Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L.

Zhang, Bin; Liu, J.; Yang, Zhao; Chen, Er Y.; Zhang, Chao J.; Zhang, Xue Y.; Li, Fu G.

doi:10.1186/s12864-018-4722-x

Cited by 107 publications

(106 citation statements)

References 59 publications

(85 reference statements)

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“…GRAS-transcription factors like Zm00001d048682 (Fig. 5b) have been demonstrated to be involved in the regulation of root and shoot development and in the improvement of plant resistance to abiotic stresses [48]. Genotype-specific upregulation of this gene upon cold stress has been demonstrated for several genotypes [41], although in the present study we did not observe differential regulation upon cold stress, but rather higher expression in cold tolerant genotypes (Fig.…”

Section: Transcriptomic Responses Associated With Cold Tolerancecontrasting

confidence: 49%

Transcriptomic diversity in seedling roots of European flint maize in response to cold

et al. 2020

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Background: Low temperatures decrease the capacity for biomass production and lead to growth retardation up to irreversible cellular damage in modern maize cultivars. European flint landraces are an untapped genetic resource for genes and alleles conferring cold tolerance which they acquired during their adaptation to the agroecological conditions in Europe. Results: Based on a phenotyping experiment of 276 doubled haploid lines derived from the European flint landrace "Petkuser Ferdinand Rot" diverging for cold tolerance, we selected 21 of these lines for an RNA-seq experiment. The different genotypes showed highly variable transcriptomic responses to cold. We identified 148, 3254 and 563 genes differentially expressed with respect to cold treatment, cold tolerance and growth rate at cold, respectively. Gene ontology (GO) term enrichment demonstrated that the detoxification of reactive oxygen species is associated with cold tolerance, whereas amino acids might play a crucial role as antioxidant precursors and signaling molecules. Conclusion: Doubled haploids representing a European maize flint landrace display genotype-specific transcriptome patterns associated with cold response, cold tolerance and seedling growth rate at cold. Identification of cold regulated genes in European flint germplasm, could be a starting point for introgressing such alleles in modern breeding material for maize improvement.

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Section: Transcriptomic Responses Associated With Cold Tolerancecontrasting

confidence: 49%

Transcriptomic diversity in seedling roots of European flint maize in response to cold

et al. 2020

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“…After analysis, it was found that three ginseng genes (PgGRAS26-01, PgGRAS43-01 and PgGRAS52-01) belong to the NSP1 and NSP2 sub-families. Three genes (AtGRAS20, AtGRAS33 and PgGRAS53-01) were observed in the evolutionary tree belonging to the SCL4/7 subfamily, which may be involved in the resistance system in the plant [2]. However, the SCL32 subfamily contains only two members (AtGRAS19 and AtGRAS34) of the Arabidopsis thaliana, and there are no members of the SCL32 sub-family in the Panax ginseng.…”

Section: Conserved Motif Analysis and Systematic Analysis Of Pggras Gmentioning

confidence: 99%

“…The Chinese ginseng is mainly distributed in Jilin Province and is commonly named as Jilin Ginseng. Ginseng has anti-thrombosis and anti-aging effects, prevents tumor angiogenesis and has other functions [1,2]. In recent years, the study of ginseng has become a hotspot for research.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer

Wang

et al. 2020

Plants

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GRAS transcription factors are a kind of plant-specific transcription factor that have been found in a variety of plants. According to previous studies, GRAS proteins are widely involved in the physiological processes of plant signal transduction, stress, growth and development. The Jilin ginseng (Panax ginseng C.A. Meyer) is a heterogeneous tetraploid perennial herb of the Araliaceae family, ginseng genus. Important information regarding the GRAS transcription factors has not been reported in ginseng. In this study, 59 Panax ginseng GRAS (PgGRAS) genes were obtained from the Jilin ginseng transcriptome data and divided into 13 sub-families according to the classification of Arabidopsis thaliana. Through systematic evolution, structural variation, function and gene expression analysis, we further reveal GRAS’s potential function in plant growth processes and its stress response. The expression of PgGRAS genes responding to gibberellin acids (GAs) suggests that these genes could be activated after application concentration of GA. The qPCR analysis result shows that four PgGRAS genes belonging to the DELLA sub-family potentially have important roles in the GA stress response of ginseng hairy roots. This study provides not only a preliminary exploration of the potential functions of the GRAS genes in ginseng, but also valuable data for further exploration of the candidate PgGRAS genes of GA signaling in Jilin ginseng, especially their roles in ginseng hairy root development and GA stress response.

