Comprehensive genomic survey, structural classification and expression analysis of CH-type zinc finger factor in wheat (Triticum aestivum L.).

Background: The CH-type zinc finger proteins (CH-ZFPs) are one of major classes of transcription factors that play important roles in plant growth, development and stress responses. Limit information about the CH-ZF genes hinders the molecular breeding in bread wheat (Triticum aestivum).

Results: In this study, 457 CH-ZFP proteins (including 253 splice variants), which contain four types of conserved domain (named Q, M, Z, and D), could be further classified into ten subsets. They were identified to be distributed in 21 chromosomes in T. aestivum. Subset-specific motifs, like NPL-, SFP1-, DL- (EAR-like-motif), R-, PL-, L- and EK-, might make CH-ZFP diverse multifunction. Interestingly, NPL- and SFP1-box were firstly found to be located in CH-ZFP proteins. Synteny analyses showed that only 4 pairs of CH family genes in T. aestivum, 65 genes in B. distachyon, 66 genes in A. tauschii, 68 genes in rice, 9 genes in Arabidopsis, were syntenic relationships respectively. It indicated that TaZFPs were closely related to genes in Poaceae. From the published transcriptome data, totally 198 of 204 TaCH-ZF genes have expression data. Among them, 25 TaCH-ZF genes were certificated to be significantly differentially expressed in 5 different organs and 15 different development stages by quantitative RT-PCR. The 18 TaCH-ZF genes were verified in response to heat, drought, and heat & drought stresses. According to expression pattern analysis, several TaZFPs, like Traes_5BL_D53A846BE.1, were not only highly expressed in L2DAAs, RTLS, RMS, but also endowed tolerance to drought and heat stresses, making them good candidates for molecular breeding.

Conclusions: This study systematically characterized the TaCH-ZFPs and their potential roles in T. aestivum. Our findings provide new insights into the CH-ZF genes in T. aestivum as well as a foundation for further studies on the roles of TaCH-ZF genes in T. aestivum molecular breeding.