Interaction of Light and Temperature Signaling at the Plant Interphase: From Cue to Stress

Bhattacharya, Juhi; Singh, Upendra Kumar; Ranjan, Aashish

doi:10.1007/978-81-322-3706-8_8

Cited by 4 publications

(3 citation statements)

References 153 publications

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“…The factor unfertilized embryo sac10 (UNE10) is another member of the bHLH class. It is supposed to inhibit far-red light signaling by interacting with phytochromes [ 33 ] and to play an important role during the fertilization of ovules by pollen in A. thaliana [ 34 ].…”

Section: Resultsmentioning

confidence: 99%

In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data

Klees

Lange

Bertram

et al. 2021

IJMS

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Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the knowledge about such rSNPs and TFs could provide essential information regarding different genetic programs, such as tissue development or environmental stress responses. In this study, we use a multi-omics approach by combining genomics, transcriptomics, and proteomics data of two different Brassica napus L. cultivars, namely Zhongshuang11 (ZS11) and Zhongyou821 (ZY821), with high and low oil content, respectively, to monitor the regulatory interplay between rSNPs, TFs and their corresponding genes in the tissues flower, leaf, stem, and root. By predicting the effect of rSNPs on TF-binding and by measuring their association with the cultivars, we identified a total of 41,117 rSNPs, of which 1141 are significantly associated with oil content. We revealed several enriched members of the TF families DOF, MYB, NAC, or TCP, which are important for directing transcriptional programs regulating differential expression of genes within the tissues. In this work, we provide the first genome-wide collection of rSNPs for B. napus and their impact on the regulation of gene expression in vegetative and floral tissues, which will be highly valuable for future studies on rSNPs and gene regulation.

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Section: Resultsmentioning

confidence: 99%

In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data

Klees

Lange

Bertram

et al. 2021

IJMS

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“…However, in an artificially controlled plant factory, one of the biggest challenges is the massive energy consumption due to the maintenance and regulation of light and temperature environments [1]. Light and temperature are the two most crucial environmental stimuli that regulated plant growth and development [2], and not only serve as cues to initiate multiple developmental processes, but are also required for optimal performances of biochemical and physiological cascades in the normal plant life cycle [3]. Thus, understanding the responses in the growth and development of the plants to different light and temperature levels is an essential prerequisite for deciphering appropriate strategies to regulate environmental parameters in plant factories.…”

Section: Introductionmentioning

confidence: 99%

The Positive Effects of Increased Light Intensity on Growth and Photosynthetic Performance of Tomato Seedlings in Relation to Night Temperature Level

et al. 2022

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Light and temperature are related to the growth and development of plants as well as their energy consumption in plant factories. However, most of the studies to date have focused on light and temperature extremes, while the adaptive responses and underlying mechanisms of plants to non-stress light intensity (LI) and night temperature (NT) largely remain elusive. Here, we investigated the growth and physiological responses of tomatoes grown under three LI regimes of 250 (LL), 300 (LM), and 350 (LH) μmol m−2 s−1, respectively, combined with two NT conditions. The results revealed that increased LI comprehensively improved tomato growth and physiological status at lower NT levels, but the growth stimulations induced by increasing LI were limited by higher NT. In addition, the lower NT at LM and LH conferred a relatively better endogenous physiological condition and significantly promoted tomato growth, but the higher NT significantly accelerated shoot growth at LL, indicating a compensation of higher NT for low light induced growth restriction. Taken together, the current study suggests that the adaptation mechanism of tomato plants to higher NT varied with LI levels, and higher LI plus lower NT would be an effective strategy to improve tomato growth.

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“…The factor unfertilized embryo sac10 (UNE10) is another member of the bHLH class. It is supposed to inhibit far-red light signaling by interacting with phytochromes [140] and to play an important role during the fertilization of ovules by pollen in A. thaliana [141]. Several BES1 (BRI1-EMS-SUPPRESSOR1) family members, in particular BEH2, BEH3, BEH4, and BZR1, are enriched in flower and leaf and/or stem tissues, and are known to regulate brassinosteroid-mediated genes.…”

Section: Transcription Factor Binding Site Enrichment Analysismentioning

confidence: 99%

Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

Wilhelmi

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Transcriptional regulation of gene expression in higher organisms is fundamental for numerous biological processes. These processes are mainly controlled by a special class of regulatory proteins, the transcription factors (TFs), and their combinatorial interplay. Various genetic programs, such as environmental adaptation, tissue development, or disease control, are governed by the binding of TFs to short DNA motifs, called transcription factor binding sites (TFBS), in the regulatory regions of their target genes. Single nucleotide polymorphisms (SNPs) located in promoter regions can alter TFBSs leading to a change in the binding affinity of TFs and, thus, affect gene expression. Such SNPs are referred to as regulatory SNPs (rSNPs). In recent years, rSNPs have come into the focus of research, and the underlying mechanisms resulting in a differential gene expression have been studied for many specific traits and diseases mainly in humans or model organisms, but also in agricultural species. However, these studies mostly concentrate on single regulatory variants and do not include systematic analyses. Thus, there is still a lack of such comprehensive analyses and genome-wide collections of rSNPs, and to date, only few tools and databases are available for livestock or crop species. In this work, I developed a pipeline for the detection of rSNPs and created the databases agReg-SNPdb and agReg-SNPdb-Plants, storing genome-wide collections of rSNPs and their predicted effects on TF binding for agricultural animal and plant species, respectively. agReg-SNPdb includes seven livestock and domestic species, namely cattle, pig, chicken, sheep, horse, goat, and dog and agReg-SNPdb-Plants includes 13 crop species and subspecies, namely African rice, Asian rice (with its subspecies Indica and Japonica), barley, bread wheat, durum wheat, grape, maize, rapeseed, sorghum, sunflower, tomato, and wild rice. Out of all species stored in agReg-SNPdb-Plants, rapeseed holds a special role. In contrast to the remaining species, where I used the data from Ensembl Plants as basis, in rapeseed, to date, there is no genome-wide collection of SNPs available. Therefore, I used a previously published data set based on different resequenced Brassica napus L. cultivars for the identification of rSNPs in agReg-SNPdb-Plants. Based on this data set, I investigated the regulatory mechanisms in two cultivars, namely Zhongshuang11 (ZS11), a so-called double-low accession with low content of erucic acid and glucosinolate, which is characterized by high oil content, and Zhongyou821 (ZY821), a so-called double-high accession with high content of erucic acid and glucosinolate, which is characterized by low oil content. In this way, I demonstrate the application of rSNPs together with multi-omics data to perform a systematic analysis of the complex interplay between rSNPs, TFs, and differentially expressed genes (DEGs) in four tissues (flower, leaf, stem, and root) which are underlying the oil content and -quality in rapeseed. viii Es hat mir großen Spaß ...

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Interaction of Light and Temperature Signaling at the Plant Interphase: From Cue to Stress

Cited by 4 publications

References 153 publications

In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data

In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data

The Positive Effects of Increased Light Intensity on Growth and Photosynthetic Performance of Tomato Seedlings in Relation to Night Temperature Level

Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

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