DefinePK

Research Objective

To identify and determine the genetic variability of begomoviruses infecting soybean crop in Pakistan and to identify the whitefly mitotype(s) involved in their transmission.

Methodology

Soybean plants exhibiting viral symptoms were collected. Total genomic DNA was extracted from symptomatic leaves and viruliferous whiteflies. Diagnostic PCR was used to detect begomoviruses, followed by whole genome amplification using rolling circle amplification (RCA). RCA products were cloned and sequenced. The partial cytochrome oxidase subunit I (COI) gene of whiteflies was amplified and sequenced. Sequences were assembled using Geneious R10, and BLAST analysis was performed. Similarity index matrices and phylogenetic trees were constructed using sequence demarcation tool (SDT), MEGA11, and MrBayes software.

Methodology Flowchart

                        graph TD
    A[Collect symptomatic soybean plants and whiteflies] --> B[Extract total genomic DNA from leaves and whiteflies];
    B --> C[Diagnostic PCR for Begomoviruses];
    C -- Positive --> D[Whole Genome Amplification using RCA];
    D --> E[Clone and sequence RCA products];
    B --> F[Amplify and sequence partial COI gene of whiteflies];
    E --> G[Assemble begomovirus sequences using Geneious R10];
    F --> H[Assemble whitefly COI sequences using Geneious R10];
    G --> I[BLAST analysis and sequence similarity comparison];
    H --> I;
    I --> J[Construct phylogenetic trees using SDT, MEGA11, MrBayes];
    J --> K[Identify begomovirus and whitefly mitotype];                    

Discussion

The study confirmed the presence of ToLCNDV infecting soybean in Pakistan, which is a novel report. The identification of the Asia II-1 mitotype on soybean plants in Pakistan is also a first report. This finding is significant as the Asia II-1 mitotype is considered invasive and can impact begomovirus transmission to new hosts, potentially leading to new recombinant species and variants.

Key Findings

The begomovirus Multan isolate showed 98% similarity with Tomato Leaf Curl New Delhi virus (ToLCNDV). The COI gene sequence of Bemisia tabaci showed 99.9% similarity with the Asia II-I mitotype found in Pakistan. The study confirmed the infection of ToLCNDV and the presence of Asia-II-I mitotype on soybean in Multan, Pakistan.

Conclusion

This study confirms the presence of ToLCNDV and the Asia II-1 mitotype on soybean crops in Pakistan, marking the first report of a begomovirus-whitefly complex on soybean in the country. This research will aid in developing management strategies for begomovirus-whitefly complexes in Pakistan.

Fact Check

1. Virus Identification: The study identified the begomovirus Multan isolate with 98% similarity to Tomato Leaf Curl New Delhi virus (ToLCNDV).
2. Whitefly Mitotype Identification: The study identified the whitefly mitotype with 99.9% similarity to Asia II-I.
3. Publication Date: The article was published in J. Agric. Biol. 02(2) 2024.

Mind Map