Evolution and expression patterns of cytokinin oxidase genes in Fragaria vesca

2016 ◽  
Vol 212 ◽  
pp. 115-125 ◽  
Author(s):  
Yun Jiang ◽  
Xianna Mi ◽  
Ying Lin ◽  
Han Wu ◽  
Tingting Gu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Cytokinin Oxidase ◽  
Fragaria Vesca

scholarly journals The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Liu ◽  
Wei Qu ◽  
Kaikai Zhu ◽  
Zong-Ming Cheng
Keyword(s):  
Protein Kinases ◽  
Evolutionary Dynamics ◽  
Expression Patterns ◽  
Gene Families ◽  
Gray Mold ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Go Enrichment ◽  
Potential Link ◽  
Wild Strawberry

Abstract Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.

scholarly journals Identification and Functional Characterization of Apple MdCKX5.2 in Root Development and Abiotic Stress Tolerance

Horticulturae ◽  
2022 ◽  
Vol 8 (1) ◽  
pp. 62
Author(s):  
Yang Liu ◽  
Xun Wang ◽  
Xiaofei Wang ◽  
Wensheng Gao ◽  
Chunxiang You
Keyword(s):  
Expression Analysis ◽  
Root Development ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Primary Root ◽  
Cytokinin Oxidase ◽  
Lateral Root Development ◽  
Exogenous Cytokinin

Cytokinin oxidase/dehydrogenases (CKXs) are the key enzymes in cytokinin degradation and have been widely studied in model plants. Little is known about apple’s (Malus×domestica) CKX genes. Here, using genome-wide analysis, we identified 10 MdCKX genes in apple. The phylogenetics, chromosome locations, and genome structures were then tested. Expression analysis showed that MdCKX genes had different expression profiles in apple, pointing to the different roles. Meanwhile, relative expression analysis showed that these genes have different expression patterns in response to several exogenous cytokinin factors, including trans-zeatin (ZT), thidiazuron (TDZ), and N6-furfuryladenine (KT). Finally, we introduced the MdCKX5.2 gene into Arabidopsis to evaluate its functions, and the results suggested the transgenic Arabidopsis displayed phenotypes related to promoting primary root and lateral root development, response to exogenous ZT, and conferring to drought and salt tolerant. Taken together, our results provide insights on the possible application of the MdCKX5.2 gene for molecular breeding in apples.

scholarly journals Whole-Genome Identification and Salt- and ABA-Induced Expression Trends of the Nicotiana tabacum CKX gene family

2021 ◽  
Author(s):  
Wenwen Chen ◽  
Genhong Wang ◽  
Meiqin Yi ◽  
Chunman Song ◽  
Qian Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Nicotiana Tabacum ◽  
Phylogenetic Tree ◽  
Gene Family ◽  
Dynamic Balance ◽  
Expression Patterns ◽  
Cytokinin Oxidase ◽  
Induced Expression ◽  
Network Analyses

Abstract Cytokinin hormones are indispensable for plant growth and development. Cytokinin oxidase/dehydrogenase (CKX) helps regulate the dynamic balance of endogenous cytokinin levels. However, little is known about the CKX genes of Nicotiana tabacum (NtCKXs). In silico analyses were used to isolate, characterize, and elucidate the phylogenetic relationships of 15 NtCKX genes. Multi-species phylogenetic tree construction placed NtCKX1–15 on five of the eight branches of the CKX phylogenetic tree. Protein structure and network analyses revealed that NtCKX genes located on the same phylogenetic branch generally contain several conserved motifs and have highly similar structures, with structural domains related to flavin adenine dinucleotide (FAD) and cytokinin-binding found on all of the predicted NtCKX-encoded proteins. The upstream promotor region of NtCKX genes contained a large number of abiotic stress-responsive cis-acting elements, including DRE, ERE, MBS, MYB, and MYC. Gene expression analysis revealed that each NtCKX gene has a different response to salt- and exogenous ABA-stress. Four NtCKX genes exhibited ABA-induced expression trends with varying peak times. Under salt-stress, NtCKX expression was significantly suppressed in two genes and upregulated in five others. In summary, we have provided basic in-formation about the CKX gene family of N. tabacum, and elucidated their gene expression patterns under abiotic stresses, including ABA- and salt-stress. The findings of this work can serve as a foundation for future study of the functions of N. tabacum CKX genes.

