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

Author:

Maheen Nimra1,Shafiq Muhammad2ORCID,Sadiq Saleha1,Farooq Muhammad1ORCID,Ali Qurban3ORCID,Habib Umer4,Shahid Muhammad Adnan5,Ali Asjad6ORCID,Ali Fawad67ORCID

Affiliation:

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

2. Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan

3. Department of Plant Breeding and Genetics, University of Punjab, Lahore 545900, Pakistan

4. Department of Horticulture, PMAS Arid Agriculture University, Murree Road, Rawalpindi 46000, Pakistan

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

6. Queensland Department of Agriculture and Fisheries, Mareeba, QLD 4880, Australia

7. 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 C2H2 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.

Publisher

MDPI AG

Subject

Plant Science,Agronomy and Crop Science,Food Science

Reference69 articles.

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