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

2021 ◽  
Author(s):  
Yongliang Li ◽  
Aolong Sun ◽  
Qun Wu ◽  
Xiaoxiao Zou ◽  
Fenglin Chen ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Zinc Finger ◽  
Stress Responses ◽  
Molecular Breeding ◽  
Pattern Analysis ◽  
Splice Variants ◽  
Expression Data ◽  
Rt Pcr ◽  
Expression Pattern Analysis ◽  
Conserved Domain

Abstract Background: The C2H2-type zinc finger proteins (C2H2-ZFPs) are one of major classes of transcription factors that play important roles during 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 on 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 A. thaliana, 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.

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

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yongliang Li ◽  
Aolong Sun ◽  
Qun Wu ◽  
Xiaoxiao Zou ◽  
Fenglin Chen ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Zinc Finger ◽  
Stress Responses ◽  
Molecular Breeding ◽  
Splice Variants ◽  
Triticum Aestivum L ◽  
Expression Data ◽  
Rt Pcr ◽  
Expression Pattern Analysis ◽  
Conserved Domain

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.

Cloning and function analysis of BAG family genes in wheat

2016 ◽  
Vol 43 (5) ◽  
pp. 393
Author(s):  
Shiming Ge ◽  
Zhen Kang ◽  
Ying Li ◽  
Fuzhen Zhang ◽  
Yinzhu Shen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Salinity Stress ◽  
Heat Tolerance ◽  
Expressed Sequence Tag ◽  
Function Analysis ◽  
Pcr Analysis ◽  
Subcellular Localisation ◽  
Hybrid Technique ◽  
Rt Pcr ◽  
Conserved Domain

By analysing the cDNA microarray of the salt tolerant mutant of wheat RH8706–49 under salinity stress, our results showed an expressed sequence tag fragment and acquired an unknown gene (designated as TaBAG) with a BAG conserved domain through electronic cloning and RT–PCR technology. The gene was registered into GenBank (No. FJ599765). After homologous alignment analysis, electronic cloning, and amplifying with RT–PCR, the other gene with a BAG conserved domain, TaBAG2, was obtained and registered into GenBank (No. GU471210). Quantitative PCR analysis demonstrated that TaBAG2 expression was induced by saline and heat stress. TaBAG gene expression under salinity stress increased remarkably but showed an insignificant response to heat stress. The adversity stress detection results showed that Arabidopsis overexpressing TaBAG and TaBAG2 exhibited an obvious salt tolerance increase. Under heat stress, Arabidopsis overexpressing TaBAG2 showed increased heat tolerance; however, the heat tolerance of Arabidopsis overexpressing TaBAG did not vary significantly under heat stress. Subcellular localisation results demonstrated that TaBAGs were mainly located in the cytoplasm and the cell nucleus. We applied fluorescence complementation and yeast two-hybrid technique to prove that TaBAG2 can obviously bond with TaHsp70 and TaCaMs. After the respective mutation of aspartic acid (D) and arginine (R) at high conservation in BAG domain of TaBAG2, the bonding interaction between TaBAG2 and TaHsp70 disappeared, indicating that the two amino acids were the key loci for the interaction between TaBAG2 and TaHsp70. Heat tolerance detection results demonstrated that the heat tolerance of Arabidopsis overexpressing and cotransfected with TaBAG2 and TaHsp70 was much higher than that of Arabidopsis overexpressing TaBAG2 and Arabidopsis overexpressing TaHSP70. This finding implies that the synergistic use of TaBAG2 and TaHSP70 can improve heat tolerance of plants.

scholarly journals Genetic Basis Dissection for Eating and Cooking Qualities of Japonica Rice in Northeast China

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 423
Author(s):  
Yaolong Yang ◽  
Xin Xu ◽  
Mengchen Zhang ◽  
Qun Xu ◽  
Yue Feng ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Northeast China ◽  
Genetic Basis ◽  
Pattern Analysis ◽  
Principal Component ◽  
Rice Grain ◽  
Japonica Rice ◽  
Cooked Rice ◽  
Expression Pattern Analysis ◽  
Gel Consistency

The japonica rice in Northeast China is famous because of its high quality. Eating and cooking qualities (ECQs) are the most important factors that determine cooked rice quality. However, the genetic basis of ECQ of japonica varieties in Northeast China needs further study. In this study, 200 japonica varieties that are widely distributed in Northeast China were collected to evaluate the physicochemical indices of grain ECQs. The distribution of each trait was concentrated without large variations. Correlation analysis indicated that gel consistency (GC) had a significantly negative correlation with gelatinization temperature (GT). By integrating various analyses including kinship calculation, principal component analysis (PCA), linkage disequilibrium (LD) analysis, and original parent investigation, we found that the japonica varieties in Northeast China exhibited a narrow genetic basis. An association study for grain ECQs was performed and eight quantitative trait loci (QTLs) were detected. ALK was the major locus that regulated GT and also significantly affecting GC. Through the linkage disequilibrium (LD) and expression pattern analysis, one possible candidate gene (LOC_Os02g29980) was predicted and required further research for validation. Additionally, a different allele of Wx was identified in the variety CH4126, and ALK was not fixed in these japonica varieties. These results further elucidate the genetic basis of ECQs of japonica varieties in Northeast China and provide local breeders some assistance for improving ECQs of rice grain in rice breeding.

scholarly journals Comparative Genomic Analysis of TCP Genes in Six Rosaceae Species and Expression Pattern Analysis in Pyrus bretschneideri

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Zhao ◽  
Xueqiang Su ◽  
Xinya Wang ◽  
Mengna Wang ◽  
Xujing Chi ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Prunus Avium ◽  
Pattern Analysis ◽  
Evolutionary Relationship ◽  
Comparative Genomic ◽  
Accumulation Pattern ◽  
Stone Cell ◽  
Expression Pattern Analysis ◽  
Rosaceae Species ◽  
Different Tissues

TCP is a plant-specific transcription factor that plays an important role in flowering, leaf development and other physiological processes. In this study, we identified a total of 155 TCP genes: 34 in Pyrus bretschneideri, 19 in Fragaria vesca, 52 in Malus domestica, 19 in Prunus mume, 17 in Rubus occidentalis and 14 in Prunus avium. The evolutionary relationship of the TCP gene family was examined by constructing a phylogenetic tree, tracking gene duplication events, performing a sliding window analysis. The expression profile analysis and qRT-PCR results of different tissues showed that PbTCP10 were highly expressed in the flowers. These results indicated that PbTCP10 might participated in flowering induction in pear. Expression pattern analysis of different developmental stages showed that PbTCP14 and PbTCP15 were similar to the accumulation pattern of fruit lignin and the stone cell content. These two genes might participate in the thickening of the secondary wall during the formation of stone cells in pear. Subcellular localization showed that PbTCPs worked in the nucleus. This study explored the evolution of TCP genes in six Rosaceae species, and the expression pattern of TCP genes in different tissues of “Dangshan Su” pear. Candidate genes related to flower induction and stone cell formation were identified. In summary, our research provided an important theoretical basis for improving pear fruit quality and increasing fruit yield by molecular breeding.

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