Current status, spatiotemporal dynamics and genetic recombination analysis of cucurbit aphid-borne yellows virus (CABYV) infecting cucurbits in Punjab, Pakistan

Abstract

Cucurbits are important vegetable crops of Pakistan which are severely affected by various diseases. Keeping in view the importance of viral diseases, the present study was aimed to conduct systematic surveys of the tunnel and open field cucurbit crops in Punjab, Pakistan during 2019 and 2020. The cucurbits leaf samples with virus and virus-like symptoms were collected from the farmers fields and tunnels with no prior knowledge about sanitation and subjected to reverse transcription-polymerase chain reaction (RT-PCR) for poleroviruses incidence. The mean highest disease incidence was recorded in samples collected from district Rawalpindi (47.42%) and the mean lowest disease incidence was observed in samples of district Faisalabad (30.95%) with an overall disease incidence of 40.48% observed during 2019 and 2020. Newly detected Pakistani CABYV isolates shared 99.6 % and 94.7-96.2% nucleotide identities among themselves and with isolates retrieved from NCBI GenBank. Phylogenetic analysis showed that current study isolates i.e., OL828566 and OL828567 clustered in separate clades with isolates JQ700305, JF939814 and X7693 from Taiwan, Spain and France, respectively while isolates from Thailand, China, and Korea were grouped separately. It was evident with restriction fragment length polymorphism (RFLP) analysis that the present study CABYV isolates were grouped into two types, which seemed to be genetically similar to those identified during 2011–2015 and 2015–2021. Recombination detection analysis showed that newly detected CABYV isolates are likely to be recombinant of Spanish (JF939814) and South Korean (KR231950) isolates having the recombination breakpoint between nucleotide position number 272 and 830. Comparison and recombination detection analysis of the local isolates might help in devising a breeding program to identify resistant sources against recombinant isolates.

Keywords

• Cucurbits
• Recombination
• In silico RFLP
• RT-PCR