scholarly journals Network Analysis of Different Exogenous Hormones on the Regulation of Deep Sowing Tolerance in Maize Seedlings

2021 ◽  
Vol 12 ◽  
Author(s):  
Fenqi Chen ◽  
Xiangzhuo Ji ◽  
Mingxing Bai ◽  
Zelong Zhuang ◽  
Yunling Peng
Keyword(s):  
Inbred Line ◽  
Expression Profiles ◽  
Lignin Biosynthesis ◽  
Maize Seedlings ◽  
Deep Soil ◽  
Exogenous Hormones ◽  
Mesocotyl Elongation ◽  
Gene Modules ◽  
Transcriptome Expression ◽  
Planting Method

The planting method of deep sowing can make the seeds make full use of water in deep soil, which is considered to be an effective way to respond to drought stress. However, deep sowing will affect the growth and development of maize (Zea mays L.) at seedling stage. To better understand the response of maize to deep sowing stress and the mechanism of exogenous hormones [Gibberellin (GA3), Brassinolide (BR), Strigolactone (SL)] alleviates the damaging effects of deep-sowing stress, the physiological and transcriptome expression profiles of seedlings of deep sowing sensitive inbred line Zi330 and the deep-tolerant inbred line Qi319 were compared under deep sowing stress and the conditions of exogenous hormones alleviates stress. The results showed that mesocotyl elongated significantly after both deep sowing stress and application of exogenous hormones, and its elongation was mainly through elongation and expansion of cell volume. Hormone assays revealed no significant changes in zeatin (ZT) content of the mesocotyl after deep sowing and exogenous hormone application. The endogenous GA3 and auxin (IAA) contents in the mesocotyl of the two inbred lines increased significantly after the addition of exogenous GA3, BR, and SL under deep sowing stress compared to deep sowing stress, while BR and SL decreased significantly. Transcriptome analysis showed that the deep seeding stress was alleviated by GA3, BR, and SLs, the differentially expressed genes (DEGs) mainly included cellulose synthase, expansin and glucanase, oxidase, lignin biosynthesis genes and so on. We also found that protein phosphatase 2C and GA receptor GID1 enhanced the ability of resist deep seeding stress in maize by participating in the abscisic acid (ABA) and the GA signaling pathway, respectively. In addition, we identified two gene modules that were significantly related to mesocotyl elongation, and identified some hub genes that were significantly related to mesocotyl elongation by WGCNA analysis. These genes were mainly involved in transcription regulation, hydrolase activity, protein binding and plasma membrane. Our results from this study may provide theoretical basis for determining the maize deep seeding tolerance and the mechanism by which exogenous hormones regulates deep seeding tolerance.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Expression Pattern ◽  
Noncoding Rna ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

2020 ◽  
Author(s):  
Feng Tian ◽  
Fan Zhou ◽  
Xiang Li ◽  
Wenping Ma ◽  
Honggui Wu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Human Cell ◽  
Expression Profiles ◽  
Single Cells ◽  
Cell Types ◽  
List Type ◽  
Cell Type ◽  
Genomic Architecture ◽  
Gene Modules

SummaryBy circumventing cellular heterogeneity, single cell omics have now been widely utilized for cell typing in human tissues, culminating with the undertaking of human cell atlas aimed at characterizing all human cell types. However, more important are the probing of gene regulatory networks, underlying chromatin architecture and critical transcription factors for each cell type. Here we report the Genomic Architecture of Cells in Tissues (GeACT), a comprehensive genomic data base that collectively address the above needs with the goal of understanding the functional genome in action. GeACT was made possible by our novel single-cell RNA-seq (MALBAC-DT) and ATAC-seq (METATAC) methods of high detectability and precision. We exemplified GeACT by first studying representative organs in human mid-gestation fetus. In particular, correlated gene modules (CGMs) are observed and found to be cell-type-dependent. We linked gene expression profiles to the underlying chromatin states, and found the key transcription factors for representative CGMs.HighlightsGenomic Architecture of Cells in Tissues (GeACT) data for human mid-gestation fetusDetermining correlated gene modules (CGMs) in different cell types by MALBAC-DTMeasuring chromatin open regions in single cells with high detectability by METATACIntegrating transcriptomics and chromatin accessibility to reveal key TFs for a CGM

scholarly journals Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways

2020 ◽  
Vol 21 (3) ◽  
pp. 861 ◽  
Author(s):  
Yingdan Yuan ◽  
Bo Zhang ◽  
Xinggang Tang ◽  
Jinchi Zhang ◽  
Jie Lin
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Active Ingredients ◽  
Hub Genes ◽  
Transcriptome Database ◽  
Gene Modules ◽  
Functional Investigation ◽  
First Time

