Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass

Xu, Xiaofei; Feng, Guangyan; Huang, Linkai; Yang, Zhongfu; Liu, Qiuxu; Yang, Shuai; Zhang, Xinquan

doi:10.1007/s11033-020-05279-9

Cited by 11 publications

(7 citation statements)

References 54 publications

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“…For example, the expression of four MeGRAS genes ( MeGRAS2, 11, 22 , and 32 ) peaked at 6 h but decreased after 3 d in three Cassava varieties subjected to salt treatment ( Shan et al., 2020 ). Besides, in orchardgrass, the expression levels of DgGRAS5 , DgGRAS28 , DgGRAS31 , DgGRAS42 , and DgGRAS44 fluctuated at the seeding stage, compared to the stable expression pattern observed at the mature stage ( Xu et al., 2020 ). Collectively, we identified the expression patterns of 26 BpGRASs , most of which were substantially induced by salt stress at 6 h and significantly expressed in the leaf tissues ( Figures 4 , 5 ).…”

Section: Discussionmentioning

confidence: 95%

Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla

Tian

Zhang

et al. 2022

Front. Plant Sci.

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The GRAS gene family is a plant-specific family of transcription factors and play a vital role in many plant growth processes and abiotic stress responses. Nevertheless, the functions of the GRAS gene family in woody plants, especially in Betula platyphylla (birch), are hardly known. In this study, we performed a genome-wide analysis of 40 BpGRAS genes (BpGRASs) and identified typical GRAS domains of most BpGRASs. The BpGRASs were unevenly distributed on 14 chromosomes of birch and the phylogenetic analysis of six species facilitated the clustering of 265 GRAS proteins into 17 subfamilies. We observed that closely related GRAS homologs had similar conserved motifs according to motif analysis. Besides, an analysis of the expression patterns of 26 BpGRASs showed that most BpGRASs were highly expressed in the leaves and responded to salt stress. Six BpGRASs were selected for cis-acting element analysis because of their significant upregulation under salt treatment, indicating that many elements were involved in the response to abiotic stress. This result further confirmed that these BpGRASs might participate in response to abiotic stress. Transiently transfected birch plants with transiently overexpressed 6 BpGRASs and RNAi-silenced 6 BpGRASs were generated for gain- and loss-of-function analysis, respectively. In addition, overexpression of BpGRAS34 showed phenotype resistant to salt stress, decreased the cell death and enhanced the reactive oxygen species (ROS) scavenging capabilities and proline content under salt treatment, consistent with the results in transiently transformed birch plants. This study is a systematic analysis of the GRAS gene family in birch plants, and the results provide insight into the molecular mechanism of the GRAS gene family responding to abiotic stress in birch plants.

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Section: Discussionmentioning

confidence: 95%

Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla

Tian

Zhang

et al. 2022

Front. Plant Sci.

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“…Similarly, soybean GRAS genes in the PAT1, HAM, LISCL, SHR, SCL3 subfamily showed relatively high expression levels in the root (superior to other tissues) and nodule ( Wang et al, 2020a ). Besides, previous studies have documented that orchardgrass GRAS genes in the PAT1 subfamily (DgGRAS5, DgGRAS8, and DgGRAS17) and most of Tartary buckwheat GRAS genes were also highly expressed in roots ( Liu et al, 2019 ; Xu et al, 2020 ).…”

Section: Discussionmentioning

confidence: 97%

“…3 ). This percentage is higher than Populus (54.7%), rice (55%), orchardgrass (56.52%), Medicago truncatula (64.7%), and Arabidopsis (67%), similar to tomato (77.4%), while smaller than Zea Mays L (80.23%), Prunus mume (82.2%), grapevine (88.46%) and potato (90%) ( Grimplet et al, 2016 ; Guo et al, 2017 ; Huang et al, 2015 ; Liu & Widmer, 2014 ; Lu et al, 2015 ; Song et al, 2017 ; Wang et al, 2019 ; Xu et al, 2020 ). Variety percentage among these species revealing that the structure of GRAS genes might be a species-specific and high rate of intronless genes in the plant GRAS gene family suggesting the close evolutionary relationship of GRAS proteins.…”

