes pathogenesis-related (PR) proteins, receptor-like kinases, phytohormone signaling, cell-wall integrity, cytochrome P450 monooxygenases, and transcription factors. Some of the genes were exclusively overexpressed in resistant genotype, namely, GABA transporter1, ankyrin repeat domain-containing protein, xyloglucan endotransglucosylase/hydrolase, and PR-5 (thaumatin-like). Antioxidant enzyme activities were observed to be increased after infection in both genotypes but higher activity was found in the resistant genotype, AK. This is the first report of transcriptome profiling in onion in response to PB infection and will serve as a resource for future studies to elucidate the molecular mechanism of onion-A. porri interaction and to improve PB resistance in onions.

Induced Disease Resistance and Promotion of Shallot Growth by Bacillus velezensis B-27.

BACKGROUND AND OBJECTIVES: Shallot is a vegetable crop with high economic value, but its productivity is still relatively low due to various limitations. One of the most hampering factors is moler disease and purple blotch disease caused by Fusarium sp. and Alternaria porri, respectively. Numerous efforts have been made to control these diseases either using chemical fungicides or through improvement of resistant cultivar. This study aimed to determine moler and purple disease suppression and improvement of plant growth by Bacillus as Plant Growth Promoting Rhizobacteria (PGPR) on shallot. MATERIALS AND METHODS: Molecular identification of Bacillus was performed by partial gyrB gene sequencing using universal gyrB-F/gyrB-R primers. Field observation and experiments were performed using completely randomized factorial block design single factor with 3 blocks for replication. RESULTS: The partial gyrB gene sequences showed high similarity between Bacillus isolate B-27 and Bacillus velezensis. The application of Bacillus isolate B-27 to shallots was shown to reduce the intensity of moler and purple blotch diseases by 67%. On top of that, Bacillus isolate B-27 increased the plant height up to 27.12 cm, the number of leaves up to 23 blades, tillers up to 8 bulbs and the tuber weight during harvest time up to 33.64 kg. CONCLUSION: Molecular identification based on partial gyrB gene sequence analysis suggested that Bacillus isolate B-27 has close relationship with Bacillus velezensis. Besides, the application of Bacillus isolate B-27 on shallot could reduce the disease intensity and increase height, number of tillers and plant yield significantly.

Identification of Novel Source of Resistance and Differential Response of Allium Genotypes to Purple Blotch Pathogen, Alternaria porri (Ellis) Ciferri.

Purple blotch, caused by Alternaria porri (Ellis) Cifferi, is a serious disease incurring heavy yield losses in the bulb and seed crop of onion and garlic worldwide. There is an immediate need for identification of effective resistance sources for use in host resistance breeding. A total of 43 Allium genotypes were screened for purple blotch resistance under field conditions. Allium cepa accession 'CBT-Ac77' and cultivar 'Arka Kalyan' were observed to be highly resistant. In vitro inoculation of a selected set of genotypes with A. porri, revealed that 7 days after inoculation was suitable to observe the disease severity. In vitro screening of 43 genotypes for resistance to A. porri revealed two resistant lines. An additional 14 genotypes showed consistent moderate resistance in the field as well as in vitro evaluations. Among the related Allium species, A. schoenoprasum and A. roylei showed the least disease index and can be used for interspecific hybridization with cultivated onion. Differential reaction analysis of three A. porri isolates (Apo-Chiplima, Apn-Nasik, Apg-Guntur) in 43 genotypes revealed significant variation among the evaluated Allium species (P = 0.001). All together, the present study suggest that, the newly identified resistance sources can be used as potential donors for ongoing purple blotch resistance breeding program in India.

Large-spored Alternaria pathogens in section Porri disentangled.

The omnipresent fungal genus Alternaria was recently divided into 24 sections based on molecular and morphological data. Alternaria sect. Porri is the largest section, containing almost all Alternaria species with medium to large conidia and long beaks, some of which are important plant pathogens (e.g. Alternaria porri, A. solani and A. tomatophila). We constructed a multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alt a 1 gene regions, which, supplemented with morphological and cultural studies, forms the basis for species recognition in sect. Porri. Our data reveal 63 species, of which 10 are newly described in sect. Porri, and 27 species names are synonymised. The three known Alternaria pathogens causing early blight on tomato all cluster in one clade, and are synonymised under the older name, A. linariae. Alternaria protenta, a species formerly only known as pathogen on Helianthus annuus, is also reported to cause early blight of potato, together with A. solani and A. grandis. Two clades with isolates causing purple blotch of onion are confirmed as A. allii and A. porri, but the two species cannot adequately be distinguished based on the number of beaks and branches as suggested previously. This is also found among the pathogens of Passifloraceae, which are reduced from four to three species. In addition to the known pathogen of sweet potato, A. bataticola, three more species are delineated of which two are newly described. A new Alternaria section is also described, comprising two large-spored Alternaria species with concatenate conidia.