Biocontrol strategies: an eco-smart tool for integrated pest and diseases management

For the burgeoning global population, sustainable agriculture practices are crucial for accomplishing the zero-hunger goal. The agriculture sector is very concerned about the rise in insecticide resistance and the Modern Environmental Health Hazards (MEHHs) that are problems for public health due to on pesticide exposure and residues. Currently, farming practices are being developed based on microbial bio-stimulants, which have fewer negative effects and are more efficient than synthetic agro-chemicals. In this context, one of the most important approaches in sustainable agriculture is the use of biocontrol microbes that can suppress phytopathogens and insects. Simultaneously, it is critical to comprehend the role of these microbes in promoting growth and disease control, and their application as biofertilizers and biopesticides, the success of which in the field is currently inconsistent. Therefore, editorial is part of a special issue titled "Biocontrol Strategies: An Eco-smart Tool for Integrated Pest and Disease Management" which focuses on biocontrol approaches that can suppress the biotic stresses, alter plant defense mechanisms, and offer new eco-smart ways for controlling plant pathogens and insect pests under sustainable agriculture.

First Report of Garlic virus B infecting Garlic in India

Garlic (Allium sativum L.) is an economically important spice and vegetable crop grown throughout the world. Garlic viral disease complex caused by multiple virus infections is an important constraint in exploiting the potential yield of garlic. Among these viral pathogens, allexivirus (family Alphaflexiviridae) is the genus of viruses known for their degenerative effect on garlic yield. Their coexistence with other viruses, particularly potyviruses, has an adverse effect on garlic yield and quality (Perotto et al. 2010). During Sept 2018, while screening garlic germplasm accessions for the presence of allexiviruses, symptoms like foliar mosaic and curling were observed on accession G-204, planted at an experimental plot of ICAR-DOGR, Pune, India. A total of five samples comprised of five randomly selected G-204 garlic plants were collected from the experimental plot. Each sample contained leaves from the top, middle, and bottom portion of the individual garlic plants. These samples were subjected to RNA extraction using the RNeasy Plant Mini Kit (Qiagen, Germany) followed by reverse transcription (RT) using the Transcriptor cDNA synthesis kit (Roche Diagnostics, GmbH, Germany). The extracted RNA was then tested for allexiviruses such as garlic virus A (GarV-A), garlic virus B (GarV-B), garlic virus C (GarV-C), garlic virus D (GarV-D), and garlic virus X (GarV-X) by polymerase chain reaction (PCR) (Gawande et al. 2015; Roylawar et al. 2019; Baranwal et al. 2011; Gieck et al. 2009). Leaf samples tested through RT-PCR were found positive for garlic viruses GarV-A, GarV-B, GarV-C, GarV-D, and GarV-X. Allexiviruses other than GarV-B had been previously reported in India and hence further tests were conducted to confirm GarV-B infection. RT-PCR using primers, CF 5'- ATGGGAGACAGGTCGCAA-3' and CR5'- CTAAAATGTAAGCATGAGCGGT-3' designed specific to the coat protein yielded a 735-bp amplicon from all five G-204 plants. The amplified product was purified using QIAquick PCR Purification Kit (Qiagen, Germany) and cloned in pJET1.2 vector (Thermo Scientific, Lithuania). Two clones containing the CP gene were bidirectionally sequenced, and a consensus sequence was submitted to GenBank (MN650206). BLASTn results indicated that this consensus sequence showed 97.96% nucleotide (KP657919.1) and 100% amino acid sequence (AKN19940.1) identity with the CP sequence of GarV-B isolate from Poland. The presence of GarV-B was confirmed by enzyme-linked immunosorbent assay (ELISA) using a double-antibody sandwich ELISA kit (Arsh Biotech, Delhi, India) as per the manufacturer's protocol. An absorbance of reaction was read using a microplate reader at 405 nm. The mean OD values of negative and positive controls were 0.034 and 0.373, respectively. The OD values of five samples tested ranged from 0.210 to 0.296 indicating a positive reaction for GarV-B. To assess the presence of GarV-B in the available genetic stock, we tested 30 garlic germplasm accessions for GarV-B using RT-PCR. Out of these, 17 accessions were found positive for GarV-B. GarV-B has been reported from many countries (Gieck et al. 2009). This is the first report of GarV-B from India. Globally, allexiviruses are known for their adverse impact on garlic production (Oliveira et al. 2014). GarV-B together with other viruses can be a potential threat to garlic production in India. Further, detailed evaluations are needed to study the impact of GarV-B on garlic production in India.

