Optimization of tissue and time for rapid serological and molecular detection of Apple stem pitting virus and Apple stem grooving virus in apple’

Nabi, Sajad Un; Mir, Javid Iqbal; Sharma, O.C.; Singh, D. B.; Zaffer, Shafia; Sheikh, M. A.; Masoodi, Lubna; Khan, Kamran Ahmed

doi:10.1007/s12600-018-0701-7

Cited by 15 publications

(10 citation statements)

References 26 publications

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“…A similar pattern was also found for the distribution of ASGV, ASPV, ACLSV, and ASSVd in a 15‐year‐old pear plant (Jingbaili). The distribution pattern of ASGV and ASPV in pear plants differed from that observed by Nabi et al (2018) in apple trees, where the two viruses were not present in apple fruit. A similar phenomenon has also been reported by Wang et al (2010), who found that the distribution pattern of ASGV and ACLSV in pear shoots in vitro differs from that in apple shoots in vitro (Knapp et al, 1995).…”

Section: Discussioncontrasting

confidence: 89%

Incidence of major pome fruit tree viruses and viroids in commercial pear orchards in China and in Pyrus betulifolia seedlings

Huang

et al. 2021

Plant Pathology

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Latent viral infections are common in pome fruit trees, including apple, pear, and quince, leading to significant reductions in yield and quality (reviewed by Umer et al., 2019). Twenty-one viruses, belonging to 12 genera classified into nine families, have been identified to infect pome fruit trees (Umer et al., 2019). In addition, a novel virus, provisionally named pear chlorotic leaf spot-associated virus (PCLSaV), has been recently identified in pear trees in China (Liu et al., 2020). Among them, apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), and apple mosaic virus (ApMV) are considered the most economically important viruses affecting pome fruit trees worldwide. In

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Section: Discussioncontrasting

confidence: 89%

Incidence of major pome fruit tree viruses and viroids in commercial pear orchards in China and in Pyrus betulifolia seedlings

Huang

et al. 2021

Plant Pathology

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“…In our previous studies, we reported the association of ApNMV as a more likely cause than ApMV by conducting the survey among various apple cultivars exhibiting either mosaic or mosaic–necrotic symptoms in major apple-growing districts of Kashmir valley. ApNMV was found to be associated with five cultivars of apple (Red Delicious, Golden Delicious, Oregon Spur, Royal Delicious and Fuji Aztec) whereas ApMV was found to be associated with only two cultivars (Red Delicious and Golden Delicious) [ 37 ]. Despite the presence of ApNMV in the GD cultivar, necrosis was absent, which may be due to the presence of a higher percentage of ApMV reads than ApNMV.…”

Section: Discussionmentioning

confidence: 99%

“…For RT-PCR, specific primer pairs ( Table S1 ) reported earlier was used to amplify genomic regions corresponding to the coat protein or replicase genes. RT-PCR was performed in a 30-cycle program with denaturation at 94 °C for 30 s, annealing at 50 °C for ApNMV, 53 °C for ApMV [ 35 ], 50 °C for ASGV and 55 °C for ASPV and AHVd for 45 s [ 31 , 37 ], followed by extension at 72 °C for 30 s with a final extension at 72 °C for 7 min. The reagents were the same except the cDNA template and forward and reverse primers of specific viruses/viroids.…”

Section: Methodsmentioning

confidence: 99%

High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid

Nabi

Rao

Mansoor

et al. 2022

Plants

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Many viruses have been found associated with apple mosaic disease in different parts of the world. In order to reveal and characterize the viruses and viroids in symptomatic apple plants, next-generation sequencing (RNA seq.) of rRNA-depleted total RNA using Illumina Hiseq2500 was applied to two cultivars, Oregon Spur and Golden Delicious, with symptoms of mosaic and necrosis and one cultivar, Red Fuji, which was asymptomatic. The RNA sequencing detected five viruses, viz., apple necrotic mosaic virus (ApNMV), apple mosaic virus (ApMV), apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), and one viroid i.e., apple hammerhead viroid (AHVd). RT-PCR amplification and sequencing also confirmed the presence of all these five viruses and viroids detected in HTS of total RNA. The complete genomes of five viruses and AHVd were reconstructed. The phylogenetic analysis of these viruses and AHVd revealed genetic diversity by forming subclusters with isolates from other countries. Recombination events were observed in all five viruses while single-nucleotide variants were detected only in ApMV and ApNMV. The absence of ApMV and ApNMV in asymptomatic samples from the same cultivars in an RT-PCR assay indicated that these two viruses are associated with mosaic disease of apples in India. This is the first viral genome analysis of symptomatic and asymptomatic apple plants and the first report of genome characterization of viruses associated with apple mosaic disease from India. High-throughput RNA sequencing is a powerful tool to characterize the genome of viruses and viroids in plants previously undetected by conventional methods. This would also help in the indexing and certification of large-scale germplasm.

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“…Nearly 14 viruses Letters in Applied Microbiology 74, 586--592 © 2021 The Society for Applied Microbiology and 4 viroids have been reported to infect apple crops throughout the world (Nabi et al 2020a). The major viruses infecting apples throughout the world including India are apple mosaic virus (ApMV), apple stem pitting virus (ASPV), apple stem grooving virus (ASGV) and apple chlorotic leaf spot virus (ACLSV) (Padder et al 2011;Verma et al 2014;Katwal et al 2016;Nabi et al 2018Nabi et al , 2019. Recently, a new virus (ApNMV) and viroid (apple hammerhead viroid-AHVd) have been reported from the mosaic affected apple cultivars in India (Nabi and Baranwal 2020;Nabi et al 2020a).…”

Section: Introductionmentioning

confidence: 99%

Development of multiplex RT-PCR assay for simultaneous detection of four viruses infecting apple (Malus domestica)

Nabi

Madhu

Rao³

2022

Letters in Applied Microbiology

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Significance and Impact of the Study: In India, a new virus, apple necrotic mosaic virus (ApNMV), has been found to infect the apple trees along with ApMV, apple stem pitting virus (ASPV) and apple stem grooving virus (ASGV). This study was designed to detect the ApNMV along with three other viruses (ApMV, ASPV and ASGV) simultaneously using multiplex RT-PCR in a single tube. The assay developed in this study will be an effective detection tool for large-scale surveys and indexing of large apple germplasm for the production of virus-free planting material in temperate fruits. This will also help in studying the distribution of all the four viruses in apple growing regions of India and abroad.

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Optimization of tissue and time for rapid serological and molecular detection of Apple stem pitting virus and Apple stem grooving virus in apple’

Cited by 15 publications

References 26 publications

Incidence of major pome fruit tree viruses and viroids in commercial pear orchards in China and in Pyrus betulifolia seedlings

Incidence of major pome fruit tree viruses and viroids in commercial pear orchards in China and in Pyrus betulifolia seedlings

High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid

Development of multiplex RT-PCR assay for simultaneous detection of four viruses infecting apple (Malus domestica)

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