Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

Yan, Feng; Zhou, Huijuan; Yue, Ming; Ge, Yang; Li, Huaizhu; Zhang, Shuoxin; Zhao, Peng

doi:10.3390/f10030275

Cited by 13 publications

(6 citation statements)

References 71 publications

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“…The WRKY gene family in walnut can be divided into four groups, similar to the classification of WRKY genes in Musa acuminate and Musa balbisiana , Castor bean, pineapple, soybean, C. sinensis , C. clementina and C. unshiu , Eucalyptus grandis , Quinoa, Dimocarpus longan , Raphanus sativus , potato, moso bamboo, G. raimondii and G. arboretum , Cassava, willow, Oryza officinalis , peach and Dendrobium officinale . The division of the family in such a manner suggests that the results of our classification were reasonable and reliable [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ]. In view of the conserved motifs, motifs 5, 9, 1, 2, 8, 10 and 7 were the typical motifs of group I; motifs 1 and 2 were the typical motifs of group II; and motifs 4, 1 and 2 were the typical motifs of group III.…”

Section: Discussionmentioning

confidence: 97%

“…There is no previous study regarding the WRKY gene in common walnut ( J. regia ) [ 33 , 34 ]. In a recent publication of high-quality common walnut genome data, some gene families and transcript factors were reported in common walnut, such phenylalanine ammonialyase ( PAL) , F-box , fatty acid desaturase ( FAD) , heat stress transcription factors ( HSFs ), nascent polypeptide-associated complex protein ( NAC) and repressor of GAI; gibberellic acid-insensitive RGA and scarecrow SCR ( GRAS ) were also reported [ 35 , 36 , 37 , 38 , 39 , 40 ]. However, comprehensive information regarding the functional characterization of the WRKY gene family in common walnut is still unclear.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

Fan

Zhou

et al. 2021

Genes

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The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

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Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

Fan

Zhou

et al. 2021

Genes

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“…Various gene families may often be somewhat selective for the type of tissue, as is the case for RNAi-associated gene families (Hsu et al, 2021;Cao et al, 2016;Sabbione et al, 2019;Yan et al, 2019b). At the same time, these genes that produce tissue specificity can often also produce important effects on specific tissue life activities or tissue resistance.…”

Section: Function Of Rnai-related Genes In Plantsmentioning

confidence: 99%

“…In recent years, a high-quality walnut genome (Juglans regia) has been completely sequenced (Zhang et al, 2020), and the evolutionary study of its RNAi system based on feasible methods is an important part of facilitating the application of model plant research on walnut plants. Second, the process of testing preliminary walnut disease resistance using gene expression will also enhance our understanding of natural resistance to walnut diseases and the functional differentiation of genes (Yan et al, 2019b;Yan et al, 2019a;Feng et al, 2021). To this end, we comprehensively analysed the DCL, RDR, DRB, and AGO genes possessed by the walnut genome and investigated their structure, evolution, and possible interactions.…”

Section: Introductionmentioning

confidence: 99%

RNA Interference Pathways in <em>Juglandaceae</em>: Based on Gene Diversity, Evolution, and Functional Differentiation

Fang¹,

Wei²,

Huang³

et al. 2022

Preprint

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RNA interference (RNAi) is one of the main mechanisms for disease resistance and small RNA production in plants. The main proteins involved in RNAi include Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), double-stranded RNA-binding (DRB), and Argonaute (AGO). Juglandaceae contains a variety of important woody plants, and walnuts are one of the four major woody plant groups and one of the four major dried fruits in the world. To clarify the evolution and functional differentiation of RNAi-related proteins in the walnut (Juglans regia) genome, this study integrated various web resources from gene family acquisition to structural analysis and transcriptome data to correlate walnuts and their congeners. The walnut genome has 5 DCL, 13 RDR, 15 DRB and 15 AGO genes, similar genes encoding conserved protein structural domains and conserved motifs with similar subcellular localization. Walnut AGO proteins are classified into three classes and seven subclasses. The DCL is divided into four categories, while RDR is mainly divided into four categories, and DRB can be divided into six categories. The exception is that the copy number of walnut RDR1 is 9, in which seven RDR1 are distributed in clusters on chromosome 16. Purifying selection drove the formation of walnut genes, but protein classes were subjected to varying degrees of purifying selection. Additionally, these results showed some similarity in other plants of the walnut family. Moreover, different RNAi-related genes of walnut produced abundant selective expression in response to different tissues and stresses. In this study, DCL, RDR, DRB and AGO gene families were identified and analysed in the genome of the walnut family for the first time and preliminarily examined the evolution, structure and expression characteristics of these families to provide a preliminary basis for the evolution of the walnut RNAi pathway and breeding research.

