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

Genome-wide analysis of C2H2 zinc finger family and their response to abiotic stresses in apple

C2H2-type zinc finger proteins are one of the most widely studied families in plants and play important roles in abiotic stress responses. In the present study, the physicochemical properties, chromosomal locations, evolutionary relationships, and gene structures of 54 C2H2 zinc finger protein (ZFP) family members were analyzed in apple. The MdC2H2-ZFP genes were phylogenetically clustered into seven subfamilies distributed in different densities on 16 chromosomes. The RNA-seq data from various tissues revealed that MdC2H2-ZFPs differentially expressed among root, stem, leaf, flower, and fruits. Quantitative analysis of its expression characteristics showed that the MdC2H2-ZFP genes were rapidly induced as exposure to abiotic stresses such as drought, salt and low temperature etc. Under drought stress, the expression of eight members was significantly up-regulated, and the highest was obtained from MdC2H2-17; as exposure to salt stress, nine MdC2H2-ZFPs was obviously up-regulated, with the highest expression of MdC2H2-13; and under low temperature stress, the expression of seven members was highly up-regulated, and MdC2H2-13 also demonstrated the highest expression which is same as the case under salt stress. Therefore, some members of MdC2H2-ZFP gene family considerably involve in the multiple abiotic stress responses, which may better understand the function of this family and facilitate the breeding of apple for stress tolerance.

Genome-wide analysis of the C2H2-ZFP gene family in Stevia rebaudiana reveals involvement in abiotic stress response

Stevia (Stevia rebaudiana Bertoni) is a natural sweetener plant that accumulates highly sweet steviol glycosides (SGs) especially in leaves. Stevia is native to humid areas and does not have a high tolerance to drought which is the most serious abiotic stress restricting its production worldwide. C2H2 zinc finger proteins (C2H2-ZFPs) are a group of well-known transcription factors that involves in various developmental, physiological and biochemical activities as well as in response to abiotic stresses. Here we analyzed C2H2-ZFP gene family in stevia and identified a total of 185 putative SrC2H2-ZF proteins from the genome sequence of S. rebaudiana. We further characterized the identified C2H2-ZF domains and their organization, additional domains and motifs and analyzed their physicochemical properties, localization and gene expression patterns. The cis-element analysis suggested multiple roles of SrC2H2-ZFPs in response to light, phytohormone, and abiotic stresses. In silico analysis revealed that the stevia C2H2-ZFP genes are interactively expressed in different tissues and developmental stages and some C2H2-ZFP genes are involved in response to drought stress. This study provides a background for future exploration of the functional, and regulatory aspects of the C2H2-ZFP gene family in S. rebaudiana.

Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae)

Background: C2H2-zinc finger transcription factors comprise one of the largest and most diverse gene superfamilies and are involved in the transcriptional regulation of flowering. Although a large number of C2H2 zinc-finger proteins (C2H2-ZFPs) have been well characterized in a number of model plant species, little is known about their expression and function in Coptis teeta. C. teeta displays two floral phenotypes (herkogamy phenotypes). It has been proposed that the C2H2-zinc finger transcription factor family may play a crucial role in the formation of floral development and herkogamy observed in C. teeta. As such, we performed a genome-wide analysis of the C2H2-ZFP gene family in C. teeta. Results: The complexity and diversity of C. teeta C2H2 zinc finger proteins were established by evaluation of their physicochemical properties, phylogenetic relationships, exon-intron structure, and conserved motifs. Chromosome localization showed that 95 members of the C2H2 zinc-finger genes were unevenly distributed across the nine chromosomes of C. teeta, and that these genes were replicated in tandem and segmentally and had undergone purifying selection. Analysis of cis-acting regulatory elements revealed a possible involvement of C2H2 zinc-finger proteins in the regulation of phytohormones. Transcriptome data was then used to compare the expression levels of these genes during the growth and development of the two floral phenotypes (F-type and M-type). These data demonstrate that in groups A and B, the expression levels of 23 genes were higher in F-type flowers, while 15 genes showed higher expressions in M-type flowers. qRT-PCR analysis further revealed that the relative expression was highly consistent with the transcriptome data. Conclusion: These data provide a solid basis for further in-depth studies of the C2H2 zinc finger transcription factor gene family in this species and provide preliminary information on which to base further research into the role of the C2H2 ZFPs gene family in floral development in C. teeta.

