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

Nimra Maheen, Muhammad Shafiq (), Saleha Sadiq, Muhammad Farooq, Qurban Ali, Umer Habib, Muhammad Adnan Shahid, Asjad Ali and Fawad Ali ()
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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

Agriculture, 2023, vol. 13, issue 6, 1-21

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.

Keywords: Citrus reticulata; expression pattern; genome; WRKY transcription factor gene family (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2023
References: View references in EconPapers View complete reference list from CitEc
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