Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.)

Sandhya Tyagi; Shailendra Kumar Jha; Anuj Kumar; Gautam Saripalli; Ramesh Bhurta; Deepak T Hurali; Lekshmy Sathee; Niharika Mallick; Reyazul Rouf Mir; Viswanathan Chinnusamy; Vinod

doi:10.3389/fgene.2022.972474

Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.)

Front Genet. 2022 Sep 30:13:972474. doi: 10.3389/fgene.2022.972474. eCollection 2022.

Affiliations

¹ Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
² Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.
³ Centre for Agricultural Bioinformatics (CABin), Indian Agricultural Statistics Research Institute, New Delhi, India.
⁴ Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States.
⁵ Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Wadura Campus, Srinagar, India.

Abstract

Cyclophilins (CYPs) are a group of highly conserved proteins involved in host-pathogen interactions in diverse plant species. However, the role of CYPs during disease resistance in wheat remains largely elusive. In the present study, the systematic genome-wide survey revealed a set of 81 TaCYP genes from three subfamilies (GI, GII, and GIII) distributed on all 21 wheat chromosomes. The gene structures of TaCYP members were found to be highly variable, with 1-14 exons/introns and 15 conserved motifs. A network of miRNA targets with TaCYPs demonstrated that TaCYPs were targeted by multiple miRNAs and vice versa. Expression profiling was done in leaf rust susceptible Chinese spring (CS) and the CS-Ae. Umbellulata derived resistant IL "Transfer (TR). Three homoeologous TaCYP genes (TaCYP24, TaCYP31, and TaCYP36) showed high expression and three homoeologous TaCYP genes (TaCYP44, TaCYP49, and TaCYP54) showed low expression in TR relative to Chinese Spring. Most of the other TaCYPs showed comparable expression changes (down- or upregulation) in both contrasting TR and CS. Expression of 16 TaCYPs showed significant association (p < 0.05) with superoxide radical and hydrogen peroxide abundance, suggesting the role of TaCYPs in downstream signaling processes during wheat-leaf rust interaction. The differentially expressing TaCYPs may be potential targets for future validation using transgenic (overexpression, RNAi or CRISPR-CAS) approaches and for the development of leaf rust-resistant wheat genotypes.

Keywords: bread wheat; cyclophilin; genome-wide identification; leaf rust resistance; reactive oxygen species.