Dendrobium is widely used in traditional Chinese medicine, which contains many kinds of active ingredients. In recent years, many Dendrobium transcriptomes have been sequenced. Hence, weighted gene co-expression network analysis (WGCNA) was used with the gene expression profiles of active ingredients to identify the modules and genes that may associate with particular species and tissues. Three kinds of Dendrobium species and three tissues were sampled for RNA-seq to generate a high-quality, full-length transcriptome database. Based on significant changes in gene expression, we constructed co-expression networks and revealed 19 gene modules. Among them, four modules with properties correlating to active ingredients regulation and biosynthesis, and several hub genes were selected for further functional investigation. This is the first time the WGCNA method has been used to analyze Dendrobium transcriptome data. Further excavation of the gene module information will help us to further study the role and significance of key genes, key signaling pathways, and regulatory mechanisms between genes on the occurrence and development of medicinal components of Dendrobium.

scholarly journals Red Light-inhibited Mesocotyl Elongation in Maize Seedlings

1978 ◽  
Vol 61 (4) ◽  
pp. 534-537 ◽  
Author(s):  
Larry N. Vanderhoef ◽  
Winslow R. Briggs
Keyword(s):  
Red Light ◽  
Maize Seedlings ◽  
Mesocotyl Elongation

scholarly journals Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10741
Author(s):  
Nan Chao ◽  
Qi Qi ◽  
Shuang Li ◽  
Brent Ruan ◽  
Xiangning Jiang ◽  
...  
Keyword(s):  
Shikimic Acid ◽  
Lignin Content ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Functional Divergence ◽  
Lignin Biosynthesis ◽  
Populus Tomentosa ◽  
Motif Analysis ◽  
Monolignol Biosynthesis ◽  
Populus Tomentosa Carr

Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content. Ten HCT homologs were identified in the Populus trichocarpa (Torr. & Gray) genome. Both genome duplication and tandem duplication resulted in the expansion of HCT orthologs in Populus. Comprehensive analysis including motif analysis, phylogenetic analysis, expression profiles and co-expression analysis revealed the divergence and putative function of these candidate PoptrHCTs. PoptrHCT1 and 2 were identified as likely involved in lignin biosynthesis. PoptrHCT9 and 10- are likely to be involved in plant development and the response to cold stress. Similar functional divergence was also identified in Populus tomentosa Carr. Enzymatic assay of PtoHCT1 showed that PtoHCT1 was able to synthesize caffeoyl shikimate using caffeoyl-CoA and shikimic acid as substrates.

scholarly journals Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10492
Author(s):  
Ahmed Khadr ◽  
Guang-Long Wang ◽  
Ya-Hui Wang ◽  
Rong-Rong Zhang ◽  
Xin-Rui Wang ◽  
...  
Keyword(s):  
Butyric Acid ◽  
Growth Parameters ◽  
Lignin Content ◽  
Expression Profiles ◽  
Morphological Characteristics ◽  
Gene Expression Profiles ◽  
Lignin Biosynthesis ◽  
Gene Profiles ◽  
High Antioxidant Activity ◽  
Lignin Accumulation

Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants.

scholarly journals Assay system for mesocotyl elongation and hydrotropism of maize primary root in response to low moisture gradient

BioTechniques ◽  
2021 ◽  
Vol 71 (4) ◽  
pp. 516-527
Author(s):  
Mery Nair Sáenz-Rodríguez ◽  
Gladys Iliana Cassab López
Keyword(s):  
Primary Root ◽  
Test System ◽  
Moisture Gradient ◽  
Maize Seedlings ◽  
Growth Environment ◽  
Mesocotyl Elongation ◽  
Maize Genetic ◽  
Emergence Phase ◽  
Gradient Condition ◽  
Potential Use

We designed and validated a test system that simulates a growth environment for  Zea mays L. maize seedlings under conditions of low moisture gradient in darkness. This system allowed us to simultaneously measure mesocotyl elongation and the primary root hydrotropic response in seedlings before the emergence phase in a collection of maize hybrids. We found great variation in these two traits with statistically significant reduction of their elongations under the low moisture gradient condition that indicate the richness of maize genetic diversity. Hence, the objective of designing a new test system that evaluates the association between these underground traits with the potential use to measure other traits in maize seedlings related to early vigor was achieved.

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