Genome-Wide Analysis and Expression Profiles of Ethylene Signal Genes and Apetala2/Ethylene-Responsive Factors in Peanut (Arachis hypogaea L.)

Cui, Yuanyuan; Bian, Jianxin; Guan, Yu; Xu, Fangtao; Han, Xue; Deng, Xing‐Wang; Liu, Xiaoqin

doi:10.3389/fpls.2022.828482

Cited by 7 publications

(7 citation statements)

References 61 publications

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“…The number of AP2/ERF genes was greatest on chromosome 2 (22), chromosome 16 had the fewest (5), and the number on the other chromosomes ranged from 7 to 21. Most of the genes were on both ends of the chromosomes, which was similar to studies in Arabidopsis and other species [ 5 , 32 , 33 ]. The distribution similarity of genes on chromosomes indicates functional consistency.…”

Section: Resultssupporting

confidence: 84%

“…Analyzing the exon-intron structure of the JmAP2/ERF gene revealed that 64 members of this family possessed introns, including 27 JmAP2 genes, 2 JmRAV genes, 4 JmSoloist genes, 9 JmDREB genes, and 22 JmERF genes. Among them, the JmAP2 subfamily contained more introns than other families; however, zero or few introns were observed in the JmERF and JmDREB subfamilies; similar results have been found in C. olitorius L. [ 12 ], A. hypogaea L. [ 32 ], and C. illinoinensis [ 33 ]. This seemed to be related to the 122 pairs of segmental duplication events in this study and further confirmed that segmental duplication leads to intron loss with a higher probability than gain [ 36 ].…”

Section: Discussionsupporting

confidence: 68%

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Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

Zhao

Xie

Zhang

et al. 2022

IJMS

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Juglans mandshurica has strong freezing resistance, surviving temperatures as low as −40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily of transcription factors that regulates plant development, growth, and the response to biotic and abiotic stress. In this study, phylogenetic analysis was used to identify 184 AP2/ERF genes in the J. mandshurica genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, and JmERF). A significant amount of discordance was observed in the 184 AP2/ERF genes distribution of J. mandshurica throughout its 16 chromosomes. Duplication was found in 14 tandem and 122 segmental gene pairs, which indicated that duplications may be the main reason for JmAP2/ERF family expansion. Gene structural analysis revealed that 64 JmAP2/ERF genes contained introns. Gene evolution analysis among Juglandaceae revealed that J. mandshurica is separated by 14.23 and 15 Mya from Juglans regia and Carya cathayensis, respectively. Based on promoter analysis in J. mandshurica, many cis-acting elements were discovered that are related to light, hormones, tissues, and stress response processes. Proteins that may contribute to cold resistance were selected for further analysis and were used to construct a cold regulatory network based on GO annotation and JmAP2/ERF protein interaction network analysis. Expression profiling using qRT‒PCR showed that 14 JmAP2/ERF genes were involved in cold resistance, and that seven and five genes were significantly upregulated under cold stress in female flower buds and phloem tissues, respectively. This study provides new light on the role of the JmAP2/ERF gene in cold stress response, paving the way for further functional validation of JmAP2/ERF TFs and their application in the genetic improvement of Juglans and other tree species.

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Section: Resultssupporting

confidence: 84%

Section: Discussionsupporting

confidence: 68%

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

Zhao

Xie

Zhang

et al. 2022

IJMS

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“…The FPKM value of EIN3 was upregulated by 2.38 times in the L3S vs. D3S comparison in response to light ( Figure 5E ). Our previous study also showed that EIN3 was significantly expressed during pod development ( Cui et al, 2022 ). Three JAZ ( NLIW19 , 76C240 , and W1F2QM ) were significantly upregulated after the loss of mechanical stress and darkness.…”

Section: Resultsmentioning

confidence: 70%

Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress

Cui

Bian²,

Lv³

et al. 2022

Front. Plant Sci.