Section: Discussionmentioning

confidence: 99%

“…Meanwhile, more than a dozen GRAS gene families in various plants have been identified in the past 5 years. A total of 12 GRAS genes identified from Tamarix hispida , 46 GRAS genes from orchardgrass, 150 GRAS genes from Gossypium hirsutum L , 87 putative GRAS genes in the Brassica napus , 23 GRAS genes in Chrysanthemum morifolium , and 52 GRASs were identified in potato and walnut ( Gao et al, 2018 ; Guo et al, 2019 ; Quan et al, 2019 ; Wang et al, 2018 ; Wang et al, 2019 ; Xu et al, 2020 ; Zhang et al, 2018 ). Moreover, Chinese cabbage , Grapevine , and Zea mays L have also been investigated; however, research on the evolution, classification, and functional characteristics of the GRAS family in watermelon is scarce ( Grimplet et al, 2016 ; Guo et al, 2017 ; Song et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations

Zheng

Duan

et al. 2021

PeerJ

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The family of GRAS plant-specific transcription factor plays diverse roles in numerous biological processes. Despite the identification and characterization of GRAS genes family in dozens of plant species, until now, GRAS members in watermelon (Citrullus lanatus) have not been investigated comprehensively. In this study, using bioinformatic analysis, we identified 37 GRAS genes in the watermelon genome (ClGRAS). These genes are classified into 10 distinct subfamilies based on previous research, and unevenly distributed on 11 chromosomes. Furthermore, a complete analysis was conducted to characterize conserved motifs and gene structures, which revealed the members within same subfamily that have analogous conserved gene structure and motif composition. Additionally, the expression pattern of ClGRAS genes was characterized in fruit flesh and rind tissues during watermelon fruit development and under red light (RL) as well as root knot nematode infestation. Finally, for verification of the availability of public transcriptome data, we also evaluated the expression levels of randomly selected four ClGRAS genes under RL and nematode infection by using qRT-PCR. The qRT-PCR results indicated that several ClGRAS genes were differentially expressed, implying their vital role in RL induction of watermelon resistance against root-knot nematodes. The results obtained in this study could be useful in improving the quality of watermelon.

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“…In recent years, with the rapid development of the next-generation sequencing (NGS) technology and the assembly of orchardgrass genome, a better platform for evaluating molecular and genetic information of orchardgrass is available ( McCombie et al., 2019 ; Huang et al., 2020 ). WRKY , GRAs , and C2H2-type zinc finger gene family have previously been studied in orchardgrass ( Xu et al., 2020 ; Ren et al., 2021 ; Shuai et al., 2022 ). Studies on biotic and abiotic stress reports of orchardgrass and other cold-season forage grasses had mainly focused on drought, high temperature, and rust ( Huang et al, 2015 ; Ji et al, 2018 ; Yan et al, 2013 , 2016 ; Hu et al, 2014 ; Sun et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomic analysis of the gene expression and underlying molecular mechanism of submergence stress response in orchardgrass roots

Zheng

et al. 2023

Front. Plant Sci.

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IntroductionSubmergence stress creates a hypoxic environment. Roots are the first plant organ to face these low-oxygen conditions, which causes damage and affects the plant growth and yield. Orchardgrass (Dactylis glomerata L.) is one of the most important cold-season forage grasses globally. However, their submergence stress-induced gene expression and the underlying molecular mechanisms of orchardgrass roots are still unknown.MethodsUsing the submergence-tolerant ‘Dianbei’ and submergence-sensitive ‘Anba’, the transcriptomic analysis of orchardgrass roots at different time points of submergence stress (0 h, 8 h, and 24 h) was performed.ResultsWe obtained 118.82Gb clean data by RNA-Seq. As compared with the control, a total of 6663 and 9857 differentially expressed genes (DEGs) were detected in Dianbei, while 7894 and 11215 DEGs were detected in Anba at 8 h and 24 h post-submergence-stress, respectively. Gene Ontology (GO) enrichment analysis obtained 986 terms, while Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis obtained 123 pathways. Among them, the DEGs in plant hormones, mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction were significantly differentially expressed in Dianbei, but not in Anba.DiscussionThis study was the first to molecularly elucidate the submergence stress tolerance in the roots of two orchardgrass cultivars. These findings not only enhanced our understanding of the orchardgrass submergence tolerance, but also provided a theoretical basis 36 for the cultivation of submergence-tolerant forage varieties.

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Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass

Cited by 11 publications

References 54 publications

Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla

Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla

The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations

Comparative transcriptomic analysis of the gene expression and underlying molecular mechanism of submergence stress response in orchardgrass roots

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