Effect of exogenous indole-3-butanoic acid (IBA) application on the morphology, hormone status, and gene expression of developing lateral roots in Malus hupehensis

Abstract Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.

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Effects of dietary supplementation of DL-2-hydroxy-4(methylthio) butanoic acid on antioxidant capacity and its related gene expression in lung and liver of broilers exposed to low temperature

Poultry Science ◽

10.3382/ps/pey371 ◽

2019 ◽

Vol 98 (1) ◽

pp. 341-349 ◽

Cited By ~ 2

Author(s):

Jianping Wang ◽

Geling Yang ◽

Keying Zhang ◽

Xuemei Ding ◽

Shiping Bai ◽

...

Keyword(s):

Gene Expression ◽

Low Temperature ◽

Antioxidant Capacity ◽

Dietary Supplementation ◽

Related Gene ◽

Butanoic Acid

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Thyroid hormone status interferes with estrogen target gene expression in breast cancer samples of menopausal women

The FASEB Journal ◽

10.1096/fasebj.27.1_supplement.609.3 ◽

2013 ◽

Vol 27 (S1) ◽

Author(s):

Sandro José Conde ◽

Renata de Azevedo M. Luvizotto ◽

Maria Teresa Síbio ◽

Célia Regina Nogueira

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Thyroid Hormone ◽

Target Gene ◽

Target Gene Expression ◽

Menopausal Women ◽

Hormone Status

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Cortex cell hydraulic conductivity, endodermal apoplastic barriers and root hydraulics change in barley (Hordeum vulgare L.) in response to a low supply of N and P

Annals of Botany ◽

10.1093/aob/mcz113 ◽

2019 ◽

Cited By ~ 2

Author(s):

Thomas Armand ◽

Michelle Cullen ◽

Florentin Boiziot ◽

Lingyu Li ◽

Wieland Fricke

Keyword(s):

Gene Expression ◽

Hydraulic Conductivity ◽

Water Flow ◽

Lateral Roots ◽

Area Ratio ◽

Main Axis ◽

Mineral Nutrient ◽

Partial Recovery ◽

Cortex Cell ◽

Apoplastic Barriers

Abstract Background Mineral nutrient limitation affects the water flow through plants. We wanted to test on barley whether any change in root-to-shoot ratio in response to low supply of nitrogen and phosphate is accompanied by changes in root and cell hydraulic properties and involves changes in aquaporin (AQP) gene expression and root apoplastic barriers (suberin lamellae, Casparian bands). Methods Plants were grown hydroponically on complete nutrient solution or on solution containing only 3.3 % or 2.5 % of the control level of nutrient. Plants were analysed when they were 14–18 d old. Results Nutrient-limited plants adjusted water flow to an increased root-to-shoot surface area ratio through a reduction in root hydraulic conductivity (Lp) as determined through exudation analyses. Cortex cell Lp (cell pressure probe analyses) decreased in the immature but not the mature region of the main axis of seminal roots and in primary lateral roots. The aquaporin inhibitor HgCl2 reduced root Lp most in nutrient-sufficient control plants. Exchange of low-nutrient for control media caused a rapid (20–80 min) and partial recovery in Lp, though cortex cell Lp did not increase in any of the root regions analysed. The gene expression level (qPCR analyses) of five plasma membrane-localized AQP isoforms did not change in bulk root extracts, while the formation of apoplastic barriers increased considerably along the main axis of root and lateral roots in low-nutrient treatments. Conclusions Decrease in root and cortex cell Lp enables the adjustment of root water uptake to increased root-to-shoot area ratio in nutrient-limited plants. Aquaporins are the prime candidate to play a key role in this response. Modelling of water flow suggests that some of the reduction in root Lp is due to increased formation of apoplastic barriers.

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Effect of Exogenous Abscisic acid (ABA) on the Morphology, Phytohormones, and Related Gene Expression of Developing Lateral Roots in ‘Qingzhen 1’

10.21203/rs.3.rs-670691/v1 ◽

2021 ◽

Author(s):

Xiaoyun Zhang ◽

Shaohuan Li ◽

Ting Tang ◽

Jiangping Mao ◽

Ke Li ◽

...

