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    Prediction of RNA editing sites and genome-wide characterization of PERK gene family in maize (Zea mays L.) in response to drought stress
    (Elsevier, 2022) Shahid, Shahmeer; Sher, Muhammad Ali; Ahmad, Furqan; Rehman, Shoaib Ur; Farid, Babar; Raza, Humayun; Ali, Zulfiqar
    Objectives: Inadvertent climate changes continuously threating the crops production and thus affecting the livelihood of peoples across the world. The maize production at world level has severely been hampered by the drought stress. Proline-rich extensin-like receptor kinases (PERKs) are considered among the sub-class of plants larger protein family, receptor kinases. Member of PERK gene family play significant role in both abiotic and biotic stress and in various plant metabolic activities and pathways.Methods: As of now, no comprehensive research is reported for PERK genes in maize. We have performed a genome wide in-silico analysis and identify twenty-three PERK genes in maize. We performed phylogenetic analysis, sequence logos, motif analysis, promoter analysis, chromosomal and subcellular localization, synteny and expression analysis using RNA seq data under drought stress. We also predict RNA editing sites in mitochondrial and chloroplast genome.Results: Phylogenetic study of PERK genes from eight different plant species divided into four distinct clades. Four subclasses group of ZmPERKs were observed based on domain organization, motif pattern, and phylogenetic analysis. The exon-intron arrangement of the ZmPERK were conserved among members of the same subclasses. In the promoter region different cis-elements were found those were involved in the growth and development, as well as light and stress response. Through gene duplication analysis it was observed that segmental duplications in ZmPERKs played major role in maize evolution. The Ka/Ks ratios indicated that most ZmPERK genes during the evolution have experienced strong purifying selection. The conversion of cytosine (C) to uracil (U) was observed in all predicted editing sites (U). These transitions were mostly based on changes in the first and second codon bases. The in-silico expression analysis of transcriptome data revealed the differential expression of ZmPERK genes in response to drought stress and oil content accumulation.Conclusion: The current study provides base information on the PERK gene family in maize. Our findings can serve as a reference for further functional analysis of ZmPERKs. These genes can be further explored and used in breeding program to develop cultivars resilient to drought stress. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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    Sero-RAPD makers based evaluation of chilli pepper germplasm for resistance to chilli veinal mottle virus
    (Elsevier, 2022) Saba, Sehrish; Ashfaq, Muhammad; Mehmood, Mirza Abid; Ahmad, Furqan; Alfarraj, Saleh; Ansari, Mohammad Javed; Maqbool, Amir
    Background: Chilli veinal mottle virus is a remarkable threat to chilli crops worldwide including Pakistan. Methods: In the present study, 18 chilli pepper genotypes were catalogued against ChiVMV ATIPK isolate by using DAS-ELISA with virus-specific polyclonal antisera. Results: Out of 18 genotypes, four genotypes viz., Loungi pepper, Sanam, Red Pepper, and CV-1 were categorized as highly susceptible followed by three susceptible (Soofi, Royal Wonder, Pepper PLSQ) and four (Yolo wonder, Bhakkar Local, CIM-506, CR-25) were moderately susceptible. The plants of these genotypes exhibited characteristic symptoms of ChiVMV and accumulated a high level of virus titer. The rest of three (California wonder, Gola Peshawar, Red top) and four (CV-7, Hot Pepper, Doni Pepper, Ghotki) genotypes were grouped as resistant and moderately resistant, respectively. Three resistant and three highly susceptible genotypes were further appraised for genetic diversity by RAPD markers and a total of 75 bands were scored, 76% of them unveiled polymorphism with an amplification range of 5-9 bands. Genetic analysis revealed 44-78.67% similarities with Mean Similarity Index (MSI) ranging from 59.46 to 65.86%. Most of the primers were highly informative with PIC value fluctuated from 0.388 to 0.666, with an average value of 0.512. Cluster analysis further confirmed and clustered both groups of genotypes in a separate clade. Conclusion: It is concluded that genotypes; California Wonder and Red Top showed diverse response from other genotypes, not only based on symptoms and ELISA but also on markers' basis. Therefore, these genotypes could be useful as ChiVMV resistant sources in the chilli breeding program. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of King Saud University.