Co-expression network analysis reveals PbTGA4 and PbAPRR2 as core transcription factors of drought response in an important timber species Phoebe bournei

Phoebe bournei is one of the main afforestation tree species in subtropical regions of China and is famous for its timber. Its distribution and growth are significantly impaired by water conditions. Thus, it is essential to understand the mechanism of the stress response in P. bournei. Here, we analyzed the phenotypic changes and transcriptomic rearrangement in the leaves and roots of P. bournei seedlings grown for 0 h, 1 h, 24 h, and 72 h under simulated drought conditions (10% PEG 6000). The results showed that drought stress inhibited plant photosynthesis and increased oxidoreductase activity and abscisic acid (ABA) accumulation. Spatio-temporal transcriptomic analysis identified 2836 and 3704 differentially expressed genes (DEGs) in leaves and roots, respectively. The responsive genes in different organs presented various expression profiles at different times. Gene co-expression network analysis identified two core transcription factors, TGA4 and APRR2, from two modules that showed a strong positive correlation with ABA accumulation. Our study investigated the different responses of aboveground and belowground organs of P. bournei to drought stress and provides critical information for improving the drought resistance of this timber species.

Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet

A plant's Q-type C2H2-type ZFP plays key roles in plant growth and development and responses to biotic and abiotic stresses. Sugar beet (Beta vulgaris L.) is an important crop for sugar production. Salt stress and viral infection significantly reduce the root yield and sugar content of sugar beet. However, there is a lack of comprehensive genome-wide analyses of Q-type C2H2 ZFPs and their expression patterns in sugar beet under stress. In this study, 35 sugar beet Q-type C2H2 ZFPs (BvZFPs) containing at least one conserved "QALGGH" motif were identified via bioinformatics techniques using TBtools software. According to their evolutionary relationship, the BvZFPs were classified into five subclasses. Within each subclass, the physicochemical properties and motif compositions showed strong similarities. A Ka/Ks analysis indicated that the BvZFPs were conserved during evolution. Promoter cis-element analysis revealed that most BvZFPs are associated with elements related to phytohormone, biotic or abiotic stress, and plant development. The expression data showed that the BvZFPs in sugar beet are predominantly expressed in the root. In addition, BvZFPs are involved in the response to abiotic and biotic stresses, including salt stress and viral infection. Overall, these results will extend our understanding of the Q-type C2H2 gene family and provide valuable information for the biological breeding of sugar beet against abiotic and biotic stresses in the future.

Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi

BACKGROUND

C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far.

RESULTS

In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus.

CONCLUSION

The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.

Genome-Wide Association Study and Genomic Prediction on Plant Architecture Traits in Sweet Corn and Waxy Corn

Sweet corn and waxy corn has a better taste and higher accumulated nutritional value than regular maize, and is widely planted and popularly consumed throughout the world. Plant height (PH), ear height (EH), and tassel branch number (TBN) are key plant architecture traits, which play an important role in improving grain yield in maize. In this study, a genome-wide association study (GWAS) and genomic prediction analysis were conducted on plant architecture traits of PH, EH, and TBN in a fresh edible maize population consisting of 190 sweet corn inbred lines and 287 waxy corn inbred lines. Phenotypic data from two locations showed high heritability for all three traits, with significant differences observed between sweet corn and waxy corn for both PH and EH. The differences between the three subgroups of sweet corn were not obvious for all three traits. Population structure and PCA analysis results divided the whole population into three subgroups, i.e., sweet corn, waxy corn, and the subgroup mixed with sweet and waxy corn. Analysis of GWAS was conducted with 278,592 SNPs obtained from resequencing data; 184, 45, and 68 significantly associated SNPs were detected for PH, EH, and TBN, respectively. The phenotypic variance explained (PVE) values of these significant SNPs ranged from 3.50% to 7.0%. The results of this study lay the foundation for further understanding the genetic basis of plant architecture traits in sweet corn and waxy corn. Genomic selection (GS) is a new approach for improving quantitative traits in large plant breeding populations that uses whole-genome molecular markers. The marker number and marker quality are essential for the application of GS in maize breeding. GWAS can choose the most related markers with the traits, so it can be used to improve the predictive accuracy of GS.

Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

Background

RING (Really Interesting New Gene) zinc finger (RING-zf) proteins belong to an important subclass of zinc fingers superfamily, which play versatile roles during various developmental stages and in abiotic stress responses. Based on the conserved cysteine and histidine residues, the RING-zf domains are classified into RING-HC (C3HC4), RING-H2 (C3H2C3), RING-v, RING-D, RING-S/T, RING-G, and RING-C2. However, little is known about the function of the RING-zfs of wheat.