Heteroplasmy due to coexistence of mtCOI haplotypes from different lineages of the Thrips tabaci cryptic species group

Heteroplasmy is the existence of multiple mitochondrial DNA haplotypes within the cell. Although the number of reports of heteroplasmy is increasing for arthropods, the occurrence, number of variants, and origins are not well studied. In this research, the occurrence of heteroplasmy was investigated in Thrips tabaci, a putative species complex whose lineages can be distinguished by their mitochondrial DNA haplotypes. The results from this study showed that heteroplasmy was due to the occurrence of mitochondrial cytochrome oxydase I (mtCOI) haplotypes from two different T. tabaci lineages. An assay using flow cytometry and quantitative real-time PCR was then used to quantify the per cell copy number of the two mtCOI haplotypes present in individuals exhibiting heteroplasmy from nine geographically distant populations in India. All of the T. tabaci individuals in this study were found to exhibit heteroplasmy, and in every individual the per cell copy number of mtCOI from lineage 3 comprised 75-98% of the haplotypes detected and was variable among individuals tested. There was no evidence to suggest that the presense of lineage-specific haplotypes was due to nuclear introgression; however, further studies are needed to investigate nuclear introgression and paternal leakage during rare interbreeding between individuals from lineages 2 and 3.

First Report of Iris yellow spot virus Infecting Allium tuberosum in India

Allium tuberosum L., commonly known as garlic chives, is an important spice in northeastern India as well as in many other parts of the world. Iris yellow spot virus (IYSV; genus Tospovirus, family Bunyaviridae) is an important pathogen of onion (4) and other related Alliums such as garlic (3) and leek (2). During April 2013, symptoms potentially induced by IYSV such as chlorotic and straw-colored spindle-like lesions were observed on leaves of A. tuberosum accession Hanzong Winter (CGN 20779) plants in the wild species garden at the Directorate of Onion and Garlic Research (DOGR), Rajgurunagar, Pune, Maharashtra, India. Ten plant samples of A. tuberosum were randomly collected from the wild species garden and the upper, middle, and lower portions of the leaves were pooled and tested by double-antibody sandwich (DAS)-ELISA using a commercially available kit (Agdia Inc., Elkhart, IN) for IYSV. All of them showed positive results for IYSV incidence. Total RNA from the ELISA positive leaf samples of A. tuberosum was extracted using the RNeasy Plant Mini kit (Qiagen GmbH, Hilden, Germany). The primer pair IYSV-F (5'-TCAGAAATCGAGAAACTT-3') and IYSV-R (5'-TAATTATATCTATCTTTCTTGG-3') (1) was used for RT-PCR. The primer pair was specific to amplify 797 bp of the nucleocapsid (N) gene of IYSV. The amplified product derived from A. tuberosum isolate was purified by QIAquick PCR Purification Kit (Qiagen) and cloned using the vector pDrive (Qiagen). The recombinant clone was sequenced (Accession No. KF624624). Sequence analysis performed on CLC Main Workbench Version 6.8.4 confirmed that the fragment was of IYSV. Nucleotide sequence comparison of our virus with other IYSV isolates revealed that the highest nucleotide identity (99%) was with the IYSV garlic isolate (HM173691) from India. Further, maximum 96% protein identity was with IYSV onion isolate (ACA09432) and garlic isolate (ADK56108) from India. To our knowledge, this is the first report of IYSV naturally occurring on A. tuberosum in India. It is evident from previous studies that IYSV causes significant losses in onions (1) and from this study, that its symptoms have direct impact on quality of garlic chives. Further detailed studies are required to assess the magnitude of the impact of IYSV infection on yield and quality of A. tuberosum. References: (1) A. Bulajic et al. Plant Dis. 93:976, 2009. (2) M. C. Córdoba-Sellés et al. Plant Dis. 91:1365, 2007. (3) S. J. Gawande et al. Plant Dis. 94:1066, 2010. (4) B. Mandal et al. Plant Dis. 96:468, 2012.