scholarly journals Genome-Wide Characterization and Expression Analysis of the Growth Regulating Factor (GRF) Gene Family in Strawberry (Fragaria vesca)

2021 ◽  
Vol 25 (05) ◽  
pp. 1051-1060
Author(s):  
Xuwen Jiang
Keyword(s):  
Transcriptional Regulation ◽  
Gene Family ◽  
Chromosomal Location ◽  
Expression Patterns ◽  
Fragaria Vesca ◽  
Fundamental Knowledge ◽  
Genome Wide ◽  
Young Leaves ◽  
Functional Analyses ◽  
Post Transcriptional Regulation

As one of the transcription factors only found in plants, the growth regulating factor (GRF) gene family has been reported in some plant species, but information on this gene family in strawberries remains unclear. Here, Fragaria vesca GRF (FvGRF) genes were systematically studied, including chromosomal location, gene structure, conserved motif, phylogenetic, expression profiling, post-transcriptional regulation, and functional analyses. The identified 10 FvGRFs were phylogenetically classified into two groups and five subgroups. Of these, nine FvGRFs were distributed on the five chromosomes, while FvGRF2 was located on the scf0512956. Motifs 2 and 1 corresponding to QLQ and WRC domains existed in all the FvGRF proteins. FvGRFs showed different expression patterns based on RT-qPCR analyses, for example, FvGRF1, FvGRF3, FvGRF6 and FvGRF8 were predominantly expressed in buds and blooming flowers, FvGRF4 and FvGRF5 were mainly expressed in young leaves, indicating that the roles of these genes are diverse and redundant in strawberry growth and development. Furthermore, FvGRF2 and FvGRF8 were experimentally validated to be the targets of strawberry miR396, suggesting the significance and conservation of miR396 in post-transcriptional regulation of FvGRFs. These results provide fundamental knowledge for further functional analyses of FvGRFs in strawberries. © 2021 Friends Science Publishers

scholarly journals Regulation of rose petal dehydration tolerance and senescence by RhNAP transcription factor via the modulation of cytokinin catabolism

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Jing Zou ◽  
Peitao Lü ◽  
Liwei Jiang ◽  
Kun Liu ◽  
Tao Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Expression Patterns ◽  
Limiting Factor ◽  
Cytokinin Oxidase ◽  
Mobility Shift ◽  
Independent Manner ◽  
Flower Opening ◽  
Dehydration Tolerance ◽  
Petal Senescence ◽  
Rose Petals

AbstractPetals and leaves share common evolutionary origins but have different phenotypic characteristics, such as the absence of stomata in the petals of most angiosperm species. Plant NAC transcription factor, NAP, is involved in ABA responses and regulates senescence-associated genes, and especially those that affect stomatal movement. However, the regulatory mechanisms and significance of NAP action in senescing astomatous petals is unclear. A major limiting factor is failure of flower opening and accelerated senescence. Our goal is to understand the finely regulatory mechanism of dehydration tolerance and aging in rose flowers. We functionally characterized RhNAP, an AtNAP-like transcription factor gene that is induced by dehydration and aging in astomatous rose petals. Cytokinins (CKs) are known to delay petal senescence and we found that a cytokinin oxidase/dehydrogenase gene 6 (RhCKX6) shares similar expression patterns with RhNAP. Silencing of RhNAP or RhCKX6 expression in rose petals by virus induced gene silencing markedly reduced petal dehydration tolerance and delayed petal senescence. Endogenous CK levels in RhNAP- or RhCKX6-silenced petals were significantly higher than those of the control. Moreover, RhCKX6 expression was reduced in RhNAP-silenced petals. This suggests that the expression of RhCKX6 is regulated by RhNAP. Yeast one-hybrid experiments and electrophoresis mobility shift assays showed that RhNAP binds to the RhCKX6 promoter in heterologous in vivo system and in vitro, respectively. Furthermore, the expression of putative signal transduction and downstream genes of ABA-signaling pathways were also reduced due to the repression of PP2C homolog genes by RhNAP in rose petals. Taken together, our study indicates that the RhNAP/RhCKX6 interaction represents a regulatory step enhancing dehydration tolerance in young rose petals and accelerating senescence in mature petals in a stomata-independent manner.