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Peanut is an oil crop with important economic value that is widely cultivated around the world. It blooms on the ground but bears fruit underground. When the peg penetrates the ground, it enters a dark environment, is subjected to mechanical stress from the soil, and develops into a normal pod. When a newly developed pod emerges from the soil, it turns green and stops growing. It has been reported that both darkness and mechanical stress are necessary for normal pod development. In this study, we investigated changes in gene expression during the reverse process of peg penetration: developmental arrest caused by pod (Pattee 3 pods) excavation. Bagging the aerial pods was used to simulate loss of mechanical pressure, while direct exposure of the aerial pods was used to simulate loss of both mechanical pressure and darkness. After the loss of mechanical stress and darkness, the DEGs were significantly enriched in photosynthesis, photosynthesis–antenna proteins, plant–pathogen interaction, DNA replication, and circadian rhythm pathways. The DNA replication pathway was enriched by down-regulated genes, and the other four pathways were enriched by upregulated genes. Upregulated genes were also significantly enriched in protein ubiquitination and calmodulin-related genes, highlighting the important role of ubiquitination and calcium signaling in pod development. Further analysis of DEGs showed that phytochrome A (Phy A), auxin response factor 9 (IAA9), and mechanosensitive ion channel protein played important roles in geocarpy. The expression of these two genes increased in subterranean pods but decreased in aerial pods. Based on a large number of chloroplast-related genes, calmodulin, kinases, and ubiquitin-related proteins identified in this study, we propose two possible signal transduction pathways involved in peanut geocarpy, namely, one begins in chloroplasts and signals down through phosphorylation, and the other begins during abiotic stress and signals down through calcium signaling, phosphorylation, and ubiquitination. Our study provides valuable information about putative regulatory genes for peanut pod development and contributes to a better understanding of the biological phenomenon of geocarpy.

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“…In recent years, extensive studies have revealed the key regulatory roles of auxin, ethylene, cytokinin, abscisic acid, and gibberellin in peanut pod development, maturation, and response to biotic/abiotic stresses. 36,37 The comparative transcriptome data present in this study showed that plant hormone signaling pathway genes in the peanut pod varied greatly when faced with microplastics contamination and biochar amendment, especially those involved in the auxin signal transduction pathway. All high-abundance DEGs of the auxin signal transduction pathway exhibited opposite expression trends in the comparisons T1-v-T2 and T2-v-T3.…”

Section: Discussionmentioning

confidence: 83%

Biochar alleviated the toxic effects of microplastics‐contaminated geocarposphere soil on peanut (Arachis hypogaea L.) pod development: roles of pod nutrient metabolism and geocarposphere microbial modulation

Yang,

Liang,

et al. 2023

J Sci Food Agric

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BACKGROUNDThe accumulation of microplastics in agricultural soil poses a threat to the sustainability of agriculture, impacting crop growth and soil health. Due to the geocarpy feature of peanut, geocarposphere soil environment is critical to pod development and its nutritional quality. While the effects of microplastics in the rhizosphere have been studied, their impact on peanut pod in the geocarposphere remains unknown. Biochar has emerged as a potential soil agent with the ability to remediate soil contamination. However, the mechanisms of biochar in mitigating the toxic effects of microplastics‐contaminated geocarposphere soil on peanut pod development remain largely unexplored.RESULTSWe evaluated the peanut pod performance and microbiome when facing microplastics contamination and biochar amendment in geocarposphere soil. The results showed that microplastics present in geocarposphere soil could directly enter the peanut pod, cause pod developmental disorder and exert adverse effects on nutritional quality. Aberrant expression of key genes associated with amino acid metabolism, lipid synthesis, and auxin and ethylene signaling pathways were the underlying molecular mechanisms of microplastics‐induced peanut pod developmental inhibition. However, these expression abnormalities could be reversed by biochar application. In addition, peanut geocarposphere microbiome results showed that biochar application could restore the diversity of microbial communities inhibited by microplastics contamination and promote the relative abundance of bacteria correlated with pathogen resistance and nitrogen cycle of geocarposphere soil, further promoting peanut pod development.CONCLUSIONThis study demonstrated that biochar application is an effective strategy to mitigate the toxic effects of microplastics‐contaminated geocarposphere soil on pod development and nutritional quality. © 2023 Society of Chemical Industry.

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Genome-Wide Analysis and Expression Profiles of Ethylene Signal Genes and Apetala2/Ethylene-Responsive Factors in Peanut (Arachis hypogaea L.)

Cited by 7 publications

References 61 publications

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress

Biochar alleviated the toxic effects of microplastics‐contaminated geocarposphere soil on peanut (Arachis hypogaea L.) pod development: roles of pod nutrient metabolism and geocarposphere microbial modulation

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