Cis-element amplified polymorphism (CEAP), a novel promoter- and gene-targeted molecular marker of plants

Chen, Mei-Yan; He, Xinhua; Huang, Xing; Lu, Ting-ting; Zhang, Yili; Zhu, Jiawei; H, Yu; Luo, Cong

doi:10.1007/s12298-022-01212-5

Cited by 4 publications

(2 citation statements)

References 44 publications

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“…ACGTG is a cis-element closely related to plant growth, development, signal transduction, and stress response. It, along with other cis-elements, can serve as valuable tools for studying genetic diversity, analyzing relationships between different species, and facilitating breeding efforts ( Chen et al, 2022 ). CACGTG is a cis-element known for its importance in plant defense against pathogens.…”

Section: Resultsmentioning

confidence: 99%

Identification, characterization, and validation of NBS-encoding genes in grass pea

Alsamman

Mousa²,

Nassar³

et al. 2023

Front. Genet.

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Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 μM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop.

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Section: Resultsmentioning

confidence: 99%

Identification, characterization, and validation of NBS-encoding genes in grass pea

Alsamman

Mousa²,

Nassar³

et al. 2023

Front. Genet.

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“…Many cis-elements were predicted to be involved in plant growth and development, signal transduction, and stress response [51]. The highly enriched cis-elements about light response, transcription enhancement, and ABRE revealed the function of PEAR candidates in plant growth regulation and stress response (Figure 2D, Table S3) [4,[36][37][38][39][40].…”

Section: Discussionmentioning

confidence: 96%

Function and Characteristic Analysis of Candidate PEAR Proteins in Populus yunnanensis

Li,

Wang,

Jiang

et al. 2023

IJMS

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PEAR proteins are a type of plant-specific DNA binding with one finger (Dof) transcription factors that play a key role in the regulation of plant growth, especially during phloem cell growth and seed germination in Arabidopsis. However, the identification, characteristics and function of PEAR proteins, particularly in woody plants, need to be further studied. In the present study, 43 candidate PEAR proteins harboring the conserved Zf-Dof domain were obtained in Populus yunnanensis. Based on phylogenetic and structural analysis, 10 representative PEAR candidates were selected, belonging to different phylogenetic groups. The functions of PEAR proteins in the stress response, signal transduction, and growth regulation of stem cambium and roots undergoing vigorous cell division in Arabidopsis were revealed based on their expression patterns as characterized by qRT-PCR analysis, in accordance with the results of cis-element analysis. In vitro experiments showed that the interaction of transcription factor (E2F) and cyclin indirectly reflects the growth regulation function of PEAR through light signaling and cell-cycle regulation. Therefore, our results provide new insight into the identity of PEAR proteins and their function in stress resistance and vigorous cell division regulation of tissues in P. yunnanensis, which may serve as a basis for further investigation of the functions and characteristics of PEAR proteins in other plants.

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Genetic Diversity Analysis of Red Beet Germplasm Resources Using CEAP Molecular Markers

Wang,

Wu,

et al. 2024

Sugar Tech

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Cis-element amplified polymorphism (CEAP), a novel promoter- and gene-targeted molecular marker of plants

Cited by 4 publications

References 44 publications

Identification, characterization, and validation of NBS-encoding genes in grass pea

Identification, characterization, and validation of NBS-encoding genes in grass pea

Function and Characteristic Analysis of Candidate PEAR Proteins in Populus yunnanensis

Genetic Diversity Analysis of Red Beet Germplasm Resources Using CEAP Molecular Markers

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