Genome-wide identification and expression profiles of ABCB gene family in Chinese hickory (Carya cathayensis Sarg.) during grafting

Yang, Ying; Huang, Qiaoyu; Wang, Xiaofei; Mei, Jiaqi; Sharma, Anket; Tripathi, Durgesh Kumar; Yuan, Huwei; Zheng, Bingsong

doi:10.1016/j.plaphy.2021.10.029

Cited by 8 publications

(8 citation statements)

References 53 publications

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“…Based on the transcriptome data of Chinese hickory grafting, auxin-related unigenes were identified as differentially expressed genes (DEGs) during the grafting process ( Qiu et al., 2016 ). Further investigation revealed that the expression of Aux/IAA , GH3 , and ABCB family genes changed dramatically during graft healing ( Yuan et al., 2018 ; Xu et al., 2020 ; Yang et al., 2021 ). The AUX/LAX transporter is an auxin transporter that aids in the transport of auxin between cells and the formation of vascular bundles.…”

Section: Discussionmentioning

confidence: 99%

“…The content of auxin in the healing area increased significantly after grafting and remained high levels throughout the healing process ( Sharma and Zheng, 2019 ). Several studies about Chinese hickory grafting have identified the key stages important for survival ( Liu et al., 2002 ), and have concluded that auxin plays an important role during the grafting success ( Zheng et al., 2002 ; Qiu et al., 2016 ; Xu et al., 2017 ; Saravana Kumar et al., 2018 ; Yuan et al., 2018 ; Xu et al., 2020 ; Yang et al., 2021 ). Despite the significant advances in the studies of Chinese hickory and Chinese hickory grafting, little is known about the genetic roles of key genes, including auxin influx carriers under abiotic stress treatments and during grafting.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and expression analysis of AUX/LAX family genes in Chinese hickory (Carya cathayensis Sarg.) Under various abiotic stresses and grafting

Yang

Wang

et al. 2023

Front. Plant Sci.

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Auxin is essential for regulating plant growth and development as well as the response of plants to abiotic stresses. AUX/LAX proteins are auxin influx transporters belonging to the amino acid permease family of proton-driven transporters, and are involved in the transport of indole-3-acetic acid (IAA). However, how AUX/LAX genes respond to abiotic stresses in Chinese hickory is less studied. For the first time identification, structural characteristics as well as gene expression analysis of the AUX/LAX gene family in Chinese hickory were conducted by using techniques of gene cloning and real-time fluorescent quantitative PCR. Eight CcAUX/LAXs were identified in Chinese hickory, all of which had the conserved structural characteristics of AUX/LAXs. CcAUX/LAXs were most closely related to their homologous proteins in Populus trichocarpa , which was in consistence with their common taxonomic character of woody trees. CcAUX/LAXs exhibited different expression profiles in different tissues, indicating their varying roles during growth and development. A number of light-, hormone-, and abiotic stress responsive cis-acting regulatory elements were detected on the promoters of CcAUX/LAX genes. CcAUX/LAX genes responded differently to drought and salt stress treatments to varying degrees. Furthermore, CcAUX/LAX genes exhibited complex expression changes during Chinese hickory grafting. These findings not only provide a valuable resource for further functional validation of CcAUX/LAXs, but also contribute to a better understanding of their potential regulatory functions during grafting and abiotic stress treatments in Chinese hickory.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of AUX/LAX family genes in Chinese hickory (Carya cathayensis Sarg.) Under various abiotic stresses and grafting

Yang

Wang

et al. 2023

Front. Plant Sci.

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“…The genes from the transcription category include those related to both the transcription factors and other factors that regulate the activity of these transcription factors. For example, the transcription factor family of WRKY is prominent, as well as being the largest member of the gene family involved in the modulation of different network pathways related to stresses [80][81][82].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and Metabolome Analyses of Salt Stress Response in Cotton (Gossypium hirsutum) Seed Pretreated with NaCl

