The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn)

Chen, Jingwen; Yan, Qian; Li, Jiawei; Feng, Lei; Zhang, Yi; Xu, Jing; Xia, Rui; Zeng, Zaohai; Liu, Yuanlong

doi:10.1186/s12870-021-03193-1

Cited by 8 publications

(8 citation statements)

References 102 publications

(145 reference statements)

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“…Members of the GRAS family played an important regulatory role in multiple biological processes [ 63 , 64 ]. In rice, OsGRAS23 was demonstrated to be involved in the drought stress response by binding to the promoters of stress-responsive genes [ 65 ].…”

Section: Discussionmentioning

confidence: 99%

Evolution and functional analysis of the GRAS family genes in six Rosaceae species

et al. 2022

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Background GRAS genes formed one of the important transcription factor gene families in plants, had been identified in several plant species. The family genes were involved in plant growth, development, and stress resistance. However, the comparative analysis of GRAS genes in Rosaceae species was insufficient. Results In this study, a total of 333 GRAS genes were identified in six Rosaceae species, including 51 in strawberry (Fragaria vesca), 78 in apple (Malus domestica), 41 in black raspberry (Rubus occidentalis), 59 in European pear (Pyrus communis), 56 in Chinese rose (Rosa chinensis), and 48 in peach (Prunus persica). Motif analysis showed the VHIID domain, SAW motif, LR I region, and PFYRE motif were considerably conserved in the six Rosaceae species. All GRAS genes were divided into 10 subgroups according to phylogenetic analysis. A total of 15 species-specific duplicated clades and 3 lineage-specific duplicated clades were identified in six Rosaceae species. Chromosomal localization presented the uneven distribution of GRAS genes in six Rosaceae species. Duplication events contributed to the expression of the GRAS genes, and Ka/Ks analysis suggested the purification selection as a major force during the evolution process in six Rosaceae species. Cis-acting elements and GO analysis revealed that most of the GRAS genes were associated with various environmental stress in six Rosaceae species. Coexpression network analysis showed the mutual regulatory relationship between GRAS and bZIP genes, suggesting the ability of the GRAS gene to regulate abiotic stress in woodland strawberry. The expression pattern elucidated the transcriptional levels of FvGRAS genes in various tissues and the drought and salt stress in woodland strawberry, which were verified by RT-qPCR analysis. Conclusions The evolution and functional analysis of GRAS genes provided insights into the further understanding of GRAS genes on the abiotic stress of Rosaceae species.

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Section: Discussionmentioning

confidence: 99%

Evolution and functional analysis of the GRAS family genes in six Rosaceae species

et al. 2022

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“…The GRAS gene family has been identified and analyzed in many model plants, such as A. thaliana ( Lee et al., 2008 ), P. trichocarpa ( Liu and Widmer, 2014 ), and Z. mays ( Guo et al., 2017 ). In addition, their regulation with respect to root and fruit development ( Chen et al., 2021 ) also prompted people to study their function in many economic species, including pepper ( C. annuum L.) ( Liu et al., 2018 ), apple ( M. domestica ) ( Fan et al., 2017 ), and Prunus persica ( Jiang et al., 2022 ). However, the classification of subfamilies is still uncertain, and the number of genes varies greatly among different species.…”

Section: Discussionmentioning

confidence: 99%

“…The development stage, tissue, environmental conditions, and genotype affect expression levels ( Hirsch and Oldroyd, 2009 ), and this is consistent with the results of our qRT-PCR and transcriptome data. Moreover, it has been reported that GRAS is involved in maintaining the normal development of seeds ( Chen et al., 2021 ). The transcriptome data show that LcGRAS is expressed during somatic embryogenesis from the globular embryo stage.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of the GRAS gene family in Liriodendron chinense reveals the putative function in abiotic stress and plant development

Weng,

Chen,

Hao

et al. 2023

Front. Plant Sci.

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IntroductionGRAS genes encode plant-specific transcription factors that play essential roles in plant growth and development. However, the members and the function of the GRAS gene family have not been reported in Liriodendron chinense. L. chinense, a tree species in the Magnolia family that produces excellent timber for daily life and industry. In addition, it is a good relict species for plant evolution research.MethodsTherefore, we conducted a genome-wide study of the LcGRAS gene family and identified 49 LcGRAS genes in L. chinense.ResultsWe found that LcGRAS could be divided into 13 sub-groups, among which there is a unique branch named HAM-t. We carried out RNA sequencing analysis of the somatic embryos from L. chinense and found that LcGRAS genes are mainly expressed after heart-stage embryo development, suggesting that LcGRAS may have a function during somatic embryogenesis. We also investigated whether GRAS genes are responsive to stress by carrying out RNA sequencing (RNA-seq) analysis, and we found that the genes in the PAT subfamily were activated upon stress treatment, suggesting that these genes may help plants survive stressful environments. We found that PIF was downregulated and COR was upregulated after the transient overexpression of PATs, suggesting that PAT may be upstream regulators of cold stress. DiscussionCollectively, LcGRAS genes are conserved and play essential roles in plant development and adaptation to abiotic stress.

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“…To further identify GRAS gene family members, the GRAS conserved domain HMM model (PF03514) was downloaded from the Pfam database (http://pfam.xfam.org/, accessed on 14 April 2023), using HMMER-3.2.1 (http://hmmer.org/download.html, accessed on 14 April 2023) with an e-value <10 -5 and other parameters by default. After the identification of GRAS genes in P. bournei, the online website ExPASy (https://web.expasy.org/prot-param/, accessed on 26 February 2023) was used to analyze the physical and chemical properties of the GRAS proteins that were identified [65].…”

Section: Identification and Physical And Chemical Property Analysismentioning

confidence: 99%

Genome-Wide Identification, Expression and Stress Analysis of the GRAS Gene Family in Phoebe bournei

Chang

Fan

Lan

et al. 2023

Plants

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GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source for the construction industry and building exquisite furniture. Although genome-wide identification of the GRAS gene family has been completed in many species, that of most woody plants, particularly P. bournei, has not yet begun. We performed a genome-wide investigation of 56 PbGRAS genes, which are unequally distributed across 12 chromosomes. They are divided into nine subclades. Furthermore, these 56 PbGRAS genes have a substantial number of components related to abiotic stress responses or phytohormone transmission. Analysis using qRT-PCR showed that the expression of four PbGRAS genes, namely PbGRAS7, PbGRAS10, PbGRAS14 and PbGRAS16, was differentially increased in response to drought, salt and temperature stresses, respectively. We hypothesize that they may help P. bournei to successfully resist harsh environmental disturbances. In this work, we conducted a comprehensive survey of the GRAS gene family in P. bournei plants, and the results provide an extensive and preliminary resource for further clarification of the molecular mechanisms of the GRAS gene family in P. bournei in response to abiotic stresses and forestry improvement.

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The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn)

Cited by 8 publications

References 102 publications

Evolution and functional analysis of the GRAS family genes in six Rosaceae species

Evolution and functional analysis of the GRAS family genes in six Rosaceae species

Genome-wide analysis of the GRAS gene family in Liriodendron chinense reveals the putative function in abiotic stress and plant development

Genome-Wide Identification, Expression and Stress Analysis of the GRAS Gene Family in Phoebe bournei

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