Effects of ploidy variation on DNA methylation and gene expression in Pear (Pyrus communis L.)

Liu, Jianlong; Zhou, Fangjian; Cui, Shaoqiang; Yang, Yingjie; Sun, Qiangming; Guan, Qiuzhu; Li, DingLi; Zhang, Shaoling; Wang, Ran

doi:10.1016/j.scienta.2021.110713

Cited by 5 publications

(3 citation statements)

References 53 publications

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“…The reaction system (20 μL total volume) consisted of template cDNA 2 μL, forward primer and reverse primer 1 μL each, Supermix 10 μL, and RNA-free H 2 O 6 μL. The reaction process was as follows: 95 °C for 5 min, 45 cycles at 95 °C for 15 s, 60 °C for 30 s, and 72 °C for 30 s [ 35 ]. Using PbActin1 and PbActin2 as internal reference genes, the relative expression levels for each gene were calculated by the 2 −ΔΔCT method, and each sample analysis was repeated 3 times [ 36 ].…”

Section: Methodsmentioning

confidence: 99%

Alleviation of iron deficiency in pear by ammonium nitrate and nitric oxide

Liu

Wang

et al. 2022

BMC Plant Biol

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Background Iron is essential for the growth and development of trace elements in plants, and iron deficiency can lead to leaf chlorosis. Ammonium and nitrate are the major forms of nitrogen present in soils. Ammonium nitrate alleviates the chlorosis of leaves caused by iron deficiency, but the mechanism is not clear in pear. Results Ammonium nitrate induced the increase of nitric oxide (NO) under iron deficiency. We further analyzed the effect of NO by exogenous NO treatment. The results showed that ammonium nitrate and NO increased the activity of ferric chelate reductase. NO induced the expression of multiple IRT genes and promoted the transmembrane transport of irons. Ammonium nitrate and NO promoted the activity of nitrogen assimilation-related enzymes and the nitrogen absorption capacity, and they also increased glutamine synthetase activity. Finally, ammonium nitrate and NO increased chlorophyll synthesis, with subsequent increase in the photosynthetic capacity of plants and accumulation of biomass. Conclusion Ammonium nitrate indirectly alleviates the symptoms of plant yellowing by promoting the increase of NO, which increases the response of iron transporters. Both substances increase the nitrogen accumulation in plants. This study demonstrates a new option for minimizing Fe deficiency by regulating the balance between nutrients.

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Section: Methodsmentioning

confidence: 99%

Alleviation of iron deficiency in pear by ammonium nitrate and nitric oxide

Liu

Wang

et al. 2022

BMC Plant Biol

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“…In recent studies, gene fragments methylated in pear have been shown to be associated with energy metabolism, mitochondrial regulation, calcium ion transport, phosphatase activity, arginine biosynthesis, cell shape regulation, promotion of leaf epidermal polarization growth, auxin-mediated, RNA modification, ATP binding and carbon synthesis (Liu, et al 2022). If the DNA methylation balance is disrupted, it will lead to DNA damage repair, nucleotide metabolism, and cell cycle regulation, thereby increasing the instability and fragility of the polyploid genome (Yin, et al 2021).…”

Section: Epigenetic Changesmentioning

confidence: 99%

Plant Polyploidy: Origin, Induction, Phenotypic Change Mechanisms, Population Establishment, and Distribution

Yang

Chen

2023

Preprint

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Polyploidy refers to individuals that contain two or more heritable sets of chromosomes. It is an important feature of chromosome evolution in eukaryotes and is very common in plants in nature. Polyploidy forms in nature in many ways. Researchers have also mastered a variety of polyploid induction and detection methods. In the process of plant polyploidization, a variety of genetic and epigenetic changes occur. This reduces the redundancy of polyploidy genes and changes their traits, promoting the long-term evolution and diversification of polyploidy. Polyploidy has many strategies to overcome minority cytotype exclusion (MCE) during population establishment to coexist stably with diploid parents. Due to differences in traits, polyploidy changes its interaction with the environment, and there is a certain regular distribution in natural and urban ecosystems. Polyploids have been used in several fields, including forestry, and agriculture. In this review, we summarized the natural formation of polyploidy artificial polyploids induction, detection of polyploidy, and mechanism of phenotypic differences between polyploids and diploidy.

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“…Pear is a globally cultivated fruit crops and extensive research has been conducted to investigate pear DNA methylation, using four methods: methylation-sensitive amplification polymorphism [ 36 ], methylation-specific endonuclease-PCR [ 19 , 37 , 38 ], TLC-based detection [ 39 ], and genome-wide bisulfite sequencing [ 40 ]. It is determined that DNA methylation is increased in colchicine-induced polyploidy [ 36 ] and in long-term stored and severely desiccated seeds [ 39 ]. Inhibition of DNA methylation using the DNA methylation inhibitor 5-azacytidine (5’-Aza) decreases ethylene production in suspension-cultured pear fruit cells [ 41 ].…”

Section: Introductionmentioning

confidence: 99%

Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism

Gu,

Pei,

Guo

et al. 2024

Genome Biol

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Background Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved. Results We generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, β-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening. Conclusion Our findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.

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Effects of ploidy variation on DNA methylation and gene expression in Pear (Pyrus communis L.)

Cited by 5 publications

References 53 publications

Alleviation of iron deficiency in pear by ammonium nitrate and nitric oxide

Alleviation of iron deficiency in pear by ammonium nitrate and nitric oxide

Plant Polyploidy: Origin, Induction, Phenotypic Change Mechanisms, Population Establishment, and Distribution

Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism

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