Variation of DNA methylation and phenotypic traits following unilateral sexual polyploidization in Medicago

Euphytica ◽  
2011 ◽  
Vol 186 (3) ◽  
pp. 731-739 ◽  
Author(s):  
Riccardo Aversano ◽  
Stefano Capomaccio ◽  
Domenico Carputo ◽  
Fabio Veronesi ◽  
Daniele Rosellini
Keyword(s):  
Dna Methylation ◽  
Phenotypic Traits ◽  
Sexual Polyploidization ◽  
Unilateral Sexual Polyploidization

scholarly journals Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows

2020 ◽  
Author(s):  
Dan Sun ◽  
Thomas S. Layman ◽  
Hyeonsoo Jeong ◽  
Paramita Chatterjee ◽  
Kathleen Grogan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Chromosome Pair ◽  
Dna Methyltransferases ◽  
Model Organisms ◽  
Phenotypic Traits ◽  
Zonotrichia Albicollis ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Nucleotide Resolution

ABSTRACTDNA methylation is known to play critical roles in key biological processes. Most of our knowledge on regulatory impacts of DNA methylation has come from laboratory-bred model organisms, which may not exhibit the full extent of variation found in wild populations. Here, we investigated naturally-occurring variation in DNA methylation in a wild avian species, the white-throated sparrow (Zonotrichia albicollis). This species offers exceptional opportunities for studying the link between genetic differentiation and phenotypic traits because of a non-recombining chromosome pair linked to both plumage and behavioral phenotypes. Using novel single-nucleotide resolution methylation maps and gene expression data, we show that DNA methylation and the expression of DNA methyltransferases are significantly higher in adults than in nestlings. Genes for which DNA methylation varied between nestlings and adults were implicated in development and cell differentiation and were located throughout the genome. In contrast, differential methylation between plumage morphs was localized to the non-recombining chromosome pair. One subset of CpGs on the non-recombining chromosome was extremely hypomethylated and localized to transposable elements. Changes in methylation predicted changes in gene expression for both chromosomes. In summary, we demonstrate changes in genome-wide DNA methylation that are associated with development and with specific functional categories of genes in white-throated sparrows. Moreover, we observe substantial DNA methylation reprogramming associated with the suppression of recombination, with implications for genome integrity and gene expression divergence. These results offer an unprecedented view of ongoing epigenetic reprogramming in a wild population.

Cytological mechanism of 2n pollen formation and unilateral sexual polyploidization in Lolium

Euphytica ◽  
1989 ◽  
Vol 43 (1-2) ◽  
pp. 1-6 ◽  
Author(s):  
C. A. Sala ◽  
E. L. Camadro ◽  
M. T. Salaberry ◽  
A. O. Mendiburu
Keyword(s):  
2N Pollen ◽  
Sexual Polyploidization ◽  
Unilateral Sexual Polyploidization ◽  
Pollen Formation ◽  
Cytological Mechanism

INTERSPECIFIC HYBRIDIZATION IN POTATO BY UNILATERAL SEXUAL POLYPLOIDIZATION

2012 ◽  
pp. 107-112
Author(s):  
L. Augustin ◽  
S. Salazar ◽  
M.I. Baggio ◽  
M.F. Grando ◽  
M. Valiati ◽  
...  
Keyword(s):  
Interspecific Hybridization ◽  
Sexual Polyploidization ◽  
Unilateral Sexual Polyploidization

scholarly journals Genome-wide analysis of DNA methylation reveals selection signatures of the grass carp during domestication

2021 ◽  
Author(s):  
Ermeng Yu ◽  
Yichao Li ◽  
Bing Fu ◽  
Junming Zhang ◽  
Jun Xie ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Candidate Genes ◽  
Grass Carp ◽  
Feeding Habits ◽  
Rapid Development ◽  
Phenotypic Traits ◽  
Selection Signatures ◽  
Learning Behaviors ◽  
Differentially Methylated Genes

With the rapid development of aquaculture, many fish species are domesticated and brought into cultivation. In the process of domestication, the domesticated fish undergone intense selection pressures and develop some adaptations and phenotypic traits, namely selection signatures, such as growth and metabolism, immunity, foraging and learning behaviors. However, how this selection signatures emerges is still not clear and the knowledge of molecular epigenetic mechanisms underlying selection signatures in fish is still in its infancy. Thus, we used a farmed fish, grass carp (Ctenopharyngodon idellus), as model species to detect these selection signatures and identify the candidate differentially methylated genes that are closely associated with these selection signatures at the level of whole genome, investigating the role of DNA methylation in the emergence of selection signatures during domestication. Our results showed that domesticated grass carp demonstrated four selection signatures, including growth and metabolism, immunity, foraging and learning behaviors, and 38 candidate genes were found associated with these traits. 16 genes are significant candidate genes which play major roles in the growth and metabolism, such as IGF-1 , GK , GYS1, etc. 11 genes are related to immunity, including . The GRM1, TAS1R1 and TAS1R3 genes are essential for the adaptation of domesticated grass carp to commercial feed in artificial rearing condition. The C-FOS, POMC and CBP genes may be responsible for the acquisition of novel feeding habits and contribute to faster growth indirectly by enhancing food intake. The findings here in will provide new insights to expand our understanding about the role of epigenetic modifications in shaping physiological phenotypes in this and other teleost models, which can contribute to efficient breeding of aquaculture stocks and restocking programmes.

scholarly journals An investigation of Burkholderia cepacia complex methylomes via SMRT sequencing and mutant analysis