Keyword(s):

Gene Expression ◽

Abscisic Acid ◽

Early Stage ◽

Lateral Roots ◽

Plant Stress ◽

Zeatin Riboside ◽

Regulation Mechanism ◽

Expression Levels ◽

Primary Stress ◽

Indole 3 Acetic Acid

Abstract Lateral roots (LRs) are critical for plant stress tolerance and productivity. Understanding how hormones and genes interact in a fluctuating environment to coordinate LR development is a major challenge. Abscisic acid (ABA) is the primary stress-responsive hormone and mediates LR development in various plant species. However, the effect of exogenous ABA on LR development has not been elucidated in apple. In this study, ‘Qingzhen 1’ was treated with exogenous 5 µM ABA for 20 days to investigate the regulation mechanism of ABA on LR development. Morphological observations advocated that ABA inhibited both LR and shoot development in ‘Qingzhen 1’ apple plants, where the root number was 16.94%, the root length was 30.32%, the plant height was 10.88%, and the stem thickness was 8.08% lower than those in the control plants. Meanwhile, the endogenous ABA concentration was significantly increased, but the indole-3-acetic acid (IAA), zeatin riboside (ZR), and jasmonic acid (JA) concentrations were significantly decreased with ABA treatment. Furthermore, the expression levels of ABA-related genes (MdCYP707A2, MdABI1, MdAREB2, and MdABF3) were significantly upregulated, while the expression levels of auxin-related genes (MdYUCCA3, MdYUCCA8, MdPIN1 MdPIN2, MdPIN3, and MdARF19), root development-related genes (MdWOX5 and MdWOX11), and cell cycle-related genes (MdCYCD1;1 and MdCYCD3;1) were significantly downregulated at the early stage of ABA treatment, which act together on the inhibition of LR development. Taken together, the changes in hormone levels and gene expression resulted in inhibited LR development of apple plants in response to ABA.

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In silico analyses of pericycle cell populations reinforce their relation with associated vasculature in Arabidopsis

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0227 ◽

2012 ◽

Vol 367 (1595) ◽

pp. 1479-1488 ◽

Cited By ~ 20

Author(s):

Boris Parizot ◽

Ianto Roberts ◽

Jeroen Raes ◽

Tom Beeckman ◽

Ive De Smet

Keyword(s):

Gene Expression ◽

Lateral Root ◽

Vascular Tissue ◽

Lateral Roots ◽

Specific Expression ◽

Concentric Layer ◽

Small Set ◽

Specific Proteins ◽

In Silico Analyses ◽

Pericycle Cells

In Arabidopsis , lateral root initiation occurs in a subset of pericycle cells at the xylem pole that will divide asymmetrically to give rise to a new lateral root organ. While lateral roots never develop at the phloem pole, it is unclear how the interaction with xylem and phloem poles determines the distinct pericycle identities with different competences. Nevertheless, pericycle cells at these poles are marked by differences in size, by ultrastructural features and by specific proteins and gene expression. Here, we provide transcriptional evidence that pericycle cells are intimately associated with their vascular tissue instead of being a separate concentric layer. This has implications for the identification of cell- and tissue-specific promoters that are necessary to drive and/or alter gene expression locally, avoiding pleiotropic effects. We were able to identify a small set of genes that display specific expression in the phloem or xylem pole pericycle cells, and we were able to identify motifs that are likely to drive expression in either one of those tissues.

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GmIDL2a and GmIDL4a, Encoding the Inflorescence Deficient in Abscission-Like Protein, Are Involved in Soybean Cell Wall Degradation during Lateral Root Emergence

International Journal of Molecular Sciences ◽

10.3390/ijms19082262 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2262 ◽

Cited By ~ 3

Author(s):

Chen Liu ◽

Chunyu Zhang ◽

Mingxia Fan ◽

Wenjuan Ma ◽

Meiming Chen ◽

...

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Lateral Root ◽

Cell Layer ◽

Lateral Roots ◽

Soybean Genome ◽

Cell Wall Degradation ◽

Primary Roots ◽

Cell Wall Remodeling ◽

Soybean Cell

The number of lateral roots (LRs) of a plant determines the efficiency of water and nutrient uptake. Soybean is a typical taproot crop which is deficient in LRs. The number of LRs is therefore an important agronomic trait in soybean breeding. It is reported that the inflorescence deficient in abscission (IDA) protein plays an important role in the emergence of Arabidopsis LRs. Previously, the genes which encode IDA-like (IDL) proteins have been identified in the soybean genome. However, the functions of these genes in LR development are unknown. Therefore, it is of great value to investigate the function of IDL genes in soybean. In the present study, the functions of two root-specific expressed IDL genes, GmIDL2a and GmIDL4a, are investigated. The expressions of GmIDL2a and GmIDL4a, induced by auxin, are located in the overlaying tissue, where LRs are initiated. Overexpression of GmIDL2a and GmIDL4a increases the LR densities of the primary roots, but not in the elder root. Abnormal cell layer separation has also been observed in GmIDL2a- and GmIDL4a-overexpressing roots. These results suggest that the overlaying tissues of GmIDL2a- and GmIDL4a-overexpressing roots are looser and are suitable for the emergence of the LR primordium. Further investigation shows that the expression of some of the cell wall remodeling (CWR) genes, such as xyloglucan endotransglucosylase/hydrolases, expansins, and polygalacturonases, are increased when GmIDL2a and GmIDL4a are overexpressed in hairy roots. Here, we conclude that GmIDL2a and GmIDL4a function in LR emergence through regulating soybean CWR gene expression.

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