Comprehensive genomic survey, structural classification and expression analysis of C2H2-type zinc finger factor in wheat (Triticum aestivum L.)

Abstract

Background The C2H2-type zinc finger proteins (C2H2-ZFPs) are one of major classes of transcription factors that play important roles in plant growth, development and stress responses. Limit information about the C2H2-ZF genes hinders the molecular breeding in bread wheat (Triticum aestivum). Results In this study, 457 C2H2-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 C2H2-ZFP diverse multifunction. Interestingly, NPL- and SFP1-box were firstly found to be located in C2H2-ZFP proteins. Synteny analyses showed that only 4 pairs of C2H2 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 TaC2H2-ZF genes have expression data. Among them, 25 TaC2H2-ZF genes were certificated to be significantly differentially expressed in 5 different organs and 15 different development stages by quantitative RT-PCR. The 18 TaC2H2-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 TaC2H2-ZFPs and their potential roles in T. aestivum. Our findings provide new insights into the C2H2-ZF genes in T. aestivum as well as a foundation for further studies on the roles of TaC2H2-ZF genes in T. aestivum molecular breeding.

Genome-Wide Analysis of C2H2 Zinc Finger Gene Family and Its Response to Cold and Drought Stress in Sorghum [Sorghum bicolor (L.) Moench]

“…Previous reports indicate that they play an important role in cucumber, Arabidopsis , wheat, and tomato [ 39 , 40 , 41 , 42 ]. Therefore, many researchers have tried to perform genome-wide analysis on C2H2-ZFP s in various species, such as tomato, wheat, grape, and oyster mushroom [ 43 , 44 , 45 , 46 ], but little is known about sorghum C2H2-ZFP proteins. In this study, we carried out a genome-wide study of the S. bicolor C2H2-ZFP family and identified a total of 145 SbC2H2-ZFP members.…”

Genome-Wide Identification of the Q-type C2H2 Transcription Factor Family in Alfalfa (Medicago sativa) and Expression Analysis under Different Abiotic Stresses

“…Q-Type ZFPs are a subfamily of C2H2-ZFPs, which play crucial roles in plant response to abiotic stress. Previous studies have identified many Q-type C2H2 ZFPs in plants such as Arabidopsis , rice, wheat, poplar, and potato [ 9 , 10 , 36 , 37 , 38 ]. However, there have been few studies on the molecular function of MsZFP s under abiotic stress conditions in alfalfa.…”

Genetic analysis of morphological traits in spring wheat from the Northeast of China by a genome-wide association study

“…The LD decay analysis was calculated for the whole genomes using the full matrix and sliding window options in Tassel v5.0 (Breseghello and Sorrells, 2006). The results of LD decay, population analysis, PCA, and NJ-tree analysis for the 251 spring wheat accessions have been reported by Li et al (2021). The multi-environment phenotypic data were analyzed by a one-stage approach as y 1 n μ + Xg + Ze + v + ε, where y is the n-dimensional multi-environment phenotypic records, n is the number of multi-environment phenotypic records, 1 n is an n-dimensional vector of ones, μ is the intercept, g and e are the vector of genetic and environment effects, respectively, v is the vector of genotype-by-environment interaction effects, X and Z are the design matrices of g and e, respectively, and ε is the random residuals.…”

“…Genotyping, population structure, and linkage disequilibrium decay analysis Totally, 52,503 polymorphic SNPs after filtering (MAF <0.05, missing rate >0.1) were conducted for further GWAS (Li et al, 2021). Among the SNP markers, 18323, 18691, and 15489 were from A, B, and D genomes, respectively, with an average marker density of 0.273 Mb per marker.…”

“…With the development of the gene chip and NGS technology, getting SNP quickly becomes feasible and provides an effective way to identifying genes/QTLs for complex traits (Zhu et al, 2008;Liu et al, 2017;Wang et al, 2020). Now, the 55, 90, and 660K wheat SNP arrays are gradually replacing SSR and DArT markers in genetic analysis and have been widely used in the genetic analysis for yield (Gao et al, 2015;Sun et al, 2017;Beyer et al, 2019;Li et al, 2019), disease resistance (stripe rust, leaf rust, or powdery mildew), end-use quality, procession quality, and biotic or abiotic stress tolerance (drought or flood)-related traits (Liu et al, 2016a;Liu et al, 2017;Valluru et al, 2017;Liu et al, 2019;Li et al, 2021;Quan et al, 2021). Linkage analysis and association mapping are the two main ways to uncover the genetic mechanism of complex traits (Zhu et al, 2008;Liu et al, 2016b;Liu et al, 2017).…”