Results

In this study, 129 (93.5%) of 138 members were found in nucleus, indicating TaRING-zf were primarily engaged in the degradation of transcription factors and other nuclear-localized proteins. 138 TaRING-zf domains can be divided into four canonical or modified types (RING-H2, RING-HC, RING-D, and RING-M). The RING-M was newly identified in T. aestivum, and might represent the intermediate other states between RING-zf domain and other modified domains. The consensus sequence of the RING-M domain can be described as M-X₂-R-X₁₄-Cys-X₁-H-X₂-Cys-X₂-Cys-X₁₀-Cys-X₂-Cys. Further interspecies collinearity analyses showed that TaRING-zfs were more closely related to the genes in Poaceae. According to the public transcriptome data, most of the TaRING-zfs were expressed at different 15 stages of plant growth, development, and some of them exhibited specific responses to drought/heat stress. Moreover, 4 RING-HC (TraesCS2A02G526800.1, TraesCS4A02G290600.1, TraesCS4B02G023600.1 and TraesCS4D02G021200.1) and 2 RING-H2 (TraesCS3A02G288900.1 and TraesCS4A02G174600.1) were significantly expressed at different development stages and under drought stress. These findings provide valuable reference data for further study of their physiological functions in wheat varieties.

Conclusions

Taken together, the characterization and classifications of the TaRING-zf family were extensively studied and some new features about it were revealed. This study could provide some valuable targets for further studies on their functions in growth and development, and abiotic stress responses in wheat.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08905-x.

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

Identification of the gene for agronomic traits is important for the wheat marker-assisted selection (MAS) breeding. To identify the new and stable loci for agronomic traits, including flag leaf length (FLL), flag leaf width (FLW), uppermost internode length (UIL), and plant morphology (PM, including prostrate, semi-prostrate, and erect). A total of 251 spring wheat accessions collected from the Northeast of China were used to conduct genome-wide association study (GWAS) by 55K SNP arrays. A total of 30 loci for morphological traits were detected, and each explained 4.8–17.9% of the phenotypic variations. Of these, 13 loci have been reported by previous studies, and the other 17 are novel. We have identified seven genes involved in the signal transduction, cell-cycle progression, and plant development pathway as candidate genes. This study provides new insights into the genetic basis of morphological traits. The associated SNPs and accessions with more of favorable alleles identified in this study could be used to promote the wheat breeding progresses.

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

C2H2 zinc finger protein (C2H2-ZFP) is one of the most important transcription factor families in higher plants. In this study, a total of 145 C2H2-ZFPs was identified in Sorghum bicolor and randomly distributed on 10 chromosomes. Based on the phylogenetic tree, these zinc finger gene family members were divided into 11 clades, and the gene structure and motif composition of SbC2H2-ZFPs in the same clade were similar. SbC2H2-ZFP members located in the same clade contained similar intron/exon and motif patterns. Thirty-three tandem duplicated SbC2H2-ZFPs and 24 pairs of segmental duplicated genes were identified. Moreover, synteny analysis showed that sorghum had more collinear regions with monocotyledonous plants such as maize and rice than did dicotyledons such as soybean and Arabidopsis. Furthermore, we used quantitative RT-PCR (qRT-PCR) to analyze the expression of C2H2-ZFPs in different organs and demonstrated that the genes responded to cold and drought. For example, Sobic.008G088842 might be activated by cold but is inhibited in drought in the stems and leaves. This work not only revealed an important expanded C2H2-ZFP gene family in Sorghum bicolor but also provides a research basis for determining the role of C2H2-ZFPs in sorghum development and abiotic stress resistance.

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

Q-type C2H2 zinc-finger protein (C2H2-ZFP) transcription factors are associated with many plant growth development and environmental stress responses. To date, there have been few analyses of the Q-type C2H2-ZFP gene family in alfalfa (Medicago sativa subsp. sativa). In this study, we identified 58 Q-type C2H2-ZFPs across the entire alfalfa genome, and the gene structure, motif composition, chromosomal mapping, and cis-regulatory elements were explored, as well as the expression profiles of specific tissues and the response under different abiotic stresses. According to their phylogenetic features, these 58 MsZFPs were divided into 12 subgroups. Synteny analysis showed that duplication events play a vital role in the expansion of the MsZFP gene family. The collinearity results showed that a total of 26 and 42 of the 58 MsZFP genes were homologous with Arabidopsis and M. truncatula, respectively. The expression profiles showed that C2H2-ZFP genes played various roles in different tissues and abiotic stresses. The results of subsequent quantitative real-time polymerase chain reaction (qRT-PCR) showed that the nine selected MsZFP genes were rapidly induced under different abiotic stresses, indicating that C2H2-ZFP genes are closely related to abiotic stress. This study provides results on MsZFP genes, their response to various abiotic stresses, and new information on the C2H2 family in alfalfa.