AIMC Topic: Gene Expression Regulation, Plant

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Investigating cis-regulatory elements and gene expression in multiple tomato varieties using interpretable deep learning.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Cis-regulatory elements (CREs) govern gene expression, and the relationship between non-coding regulatory elements and gene expression is inherently complex. To further elucidate how these elements influence gene expression, we refined previous model...

Evaluation of Lens culinaris germplasm against ascochyta blight by applying phenotyping and defense genes attributes.

Scientific reports
Lentil Ascochyta blight (caused by Ascochyta lentis) is one of the most important limiting factors of lentil cultivation and production in most regions of the world. Introducing resistance sources against the pathogen is a suitable strategy to conque...

Multiomic insights into sucrose accumulation in sugarcane.

Plant molecular biology
Sugarcane holds significant economic importance in sugar and biofuel production. Despite extensive research, understanding highly quantitative traits remains challenging due to its complex genomic landscape. We conducted a multiomic investigation to ...

Genetic regulations of citrus flowering: insights towards climatic factors and modern biotechnological approaches.

Planta
The review highlights the intricate relationship between genetic and molecular mechanisms that regulate floral development and responses in citrus under diverse climatic conditions. Citrus, the world's top traded and third most produced fruit crop, h...

Biomarker genes for model-based prediction of drought-stress perception levels in rice.

BMC plant biology
BACKGROUND: Drought is a global challenge that severely restricts crop yields and threatens food security. Plants respond to drought stress by modulating gene expression before visible phenotypic changes occur. However, most studies of drought resist...

Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning.

Genome biology
BACKGROUND: Transcription initiation is a key checkpoint in plant gene regulation, yet the DNA features that determine where and the frequency of the genes start transcription remain unclear.

Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock.

Nature communications
The circadian clock of plants contributes to their survival and fitness. However, understanding clock function at the transcriptome level and its response to the environment requires assaying across high resolution time-course experiments. Generating...

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions.

BMC genomics
Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript's ...

Structure and Functions of NDR1/HIN1-Like (NHL) Proteins in Plant Development and Response to Environmental Stresses.

Plant, cell & environment
The NON-RACE-SPECIFIC DISEASE RESISTANCE 1/harpin-induced 1-LIKE (NHL) gene family plays pivotal roles, including pathogen resistance, abiotic stress tolerance, and developmental regulation, underscoring their functional versatility in developmental ...

Deep Neural Network-Mining of Rice Drought-Responsive TF-TAG Modules by a Combinatorial Analysis of ATAC-Seq and RNA-Seq.

Plant, cell & environment
Drought is a critical risk factor that impacts rice growth and yields. Previous studies have focused on the regulatory roles of individual transcription factors in response to drought stress. However, there is limited understanding of multi-factor st...