scholarly journals Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4812 ◽  
Author(s):  
Li Cai ◽  
Lu Zhang ◽  
Qiantang Fu ◽  
Zeng-Fu Xu
Keyword(s):  
Seed Yield ◽  
Jatropha Curcas ◽  
Fossil Fuels ◽  
Expression Patterns ◽  
Cytokinin Oxidase ◽  
Flower Buds ◽  
P450 Monooxygenase ◽  
Real Time Quantitative Pcr ◽  
Mature Leaves ◽  
Metabolic Genes

The seed oil of Jatropha curcas is considered a potential bioenergy source that could replace fossil fuels. However, the seed yield of Jatropha is low and has yet to be improved. We previously reported that exogenous cytokinin treatment increased the seed yield of Jatropha. Cytokinin levels are directly regulated by isopentenyl transferase (IPT), cytochrome P450 monooxygenase, family 735, subfamily A (CYP735A), and cytokinin oxidase/dehydrogenase (CKX). In this study, we cloned six IPT genes, one JcCYP735A gene, and seven JcCKX genes. The expression patterns of these 14 genes in various organs were determined using real-time quantitative PCR. JcIPT1 was primarily expressed in roots and seeds, JcIPT2 was expressed in roots, apical meristems, and mature leaves, JcIPT3 was expressed in stems and mature leaves, JcIPT5 was expressed in roots and mature leaves, JcIPT6 was expressed in seeds at 10 days after pollination, and JcIPT9 was expressed in mature leaves. JcCYP735A was mainly expressed in roots, flower buds, and seeds. The seven JcCKX genes also showed different expression patterns in different organs of Jatropha. In addition, CK levels were detected in flower buds and seeds at different stages of development. The concentration of N6-(Δ2-isopentenyl)-adenine (iP), iP-riboside, and trans-zeatin (tZ) increased with flower development, and the concentration of iP decreased with seed development, while that of tZ increased. We further analyzed the function of JcCYP735A using the CRISPR-Cas9 system, and found that the concentrations of tZ and tZ-riboside decreased significantly in the Jccyp735a mutants, which showed severely retarded growth. These findings will be helpful for further studies of the functions of cytokinin metabolic genes and understanding the roles of cytokinins in Jatropha growth and development.

scholarly journals Identification of Imprinted Genes Based on Homology: An Example of Fragaria vesca

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 380
Author(s):  
Yaping Liu ◽  
Xiaotong Jing ◽  
Hong Zhang ◽  
Jinsong Xiong ◽  
Yushan Qiao
Keyword(s):  
Genomic Imprinting ◽  
Expression Patterns ◽  
Imprinted Genes ◽  
Fragaria Vesca ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Evolutionarily Conserved ◽  
Site Variation ◽  
Parent Of Origin ◽  
Tissues Expression

Genomic imprinting has drawn increasing attention in plant biology in recent years. At present, hundreds of imprinted genes have been identified in various plants, and some of them have been reported to be evolutionarily conserved in plant species. In this research, 17 candidate genes in Fragaria vesca were obtained based on the homologous imprinted genes in Arabidopsis thaliana and other species. We further constructed reciprocal crosses of diploid strawberry (F. vesca) using the varieties 10-41 and 18-86 as the parents to investigate the conservation of these imprinted genes. Potentially informative single nucleotide polymorphisms (SNPs) were used as molecular markers of two parents obtained from candidate imprinted genes which have been cloned and sequenced. Meanwhile, we analyzed the SNP site variation ratios and parent-of-origin expression patterns of candidate imprinted genes at 10 days after pollination (DAP) endosperm and embryo for the hybrids of reciprocal cross, respectively. A total of five maternally expressed genes (MEGs), i.e., FvARI8, FvKHDP-2, FvDRIP2, FvBRO1, and FvLTP3, were identified in the endosperm, which did not show imprinting in the embryo. Finally, tissues expression analysis indicated that the five imprinted genes excluding FvDRIP2 mainly expressed in the endosperm. This is the first report on imprinted genes of Fragaria, and we provide a simple and rapid method based on homologous conservation to screen imprinted genes. The present study will provide a basis for further study of function and mechanism of genomic imprinting in F. vesca.

scholarly journals Genome-Wide Identification and Expression Analysis of MYB Transcription Factors and Their Responses to Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

Horticulturae ◽  
2021 ◽  
Vol 7 (5) ◽  
pp. 97
Author(s):  
Huihui Li ◽  
Yanwei Zhou ◽  
Zongxin Ma ◽  
Xiaoqing Lu ◽  
Yunlong Li ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Fragaria Vesca ◽  
Specific Expression ◽  
Expression Levels ◽  
Woodland Strawberry ◽  
Organ Specific ◽  
Multiple Treatments ◽  
Myb Genes ◽  
Myb Proteins

