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Genome Identification and Characterization of WRKY Transcription Factor Gene Family in Mandarin ( Citrus reticulata )

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Listed:
  • Nimra Maheen

    (Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan)

  • Muhammad Shafiq

    (Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan)

  • Saleha Sadiq

    (Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan)

  • Muhammad Farooq

    (Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan)

  • Qurban Ali

    (Department of Plant Breeding and Genetics, University of Punjab, Lahore 545900, Pakistan)

  • Umer Habib

    (Department of Horticulture, PMAS Arid Agriculture University, Murree Road, Rawalpindi 46000, Pakistan)

  • Muhammad Adnan Shahid

    (Horticultural Sciences Department, University of Florida/IFAS, North Florida Research and Education Center, Quincy, FL 32351, USA)

  • Asjad Ali

    (Queensland Department of Agriculture and Fisheries, Mareeba, QLD 4880, Australia)

  • Fawad Ali

    (Queensland Department of Agriculture and Fisheries, Mareeba, QLD 4880, Australia
    Centre of Planetary Health and Food Security, Griffith University, Nathan Campus, Brisbane, QLD 4111, Australia)

Abstract

WRKY proteins are an important group of transcription factors (TFs) gene family and were identified primarily in plants. WRKY TFs play vital roles in modulating gene expression when plants face detrimental effects due to the environment. In the current study, we focused on using the mandarin citrus ( Citrus reticulata ) genome to understand the impact of the WRKY gene family on the extraction of alleles mining in mandarins. The mining of the C. reticulata genome identified 46 CrWRKY genes that were classified into three main groups (G1, G2, and G3) further with five subclasses (IIa, IIb, IIc, Iid, and IIe) in the G2 group, and all were presented on 29 scaffolds representing numerous segmental duplications of 100% events established. Multiple sequence analysis predicted the presence of the “WRKYGQK” domain and metal-chelating zinc-finger motif C 2 H 2 in 45 genes, while the “WRKYGQK” domain was replaced with “WRKYGKK” only in CrWRKY20. The comparative relationship of CrWRKY with other plant species using dual synteny analysis revealed that the divergence between C. reticulata and C. grandis occurred after the evolutionary divergence of C. clementine , C. sinensis , C. medica , and C. ichangensis . The possible functions of the CrWRKY genes in mitigating environmental effects were predicted using cis-regulatory elements analysis and in silico RNAseq analysis, for the development of plants. These results provide a robust platform and absence of knowledge for the functional identification from key genes of CrWRKY genes in the mandarin for the possible use to improve key desirable agronomic and consumer-driven fruit quality traits in mandarins and related species.

Suggested Citation

  • Nimra Maheen & Muhammad Shafiq & Saleha Sadiq & Muhammad Farooq & Qurban Ali & Umer Habib & Muhammad Adnan Shahid & Asjad Ali & Fawad Ali, 2023. "Genome Identification and Characterization of WRKY Transcription Factor Gene Family in Mandarin ( Citrus reticulata )," Agriculture, MDPI, vol. 13(6), pages 1-21, June.
    • Handle: RePEc:gam:jagris:v:13:y:2023:i:6:p:1182-:d:1161944
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    References listed on IDEAS

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    1. Rui Xia & Chengjie Chen & Suresh Pokhrel & Wuqiang Ma & Kun Huang & Parth Patel & Fuxi Wang & Jing Xu & Zhongchi Liu & Jianguo Li & Blake C. Meyers, 2019. "24-nt reproductive phasiRNAs are broadly present in angiosperms," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
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