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“…It is, therefore responsible for subsequent translation modifications of the pure nucleus proteins and sometimes methylation of deoxyribonucleic acid (Zhang et al, 2018b). The process of flowering is controlled by a group of genes made up of gene expression (Yan et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Salicylic acid and potassium nitrate promote flowering through modulating the hormonal levels and protein pattern of date palm Phoenix dactylifera ‘Sayer’ offshoot

Shareef

2019

AAS

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Salicylic acid and potassium nitrate promote flowering through modulating the hormonal levels and protein pattern of date palm Phoenix dactylifera 'Sayer' offshoot Abstract: Salicylic acid enhances the flowering process in the plant by creating new proteins under salinity stress. The study was to determine the role of salicylic acid (500 ppm) and potassium nitrate (1500 ppm), on flowering of date palm 'Sayer' offshoots under salinity effect. Application of salicylic acid increased the number of clusters, the number of new leaves, the content of carbohydrates, ascorbic acid, indoleacetic acid, zeatin, gibberellin, and abscisic acid significantly under salinity compared with control. Although the measured parameters were the highest in plants treated with salicylic acid, there was no distinction among potassium nitrate treatment under saltwater, and salicylic acid treatment with saltwater. Salicylic acid and potassium nitrate treatment demonstrated some amazing contrasts in protein patterns in light of gel electrophoresis. Plants treated with salicylic acid with fresh water and with saltwater showed five and six protein bands, respectively, that differed in the molecular mass of one polypeptide compared to control with freshwater. However, there was a difference in the molecular mass of two polypeptides compared to control with salt water, which showed six bands. In contrast, potassium nitrate application showed five protein bands, whether with freshwater or with saltwater. The findings could facilitate to elucidate the flowering mechanisms in date palm. Salicilna kislina in kalijev nitrat pospešujeta cvetenje stranskih poganjkov dateljeve palme (Phoenix dactylifera 'Sayer') z moduliranjem ravni hormonov in vzorca proteinovIzvleček: Salicilna kislina pospešuje cvetenje preko tvorbe novih proteinov v razmerah slanostnega stresa. Namen raziskave je bil določiti vlogo salicilne kisline (500 ppm) in kalijevega nitrata (1500 ppm) na cvetenje stranskih poganjkov dateljeve palme ('Sayer') v razmerah slanosti. Uporaba salicilne kisline je značilno povečala število stranskih poganjkov, število novih listov, vsebnost ogljikovih hidratov, askorbinske kisline, indolocetne kisline, zeatina, giberelina in abscizinske kisline v razmerah slanosti v primerjavi s kontrolo. Čeprav so imeli vsi merjeni parametri največje vrednosti pri obravnavanju s salicilno kislino, ni bilo razlike v obravnavanjih s kalijevim nitratom in salicilno kislino v istih razmerah. Obravnavanja s salicilno kislino in kalijevim nitratom so imela velike razlike v vzorcu proteinov, določenem z gelsko elektroforezo. Rastline, ki so bile tretirane s salicilno kislino, sladko in slano vodo so imele pet oziroma šest proteinskih trakov, ki so se razlikovali v molekulski masi enega izmed polipeptidov v primerjavi s kontrolo, kjer je bilo samo obravnavanje s sladko vodo. Kakorkoli, v primerjavi s kontrolo, kjer je bilo obravnavanje samo s slano vodo in je bilo šest proteinskih trakov, je bila razlika v molekulski masi dveh polipeptidov. Obravnavanje samo s kalijevim n...

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Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

Cited by 13 publications

References 71 publications

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

RNA Interference Pathways in <em>Juglandaceae</em>: Based on Gene Diversity, Evolution, and Functional Differentiation

Salicylic acid and potassium nitrate promote flowering through modulating the hormonal levels and protein pattern of date palm Phoenix dactylifera ‘Sayer’ offshoot

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