Woodland strawberry (Fragaria vesca) is a diploid strawberry that is widely used as a model of cultivated octoploid strawberry (Fragaria × ananassa). It has also been used as a model for Rosaceae fruits, non-climacteric fruits, and stolons. The MYB superfamily is the largest transcription factor family in plants, and its members play important roles in plant growth and development. However, the complete MYB superfamily in woodland strawberry has not been studied. In this study, a total of 217 MYB genes were identified in woodland strawberry and classified into four groups: one 4R-MYB protein, five 3R-MYB proteins, 113 2R-MYB proteins, and 98 1R-MYB proteins. The phylogenetic relationship of each MYB subgroup was consistent in terms of intron/exon structure and conserved motif composition. The MYB genes in woodland strawberry underwent loss and expansion events during evolution. The transcriptome data revealed that most FveMYB genes are expressed in several organs, whereas 15 FveMYB genes exhibit organ-specific expression, including five genes (FveMYB101, -112, -44, and -8; FveMYB1R81) in roots, two genes (FveMYB62 and -77) in stolon tips, three genes (FveMYB99 and -35; FveMYB1R96) in open flowers, and five genes (FveMYB76 and -100; FveMYB1R4, -5, and -86) in immature fruits. During fruit ripening of woodland strawberry, the expression levels of 84 FveMYB genes were decreased, of which five genes (FveMYB4, -22, -50, and -66; FveMYB1R57) decreased more than 10-fold, whereas those 18 FveMYB genes were increased, especially FveMYB10 and FveMYB74 increased more than 30-fold. In addition, the expression levels of 36, 68, 52, and 62 FveMYB genes were altered by gibberellic acid, abscisic acid, cold, and heat treatments, respectively, and among them, several genes exhibited similar expression patterns for multiple treatments, suggesting possible roles in the crosstalk of multiple signaling pathways. This study provides candidate genes for the study of stolon formation, fruit development and ripening, and abiotic stress responses.

scholarly journals Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chao Dong ◽  
Yue Xi ◽  
Xinlu Chen ◽  
Zong-Ming Cheng
Keyword(s):  
Drought Stress ◽  
Expression Pattern ◽  
Binding Protein ◽  
Abiotic Factors ◽  
Expression Patterns ◽  
Critical Role ◽  
Pcr Analysis ◽  
Fragaria Vesca ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are unique transcription factors in plants that play important roles in the abiotic stress response. Results Here, a total of 119 AP2/EREBP genes were identified in Fragaria vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and one member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 from the A-2 subgroup had the highest expression level under drought stress. Together, analyses with the expression pattern, phylogenetic relationship, motif, and promoter suggest that FvDREB18 may play a critical role in the regulation of FvDREB1 and FvDREB2 expression. Conclusions Our findings provide new insights into the characteristics and potential functions of FvDREBs. These FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry.

scholarly journals Identification and quantitative expression of cytokinin regulatory genes during seed and leaf development in wheat

2010 ◽  
Vol 14 ◽  
pp. 131-137
Author(s):  
J. Song ◽  
L. Jiang ◽  
P.E. Jameson
Keyword(s):  
Leaf Development ◽  
Flag Leaf ◽  
Expression Patterns ◽  
Mrna Level ◽  
Gene Families ◽  
Cytokinin Oxidase ◽  
Isopentenyl Transferase ◽  
Quantitative Expression ◽  
Qrt Pcr ◽  
Yield Determination

Cytokinins are intimately involved in plant growth and development and their concentration is known to change dramatically during early stages of seed development. We propose that the concentration of active cytokinin may be coordinately regulated by specific member(s) of the multi-gene families encoding biosynthesis (isopentenyl transferase, IPT), catabolism (cytokinin oxidase, CKX), and metabolism (zeatin glucosyltransferases (ZOG) and β-glucosidase (GLU)) genes. Our qRT-PCR data for 22 putative genes showed that the expression patterns of individual members of the Triticum aestivum (Ta)IPTs, TaCKXs, TaZOGs, and TaGLUs multi-gene families were tissue and development specific during seed and flag leaf development, with up to 90-fold changes in mRNA level. Key genes that may be involved in seed yield determination have been identified. Keywords: Wheat, flag leaf, cytokinin genes, quantitative expression, qRT-PCR

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