et al. 2022

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Abiotic stresses adversely influence crop productivity and salt stress is one limiting factor. Plants need to evolve their defense mechanisms to survive in such fluctuating scenarios at either the biochemical, physiological, or molecular level. The analytical/critical investigations of cotton (Gossypium hirsutum) plants that involve looking into transcriptomic and metabolomic profiles could give a comprehensive picture of the response of the cotton plant to salt stress. This study was conducted on pre-treated cotton seeds by soaking them in a 3% sodium chloride (NaCl) solution at room temperature for 0.5, 1, and 1.5 h. In total, 3738 and 285 differentially expressed genes (DEGs) and metabolites, respectively, were discovered. The prominent DEGs included AtCCC1, EP1, NHE, AtpOMT, GAST1, CLC-c, ARP, AtKIN14, AtC3H2, COP9, AtHK-2, and EID1 to code for the regulation of seed growth, abscisic acid receptor PYR/PYL, a cellular response regarding stress tolerance (especially to salt) and germination, jasmonic acid, salicylic acid, and auxin-activated signaling pathways. A more significant amount of transcription factors, including the ethylene-responsive TFs ERF (205), bHLH (252), ZF-domains (167), bHLH (101), MYB (92), NAC (83), GATA (43), auxin-responsive proteins (30), MADs-box (23), bZIP (27), and HHO (13) were discovered in samples of NaCl-pretreated cotton seedlings under different treatments. The functional annotations of DEGs exposed their important roles in regulating different phytohormones and signal-transduction-mediated pathways in salt-treated seeds. The metabolites analysis revealed differential accumulation of flavonols, phenolic acid, amino acids, and derivatives in seedling samples treated for 0.5 h with NaCl. The conjoint analysis that showed most of the DEGs were associated with the production and regulation of glucose-1-phosphate, uridine 5′-diphospho-D-glucose, and 2-deoxyribose 1-phosphate under salt stress conditions. These results indicated positive effects of NaCl 0.5 h treatments on seedlings’ germination and growth, seemingly by activating specific growth-promoting enzymes and metabolites to alleviate adverse effects of salt stress. Hence, seed pre-treatment with NaCl can be beneficial in future cotton management and breeding programs to enhance growth and development under salt stress.

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“…Candidate gene sequences of PIN in Chinese hickory ( CcPINs ) were identified from the published genome ( Huang et al, 2019 ). The process used to identify genes was the same as that used in a previous study ( Yang et al, 2021 ). Hidden Markov model (HMM) profiles of the PIN domain (PF03547) were used for analysis.…”

Section: Methodsmentioning

confidence: 99%

Expression analysis of PIN family genes in Chinese hickory reveals their potential roles during grafting and salt stress

Yang

Mei²,

Chen³

et al. 2022

Front. Plant Sci.

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Grafting is an effective way to improve Chinese hickory while salt stress has caused great damage to the Chinese hickory industry. Grafting and salt stress have been regarded as the main abiotic stress types for Chinese hickory. However, how Chinese hickory responds to grafting and salt stress is less studied. Auxin has been proved to play an essential role in the stress response through its re-distribution regulation mediated by polar auxin transporters, including PIN-formed (PIN) proteins. In this study, the PIN gene family in Chinese hickory (CcPINs) was identified and structurally characterized for the first time. The expression profiles of the genes in response to grafting and salt stress were determined. A total of 11 CcPINs with the open reading frames (ORFs) of 1,026–1,983 bp were identified. Transient transformation in tobacco leaves demonstrated that CcPIN1a, CcPIN3, and CcPIN4 were localized in the plasma membrane. There were varying phylogenetic relationships between CcPINs and homologous genes in different species, but the closest relationships were with those in Carya illinoinensis and Juglans regia. Conserved N- and C-terminal transmembrane regions as well as sites controlling the functions of CcPINs were detected in CcPINs. Five types of cis-acting elements, including hormone- and stress-responsive elements, were detected on the promoters of CcPINs. CcPINs exhibited different expression profiles in different tissues, indicating their varied roles during growth and development. The 11 CcPINs responded differently to grafting and salt stress treatment. CcPIN1a might be involved in the regulation of the grafting process, while CcPIN1a and CcPIN8a were related to the regulation of salt stress in Chinese hickory. Our results will lay the foundation for understanding the potential regulatory functions of CcPIN genes during grafting and under salt stress treatment in Chinese hickory.

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Genome-wide identification and expression profiles of ABCB gene family in Chinese hickory (Carya cathayensis Sarg.) during grafting

Cited by 8 publications

References 53 publications

Genome-wide identification and expression analysis of AUX/LAX family genes in Chinese hickory (Carya cathayensis Sarg.) Under various abiotic stresses and grafting

Genome-wide identification and expression analysis of AUX/LAX family genes in Chinese hickory (Carya cathayensis Sarg.) Under various abiotic stresses and grafting

Transcriptome and Metabolome Analyses of Salt Stress Response in Cotton (Gossypium hirsutum) Seed Pretreated with NaCl

Expression analysis of PIN family genes in Chinese hickory reveals their potential roles during grafting and salt stress

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