Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture

Rehman, Shamsur; Ahmad, Zishan; Ramakrishnan, Muthusamy; Kalendar, Ruslan; Zhuge, Qiang

doi:10.1007/s10142-023-01219-5

Cited by 5 publications

(3 citation statements)

References 270 publications

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“…As sessile organisms, plants continuously face various biotic (microbes and pests) and abiotic (temperature, salinity, and drought) stresses, which severely impact their survival [25,26]. In their adaption to these harsh environments, a series of strategies have been developed in higher plants.…”

Section: Figure 1 Bioinformatics Analysis Of Pifs Proteins (A)mentioning

confidence: 99%

Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses

Li,

Ma,

Zhang

et al. 2024

IJMS

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Plants possess the remarkable ability to sense detrimental environmental stimuli and launch sophisticated signal cascades that culminate in tailored responses to facilitate their survival, and transcription factors (TFs) are closely involved in these processes. Phytochrome interacting factors (PIFs) are among these TFs and belong to the basic helix–loop–helix family. PIFs are initially identified and have now been well established as core regulators of phytochrome-associated pathways in response to the light signal in plants. However, a growing body of evidence has unraveled that PIFs also play a crucial role in adapting plants to various biological and environmental pressures. In this review, we summarize and highlight that PIFs function as a signal hub that integrates multiple environmental cues, including abiotic (i.e., drought, temperature, and salinity) and biotic stresses to optimize plant growth and development. PIFs not only function as transcription factors to reprogram the expression of related genes, but also interact with various factors to adapt plants to harsh environments. This review will contribute to understanding the multifaceted functions of PIFs in response to different stress conditions, which will shed light on efforts to further dissect the novel functions of PIFs, especially in adaption to detrimental environments for a better survival of plants.

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Section: Figure 1 Bioinformatics Analysis Of Pifs Proteins (A)mentioning

confidence: 99%

Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses

Li,

Ma,

Zhang

et al. 2024

IJMS

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show abstract

“…In general, information about root system architecture in the field and information about the genetic control of root system architecture remains scarce (Trachsel et al 2011). Recently, Trachsel et al (2011) proposed an easily handled, efficient and cheap tool for phenotyping mature roots in a natural environment under field conditions, that are complicated and involved in multiple environmental stress, such as high/low temperature, drought and salinity stress, affecting plant growth and development, including root development (Rehman et al 2023, Saeed et al 2023). “Shovelomics” can identify several important phenes that affect root distribution, including root number, root branch density, root growth angle, etc.…”

Section: Introductionmentioning

confidence: 99%

Diversity, Variance, and Stability of Root Phenes of Peanut (Arachis hypogaea L.)

Li,

Liu

et al. 2024

Physiologia Plantarum

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Root phenes are associated with the absorptive efficiency of water and fertilizers. However, there are few reports on the genetic variation and stability of peanut (Arachis hypogaea L.) root architecture under different environments. In this study, the diversity, variance and stability of root phenes of 89 peanut varieties were investigated with shovelomics (high throughput phenotyping of root system architecture) for two years in both field and laboratory experiments. The root phenes of these peanut genotypes presented rich diversity; for example, the value of total root length (TRL) ranged from 347.84 cm to 1013.80 cm in the field in 2018, and from 55.14 cm to 206.22 cm in the laboratory tests. The root phenes of different genotypes varied differently; for example, the coefficient of variation (CV) of TRL ranged from 24.0 to 83.5 across the two‐year field test. Field and laboratory evaluations were highly correlated, especially on lateral root density (LRD) and root angle (RA), and the quadrant graph analysis of LRD and RA implied that 69.7% of the roots belong to the same type. These not only further reflect root phenes stability through different environment but also demonstrate that some root phenes identified at early stage can indicate their status at later growth stage. In addition, root phenes showed a strong correlation with shoot growth, especially root dry weight (RDW), TRL and（nodule number）NN. Thus, laboratory tests in combination with field shovelomics can efficiently screen and select genotypes with contrasting root phenes to optimize water and nutrient management.

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“…Epigenetic modifications, such as DNA methylation and post-translational modifications of histone proteins, play a crucial role in plant responses to cold stress ( Sharma et al., 2022 ; Rehman et al., 2023 ). It is widely accepted that grapevine DNA methylation variability is primarily influenced by genotype.…”

Section: Introductionmentioning

confidence: 99%

Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera

Konecny,

Nikoghosyan,

Binder

2023

Front. Plant Sci.

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IntroductionThe escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine.MethodsWe used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific “portraits” of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied.ResultsOur analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines.DiscussionApplication of Self Organizing Maps portrayal to vine transcriptomics identified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants.

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Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture

Cited by 5 publications

References 270 publications

Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses

Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses

Diversity, Variance, and Stability of Root Phenes of Peanut (Arachis hypogaea L.)

Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera

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