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    Exploring differentially expressed genes in Phaseolus vulgaris L. during BCMV infection
    (Academic Press Ltd- Elsevier Science Ltd, 2024) Yeken, Mehmet Zahit; Celik, Ali; Emiralioglu, Orkun; Ciftci, Vahdettin; Baloch, Faheem Shehzad; Ozer, Goksel
    Bean common mosaic virus (BCMV) is a significant pathogen that affects common bean, leading to substantial yield losses and reduced crop quality. To mitigate BCMV attacks, certain genes, including diacylglycerol kinases genes (PvDGKs), genes associated with defense and stress responses (PvGST, PvPAL, PvLOX, and PvPOD), as well as genes related to plant defense (PvPR1, PvPR2, and PvPR3) play an essential functional role in various stress responses in common bean. In this study, the expression levels of PvDGK1, PvDGK2, PvDGK3, PvDGK5a, PvDGK5b, PvDGK6, PvGST, PvPAL, PvLOX, PvPOD, PvPR1, PvPR2, and PvPR3 genes were investigated in the leaves of different common bean genotypes under BCMV infection conditions. Through quantitative real -time PCR analysis, we observed varying expression patterns for all these genes at different time points during viral infection. The tolerant genotype exhibited higher expression levels of all PvDGKs, PvGST, PvPAL, PvPOD, PvPR1, and PvPR2 genes compared to the susceptible genotype, with the PvPR1 gene showing the highest transcript levels. These findings provide the initial evidence of the potential roles of PvDGKs, PvGST, PvPAL, PvLOX, PvPOD, PvPR1, PvPR2, and PvPR3 in responding to the stress induced by BCMV in common bean. The results presented herein will serve as a valuable resource for guiding future breeding studies aimed at addressing BCMV-induced stress in common bean cultivation.
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    New Detection Methods for Cryphonectria Hypovirus 1 (CHV1) through SYBR Green-Based Real-Time PCR and Loop-Mediated Isothermal Amplification (LAMP)
    (Mdpi, 2024) Celik, Ali; Cakar, Deniz; Dervis, Sibel; Morca, Ali Ferhan; Simsek, Secil Akilli; Romon-Ochoa, Pedro; Ozer, Goksel
    Some mycoviruses can be considered as effective biocontrol agents, mitigating the impact of phytopathogenic fungi and consequently reducing disease outbreaks while promoting plant health. Cryphonectria parasitica, the causal agent of chestnut blight and a highly destructive pathogen, experienced a notable decrease in its virulence with the identification of cryphonectria hypovirus 1 (CHV1), a naturally occurring biocontrol agent. In this study, two innovative diagnostic protocols designed for the accurate and efficient detection of CHV1 are introduced. The ORF A and ORF B regions of CHV1 are targeted by these techniques, which employ colorimetric loop-mediated isothermal amplification (LAMP) with 2 Colorimetric LAMP Master Mix and real-time quantitative PCR (qPCR) with SYBR Green chemistry, respectively. The LAMP assay presents a discernible color transition, changing from pink to yellow after a 35 min incubation period. Comparative analysis, when assessed against two established reverse transcription-PCR (RT-PCR) techniques, reveals a significant enhancement in sensitivity for both the LAMP approach, which offers a tenfold increase, and the qPCR method, which showcases a remarkable 100-fold sensitivity improvement. Throughout the comparison phase, it was evident that the RT-PCR, LAMP, and qPCR procedures displayed superior performance compared to the Bavendamm test, relying on phenol oxidase activity, effectively distinguishing hypovirulent strains. Consequently, this study introduces two pioneer diagnostic assays for highly sensitive CHV1 detection, representing a substantial advancement in the realm of CHV1 surveillance techniques. These methodologies hold significant promise for enhancing research endeavors in the domain of the biological control of C. parasitica.
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    Turkish isolates of alfalfa mosaic virus belong to a distinct lineage among global population
    (Academic Press Ltd- Elsevier Science Ltd, 2024) Morca, Ali Ferhan; Akbas, Birol; Santosa, Adyatma Irawan; Topkaya, Serife; Celik, Ali
    Complete RNA3 sequences of 15 alfalfa mosaic virus (AMV) isolates sampled from Afyonkarahisar, Ankara, Konya, Tokat, Kayseri, and Nevs , ehir Provinces of T & uuml;rkiye were obtained using RT-PCR with two primer pairs designed in this study. Molecular and population analyses were performed on them together with 63 global isolates which full genome sequences available in NCBI GenBank. Phylogenetic analysis based on movement protein (MP) and coat protein (CP) regions showed unrelated isolates clustering between the constructed trees, and the new Turkish isolates were dispersed in different phylogroups. Particularly, three new Turkish potato isolates: B6, K1, and K2 occupied a divergent MP lineage, together with one alfalfa isolate from China: ZM1 NX3. S , eta, and k parameters of genetic diversity confirmed that CP were more conserved than MP sequences. The 15 new Turkish isolates shared 95.4 -100% nucleotide and 94 -100% amino acid, and 92.8 -100% nucleotide and 93.3 -100% amino acid identities among themselves at MP and CP regions, respectively. All tested populations were found to be under very strict purifying constraints (dN/dS ratios of 0.061 -0.219), and had undergone recent expansion, probably due to new mutations in their genome, according to diversity and neutrality tests. Fixation index ( F ST ) values obtained by pairwise comparisons of phylogroups were all above 0.33, suggested that the isolates clustering has been done convincingly.