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“…In the Arabidopsis thaliana annotation database, the homologous gene of MELO3C016746 in Arabidopsis thaliana ( AT1G29150 ) was specifically interacted with FUS6/COP11 via the C-terminal domain of FUS6/COP11 and associates with an ATPase subunit of the 19S proteasome regulatory complex, AtS6A. The mRNA is cell-to-cell mobile (Cho et al, 2006 and 2015;); the homologous gene of MELO3C015295 in Arabidopsis thaliana ( AT5G56010 ) was a member of heat shock protein 90 (HSP90) gene family and expressed in all tissues and abundant in root apical meristem, pollen and tapetum (Cha et al, 2013; Bologna et al, 2018); the homologous gene of MELO3C021706 in Arabidopsis thaliana ( AT3G18990 ) was related to regulation of flower development and vernalization response (Kinjo et al, 2012; King et al, 2013); the homologous gene of MELO3C020725 in Arabidopsis thaliana ( AT2G37650 ) was belong to GRAS family transcription factor and it related to biological processes in regulating root and shoot development, plant growth, development and stress responses (Liu et al, 2018; Zhang et al, 2018); the homologous gene of MELO3C000209 in Arabidopsis thaliana ( AT5G56030 ) was also a member of heat shock protein 90 (HSP90) gene family and the function was similar with the gene MELO3C015295 (Cha et al, 2013; Bologna et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analysis of Powdery mildew Resistance between two Melon (Cucumis melo L) with Different Thickness Peel

Cheng

Kong

Jun-feng

2019

Preprint

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8Melon (Cucumis melo L.) is wildly planted in the world and China is a major producer of muskmelon. 9Powdery mildew is one of the most common fungal diseases in the world and this disease frequently 1 7 materials were identified. All the DEGs were annotated with several database and the transcript factors 1 8 (TFs) that related to disease resistance such as MYB, ERF and WRKY among the DEGs were also 1 9identified. This research could not only provide the information about understanding the mechanism of 2 0 powdery mildew infection but also help researchers breed the varieties with powdery mildew 2 1 resistance. 2Key words Melon (Cucumis melo L.). powdery mildew. Transcript sequencing. Candidate genes. 2 3 Transcript factors 2 4 4 1 were selected. After inoculating the powdery mildew, both materials were used to do the RNA-Seq. In 4 2 total, two RNA-seq libraries were constructed and sequenced separately; generating 47,462,015 mean 4 3 clean reads with mean GC content of 49.32 and mean Q30 of 85.89%. Among all the genes in the 4 4 genome of melon, 13828 genes were expressed in the material G and 13944 genes were expressed in 4 5 the material S (RPKM>1). Through multiple comparisons between libraries, 769 DEGs were identified, 4 6 of which the 726 were up-regulated DEGs and 43 were down-regulated ones. Based on the annotation 4 7 information in gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG) and eukaryotic 4 8 orthologous groups (KOG) database, most of the DEGs were related to "nucleus", "chloroplast" and 4 9 7 7 paired-end (PE) raw reads (Personalbio, Shanghai, China). Raw data (raw reads) in FASTQ format 7 8were processed used the trimmomatic software (Bolger et al., 2014). In this step, clean data were 7 9 obtained as follows: the first, removing reads with ≥ 10% unidentified nucleotides (N); the second, 0Removing reads with > 50% bases having phred quality < 5; the third, Removing reads with > 10 nt 8 1 aligned to the adapter, allowing ≤ 10% mismatches; the fourth, removing putative PCR duplicates 8 2 generated by PCR amplification in the library construction process. After trimmomatic, the quality of the clean data was checked by the software FASTQC 3 0 8 3 0 9

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Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L.

Cited by 107 publications

References 59 publications

Transcriptomic diversity in seedling roots of European flint maize in response to cold

Transcriptomic diversity in seedling roots of European flint maize in response to cold

Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer

Comparative transcriptome analysis of Powdery mildew Resistance between two Melon (Cucumis melo L) with Different Thickness Peel

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