Shaping inheritance: how distinct reproductive strategies influence DNA methylation memory in plants

Ibañez, Verónica Noé; Quadrana, Leandro

doi:10.1016/j.gde.2022.102018

Cited by 10 publications

(7 citation statements)

References 49 publications

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“…3f and 3i). The genome-wide reduction of CHH methylation is consistent with the hypothesis that clonal reproduction reduces CHH methylation, and the effects gradually accumulate over clonal generations 51 .…”

Section: Population Epigenomic Diversity In S Polyrhizasupporting

confidence: 84%

Population genomics and epigenomics provide insights into the evolution of facultative asexuality in plants

Xu¹,

Wang²,

Pablo³

et al. 2023

Preprint

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Many organisms, particularly plants, can reproduce both sexually and asexually but with varying frequencies. Because variations in the reproductive system profoundly affect fitness and genomic diversity, natural selection should act on changes between sexual and asexual types of propagation. However, the genomic evidence of natural selection driving switches between reproductive systems remains scarce, and the evolutionary consequences of such switches on the genomic and epigenomic diversity remain controversial. Here, by analyzing population genomes and epigenomes of Spirodela polyrhiza (L.) Schleid., a facultatively asexual angiosperm, we show that while the genomic diversity and DNA methylation levels are very low, they vary among populations. These variations are associated with both the demographic history and the frequency of sexual reproduction in each population. A genome-wide scan revealed that multiple genes involved in flowering and embryogenesis were under positive selection, consistent with the hypothesis that natural selection drove the evolution of asexuality in this plant. Together, these results provide new insights into the evolution of plant reproductive systems and suggest that natural selection can drive the evolutionary changes of asexuality, which in turn alters the levels of genomic and epigenomic diversity.

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Section: Population Epigenomic Diversity In S Polyrhizasupporting

confidence: 84%

Population genomics and epigenomics provide insights into the evolution of facultative asexuality in plants

Xu¹,

Wang²,

Pablo³

et al. 2023

Preprint

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“…As reviewed in the introduction, any deviations from the non-Mendelian inheritance of a parent-of-origin expression pattern might be the effect of epigenetic regulation. The main factors of this epigenetic regulation are the balance of gene dosage [ 28 ], small interfering RNAs [ 36 , 41 ], noncoding RNAs [ 44 , 45 ], or cis - and/or trans -regulatory elements [ 34 , 35 , 36 , 37 , 38 ]. All of them might be involved in the regulation of these epigenetic types of expression patterns, especially in polyploid species.…”

Section: Discussionmentioning

confidence: 99%

“…Such nonadditive gene expression levels associated with phenotypic heterosis in F 1 plants have already been reported and reviewed [ 29 , 30 , 31 , 32 , 33 ]. These deviations from the general role are the result of different factors, such as epigenetic regulation by transcription factors [ 34 , 35 , 36 , 37 , 38 ], the balance of gene dosage [ 39 , 40 ], small interfering RNAs (sRNA) [ 36 , 41 ], histone modifications [ 42 ], R-loop formation [ 43 ], or distally acting factors [ 31 ]. Furthermore, noncoding RNAs have been described as regulators of the development of shoots and grains in barley [ 44 ] and dominant epigenetic regulators of early meiotic stages in wheat, ensuring reproductive success [ 45 ].…”

Section: Introductionmentioning

confidence: 99%

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High- or Low-Yielding F2 Progeny of Wheat Is Result of Specific TaCKX Gene Coexpression Patterns in Association with Grain Yield in Paternal Parent

Szala,

Dmochowska-Boguta,

Bocian

et al. 2024

IJMS

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Members of the TaCKX gene family (GFM) encode oxidase/dehydrogenase cytokinin degrading enzymes (CKX), which play an important role in the homeostasis of phytohormones, affecting wheat development and productivity. Therefore, the objective of this investigation was to test how the expression patterns of the yield-related TaCKX genes and TaNAC2-5A (NAC2) measured in 7 days after pollination (DAP) spikes and the seedling roots of parents are inherited to apply this knowledge in the breeding process. The expression patterns of these genes were compared between parents and their F2 progeny in crosses of one mother with different paterns of awnless cultivars and reciprocal crosses of awned and awnless lines. We showed that most of the genes tested in the 7 DAP spikes and seedling roots of the F2 progeny showed paternal expression patterns in crosses of awnless cultivars as well as reciprocal crosses of awned and awnless lines. Consequently, the values of grain yield in the F2 progeny were similar to the pater; however, the values of seedling root mass were similar to the mother or both parents. The correlation analysis of TaCKX GFMs and NAC2 in spikes and spikes per seedling roots reveals that the genes correlate with each other specifically with the pater and the F2 progeny or the mother and the F2 progeny, which shape phenotypic traits. The numbers of spikes and semi-empty spikes are mainly correlated with the specific coexpression of the TaCKX and NAC2 genes expressed in spikes or spikes per roots of the pater and F2 progeny. Variable regression analysis of grain yield and root mass with TaCKX GFMs and NAC2 expressed in the tested tissues of five crosses revealed a significant dependency of these parameters on the mother and F2 and/or the pater and F2 progeny. We showed that the inheritance of yield-related traits depends on the specific cooperative expression of some TaCKX GFMs, in some crosses coupled with NAC2, and is strongly dependent on the genotypes used for the crosses. Indications for parental selection in the breeding of high-yielding lines are discussed.

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“…In sexual reproduction, such as seed production, various mechanisms exist to limit defective and potentially problematic epigenetic variations from one generation to the next, including resetting of DNA methylation state (Quadrana & Colot, 2016). However, clonal propagation, being asexual, lacks these reset processes and is expected to affect DNA methylation stability across the genome (Ibañez & Quadrana, 2023), leading to potential slight variations in methylation patterns.…”

Section: Methylation Variation In Cannabis Clonesmentioning

confidence: 99%

Comparative Restriction Enzyme Analysis of Methylation (CREAM) Reveals Methylome Variability Within a ClonalIn VitroCannabis Population

Boissinot,

Adamek,

Jones

et al. 2023

Preprint

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The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically consistent products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid production of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to assess a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.

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Shaping inheritance: how distinct reproductive strategies influence DNA methylation memory in plants

Cited by 10 publications

References 49 publications

Population genomics and epigenomics provide insights into the evolution of facultative asexuality in plants

Population genomics and epigenomics provide insights into the evolution of facultative asexuality in plants

High- or Low-Yielding F2 Progeny of Wheat Is Result of Specific TaCKX Gene Coexpression Patterns in Association with Grain Yield in Paternal Parent

Comparative Restriction Enzyme Analysis of Methylation (CREAM) Reveals Methylome Variability Within a ClonalIn VitroCannabis Population

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