Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

Guo, Hao; Cao, Peng; Wang, Chao; Lai, Ji-Ching; Deng, Yuan; Li, Chun; Hao, Yingchen; Wu, Zeyong; Chen, Ridong; Qiang, Qi; Fernie, Alisdair R.; Yang, Jun; Wang, Shouchuang

doi:10.1007/s11427-022-2299-5

Cited by 11 publications

(6 citation statements)

References 58 publications

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“…Cultivated accessions consistently exhibit significantly higher global levels of DNA methylation across all sequence contexts and all genomic features. These observations, are in contradiction with previous studies showing that domestication induces a significant decrease in DNA methylation in rice [ 29 ] and tomato [ 30 ]. This is perhaps explained by the differences in the type of propagation used during the domestication of each species (i.e., vegetative vs. sexual propagation), which could have resulted in diametrically opposed domestication epigenetic syndromes [ 2 , 6 ].…”

Section: Discussioncontrasting

confidence: 99%

“…A reduction that is reversed in the resynthesized hexaploid wheat [ 27 ]. More recently, detailed analysis of DNA methylation in rice [ 29 ] and tomato [ 30 ] has shown that domesticated cultivars present lower levels of DNA methylation than their wild counterparts. Moreover, multiple studies have shown that differentially methylated regions associated to domestication overlap with genes linked to traits known to be under selection during domestication of soybean [ 31 ], tomato [ 30 ], maize [ 32 ], and cotton [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

“…More recently, detailed analysis of DNA methylation in rice [ 29 ] and tomato [ 30 ] has shown that domesticated cultivars present lower levels of DNA methylation than their wild counterparts. Moreover, multiple studies have shown that differentially methylated regions associated to domestication overlap with genes linked to traits known to be under selection during domestication of soybean [ 31 ], tomato [ 30 ], maize [ 32 ], and cotton [ 28 ]. However, our understanding of how these epigenetic modifications were utilized or inadvertently altered during the domestication process remains rudimentary.…”

Section: Introductionmentioning

confidence: 99%

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Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication

Rodriguez-Izquierdo,

Carrasco,

Anand

et al. 2024

BMC Plant Biol

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The domestication process in grapevines has facilitated the fixation of desired traits. Nowadays, vegetative propagation through cuttings enables easier preservation of these genotypes compared to sexual reproduction. Nonetheless, even with vegetative propagation, various phenotypes are often present within the same vineyard due to the accumulation of somatic mutations. These mutations are not the sole factors influencing phenotype. Alongside somatic variations, epigenetic variation has been proposed as a pivotal player in regulating phenotypic variability acquired during domestication. The emergence of these epialleles might have significantly influenced grapevine domestication over time. This study aims to investigate the impact of domestication on methylation patterns in cultivated grapevines. Reduced-representation bisulfite sequencing was conducted on 18 cultivated and wild accessions. Results revealed that cultivated grapevines exhibited higher methylation levels than their wild counterparts. Differential Methylation Analysis between wild and cultivated grapevines identified a total of 9955 differentially methylated cytosines, of which 78% were hypermethylated in cultivated grapevines. Functional analysis shows that core methylated genes (consistently methylated in both wild and cultivated accessions) are associated with stress response and terpenoid/isoprenoid metabolic processes. Meanwhile, genes with differential methylation are linked to protein targeting to the peroxisome, ethylene regulation, histone modifications, and defense response. Collectively, our results highlight the significant roles that epialleles may have played throughout the domestication history of grapevines.

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Section: Discussioncontrasting

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication

Rodriguez-Izquierdo,

Carrasco,

Anand

et al. 2024

BMC Plant Biol

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“…In the future, we will further utilize multi-omics techniques such as genomics, transcriptomic, metabolomic, and epigenomics to comprehensively elucidate the response mechanisms and metabolic regulatory networks of plants to selenium (Guo et al 2023 ; Lai et al 2023 ; Liu and Zhong 2024 ), especially delving into the functional mechanisms of SAT and OASTL genes. By analyzing gene expression regulation and methylation modifications, we can better understand the response mechanisms of plants to selenium, providing more insights and methods for future crop improvement, increased selenium content, and enhanced nutritional value.…”

Section: Discussionmentioning

confidence: 99%

Gene identification, expression analysis, and molecular docking of SAT and OASTL in the metabolic pathway of selenium in Cardamine hupingshanensis

Chen,

Li,

Luo

et al. 2024

Plant Cell Rep

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Key message Identification of selenium stress-responsive expression and molecular docking of serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) in Cardamine hupingshanensis. Abstract A complex coupled with serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) is the key enzyme that catalyzes selenocysteine (Sec) synthesis in plants. The functions of SAT and OASTL genes were identified in some plants, but it is still unclear whether SAT and OASTL are involved in the selenium metabolic pathway in Cardamine hupingshanensis. In this study, genome-wide identification and comparative analysis of ChSATs and ChOASTLs were performed. The eight ChSAT genes were divided into three branches, and the thirteen ChOASTL genes were divided into four branches by phylogenetic analysis and sequence alignment, indicating the evolutionary conservation of the gene structure and its association with other plant species. qRT-PCR analysis showed that the ChSAT and ChOASTL genes were differentially expressed in different tissues under various selenium levels, suggesting their important roles in Sec synthesis. The ChSAT1;2 and ChOASTLA1;2 were silenced by the VIGS system to investigate their involvement in selenium metabolites in C. hupingshanensis. The findings contribute to understanding the gene functions of ChSATs and ChOASTLs in the selenium stress and provide a reference for further exploration of the selenium metabolic pathway in plants.

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“…DNA methylation is a heritable epigenetic mark and it can affect gene transcription and thus influence development. Genomic approaches over the last decade have revealed extensive variation in intraspecific natural DNA methylation ( Schmitz et al , 2013 ; Kawakatsu et al , 2016 ; Guo et al , 2023 ). In maize, more than 25% of cytosines in the genome are methylated ( Xu et al , 2020 ).…”

Section: Introductionmentioning

confidence: 99%

The conservation of allelic DNA methylation and its relationship with imprinting in maize

Dong,

Luo,

Yao

et al. 2023

Journal of Experimental Botany

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Genomic imprinting refers to allele-specific expression of genes depending on parental origin, and it is regulated by epigenetic modifications. Intraspecific allelic variation for imprinting has been detected; however, the intraspecific genome-wide allelic epigenetic variation in maize and its correlation with imprinting variants remain unclear. Here, three reciprocal hybrids were generated by crossing Zea mays inbred lines CAU5, B73, and Mo17 in order to examine the intraspecific conservation of the imprinted genes in the kernel. The majority of imprinted genes exhibited intraspecific conservation, and these genes also exhibited interspecific conservation (rice, sorghum, and Arabidopsis) and were enriched in some specific pathways. By comparing intraspecific allelic DNA methylation in the endosperm, we found that nearly 15% of DNA methylation existed as allelic variants. The intraspecific whole-genome correlation between DNA methylation and imprinted genes indicated that DNA methylation variants play an important role in imprinting variants. Disruption of two conserved imprinted genes using CRISPR/Cas9 editing resulted in a smaller kernel phenotype. Our results shed light on the intraspecific correlation of DNA methylation variants and variation for imprinting in maize, and show that imprinted genes play an important role in kernel development.

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Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

Cited by 11 publications

References 58 publications

Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication

Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication

Gene identification, expression analysis, and molecular docking of SAT and OASTL in the metabolic pathway of selenium in Cardamine hupingshanensis

The conservation of allelic DNA methylation and its relationship with imprinting in maize

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