First Report of Leek yellow stripe virus in Allium sativum in Western India

Garlic (Allium sativum L.) is an important bulbous spice crop in India as well as other parts of world. Garlic is well known for its medicinal properties. Degeneration due to viral infections is one of the important constraints in exploiting its yield potential. Leek yellow stripe virus (LYSV), genus Potyvirus, family Potyviridae, is a prominent virus known to infect garlic worldwide (4). During July 2013, potyvirus-like symptoms such as mosaic, streaking, stunting, mottling of leaves were observed on garlic cv. G-41 and landrace Ranibennur local, collected from Karnataka, India, and maintained at the Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India. The incidence of symptomatic plants was estimated at 70% for Ranibennur local and 68% for cv. G-41. The symptomatic leaves were sampled diagonally from the field. Twenty symptomatic plants per cultivar with each sample was composited from young, middle, and lower (basal) leaves of the plant. These samples were tested by double-antibody sandwich (DAS)-ELISA for LYSV using commercially available kit (Agdia Inc., Elkhart, IN). ELISA-positive plants were further subjected to molecular studies. Total RNA from the infected leaf samples were extracted by RNeasy Plant Mini kit (Qiagen GmbH, Hilden, Germany) and assayed by reverse transcription (RT)-PCR using primer pair LYSV-F 2 (5'-GCACCATACAGTGAATTGAG-3') (1), LYSV-R (5'-GCCTCGCGCGCTCTAA-3') (3) to amplify 874 bases of partial Nib and partial coat protein gene. The amplified product of 874 bp derived from A. sativum isolate was purified (QIAquick PCR Purification Kit, Qiagen) and cloned using vector pDrive (Qiagen). The recombinant clones were sequenced and submitted in NCBI database (GenBank Accession No. KF850539). The sequence analysis performed on CLC Main Workbench Version 6.8.4 gave confirmation of LYSV. Further, phylogenetic analysis of the 874-nt sequence revealed the highest nucleotide identity (80 to 82%) with LYSV isolates (DQ925453, JN127339, AB005611, and JX429965). To the best of our knowledge, this is the first report of natural infection of garlic by LYSV in western India. LYSV is known to cause direct losses in garlic and other related Allium spp. Up to 54% reduction in bulb weight was observed due to single infection of this virus (2). Hence, our first report about this virus has significant impact on garlic production scenario, if this virus found to be widespread in the country. For this, additional surveys and genotype screenings are needed to obtain a better understanding of the potential impact of LYSV on garlic production in India. References: (1) H. Fidan and S. Baloglu. Plant Dis. 93:672, 2009. (2) H. Lot et al. Plant Dis. 82:1381, 1998. (3) P. Lunello et al. J. Virol. Methods. 118:15, 2004. (4) H. R. Pappu et al. Plant Dis. 89:205, 2005.

First Report of Iris yellow spot virus on Garlic in India

Garlic (Allium sativum) is a spice crop of prime importance in India as well as other parts of the world. Iris yellow spot virus (IYSV; genus Tospovirus, family Bunyaviridae) is an important pathogen of onion bulb and seed crops in many parts of the world (3). The virus is also known to infect garlic and other Allium spp. (2-4). IYSV infection of garlic was reported from Reunion Island (4) and the United States (1). In February 2010, straw-colored, spindle-shaped spots with poorly defined ends were observed on the leaves of a garlic crop at the research farm of the Directorate of Onion and Garlic Research in the Pune District of Maharashtra State, India, 105 days after planting. The spots coalesced to form larger patches on the leaves, suggesting possible IYSV infection. Symptoms were visible on older leaves and more prevalent on cv. G-41, G-282, AC50, AC200, AC283, and Godavari than on other cultivars. The incidence of symptomatic plants was estimated at 5% for G-41 and AC-200, 8% for G-282 and AC283, and 10% for AC50. Leaves were sampled from 40 symptomatic plants per cultivar with each sample composited from young, middle, and older (basal) leaves of the plant. Samples were assayed by double-antibody sandwich-ELISA (Loewe Biochemica GmbH, Sauerlach, Germany) and each tested positive for the virus. Total RNA was extracted from the leaves of ELISA-positive plants using the RNAeasy Plant Mini kit (Qiagen GmbH, Hilden, Germany) and tested by reverse transcription-PCR assay using primers IYSV-F (5'-TCAGAAATCGAGAAACTT-3') and IYSV-R (5'-TAATTATATCTATCTTTCTTGG-3') (2) designed to amplify 797 bp of the nucleocapsid (N) gene of IYSV. Amplicons of expected size were obtained and cloned into a pDrive vector (Qiagen GmbH). The recombinant clone was sequenced (GenBank Accession No. HM173691). Sequence comparisons showed 98 to 100% nt identity with other IYSV N gene sequences in GenBank (Nos. EU310294 and EU310286). A phylogenetic analysis of the deduced amino acid sequences of the N gene showed that the garlic isolate of IYSV grouped most closely with onion IYSV isolates from India (GenBank Nos. EU310294, EU310286, EU310300, and EU310296). To our knowledge, this is the first report of natural infection of garlic by IYSV in India. Additional surveys and evaluations are needed to obtain a better understanding of the potential impact of IYSV on garlic production in India. References: (1) S. Bag et al. Plant Dis. 93:839, 2009. (2) A. Bulajic et al. Plant Dis. 93:976, 2009. (3) D. Gent et al. Plant Dis. 90:1468, 2006. (4) I. Robène-Soustrade et al. Plant Pathol. 55:288, 2006.