2021 ◽  
Author(s):  
Olga Mannweiler ◽  
Marta Pinto-Carbó ◽  
Martina Lardi ◽  
Kirsty Agnoli ◽  
Leo Eberl
Keyword(s):  
Dna Methylation ◽  
Burkholderia Cepacia ◽  
Membrane Vesicle ◽  
Restriction Enzymes ◽  
Burkholderia Cenocepacia ◽  
Burkholderia Cepacia Complex ◽  
Phenotypic Traits ◽  
Opportunistic Pathogens ◽  
Smrt Sequencing ◽  
Foreign Dna

Bacterial genomes can be methylated at particular motifs by methyltransferases (M). This DNA modification allows restriction endonucleases (R) to discriminate between self and foreign DNA. While the accepted primary function of such restriction modification (RM) systems is to degrade incoming foreign DNA, other roles of RM systems and lone R or M components have been found in genome protection, stability and the regulation of various phenotypes. The Burkholderia cepacia complex (Bcc) is a group of closely related opportunistic pathogens with biotechnological potential. Here, we constructed and analysed mutants lacking various RM components in the clinical Bcc isolate Burkholderia cenocepacia H111 and used SMRT sequencing of single mutants to assign the B. cenocepacia H111 Ms to their cognate motifs. DNA methylation is shown to affect biofilm formation, cell shape, motility, siderophore production and membrane vesicle production. Moreover, DNA methylation had a large effect on the maintenance of the Bcc virulence megaplasmid pC3. Our data also suggest that the gp51 M-encoding gene, which is essential in H111 and is located within a prophage, is required for maintaining the bacteriophage in a lysogenic state, thereby ensuring a constant, low level of phage production within the bacterial population. Importance While genome sequence determines an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, Ms modify specific nucleotide motifs to allow discrimination of ‘self’ from ‘non-self’ DNA, e.g. from bacteriophages. Restriction enzymes detect ‘non-self’ methylation patterns and cut foreign DNA. Furthermore, methylation of promoter regions can influence gene expression and hence affect various phenotypes. In this study, we determined the methylated motifs of four strains from the Burkholderia cepacia complex of opportunistic pathogens. We deleted all genes encoding the restriction and modification components in one of these strains, Burkholderia cenocepacia H111. It is shown that DNA methylation affects various phenotypic traits, the most noteworthy being lysogenicity of a bacteriophage and maintenance of a virulence megaplasmid.

Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes

2020 ◽  
Author(s):  
Kai Wang ◽  
Pingxian Wu ◽  
Dejuan Chen ◽  
Jie Zhou ◽  
Xidi Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Meat Quality ◽  
Epigenetic Mechanism ◽  
Phenotypic Traits ◽  
Muscular Tissue ◽  
Quality Traits ◽  
Mixed Effect ◽  
Cpg Sites ◽  
Meat Quality Traits ◽  
Yorkshire Pigs

Abstract Background: DNA methylation is a key epigenetic mechanism. Most of epigenetic studies of pigs to date have focused on differential methylation analysis. However, few studies have conducted association study between DNA methylation and phenotypic traits. Thus, it is critical to link DNA methylation and phenotypic traits in order to understand the molecular mechanism on epigenomes. In this study, we aimed to identified CpG sites at which DNA methylation levels are associated with meat quality traits in 140 Yorkshire pigs, including pH at 45min (pH45min), pH at 24h (pH24h), drip loss (DL), meat redness value (a*), yellowness (b*) and lightness (L*).Results: Genome-wide methylation levels were measured in muscular tissue using reduced representation bisulfite sequencing (RRBS). Associations between DNA methylation levels and meat quality traits were examined using linear mixed-effect models that were adjusted for gender, year, month and body weight. A Bonferroni-corrected P value lower than was considered statistically significant threshold. Eight CpG sites were associated with DL, including CpG sites annotated to RBM14 gene (cpg301054, cpg301055, cpg301058, cpg301059, cpg301066, cpg301072 and cpg301073) and NCAM1 gene (cpg1802985). Two CpG sites were associated with b*, including RNFT1 and MED13 (cpg2272837) and TRIM37 gene (cpg2270611). Five CpG sites were associated with L*, including GSDMA and LRRC3C gene (cpg2252750) and ENSSSCG00000043539 and IRX1 gene (cpg2820178, cpg2820179, cpg2820181 and cpg2820182). No significant associations were observed with pH45min, pH24h or a*.Conclusion: We reported associations of meat quality traits with DNA methylation and identified some candidate genes associated with these traits, such as NCAM1, MED13 and TRIM37 gene. These results provide new insight into the epigenetic molecular mechanisms of meat quality traits in pigs.

scholarly journals Novel epigenetic determinants of type 2 diabetes in Mexican-American families

2015 ◽  
Vol 24 (18) ◽  
pp. 5330-5344 ◽  
Author(s):  
Hemant Kulkarni ◽  
Mark Z. Kos ◽  
Jennifer Neary ◽  
Thomas D. Dyer ◽  
Jack W. Kent ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Dna Methylation ◽  
Mexican Americans ◽  
Mexican American ◽  
Fasting Blood Glucose ◽  
Phenotypic Traits ◽  
High Risk Population ◽  
Cpg Sites ◽  
Increased Risk

Abstract Although DNA methylation is now recognized as an important mediator of complex diseases, the extent to which the genetic basis of such diseases is accounted for by DNA methylation is unknown. In the setting of large, extended families representing a minority, high-risk population of the USA, we aimed to characterize the role of epigenome-wide DNA methylation in type 2 diabetes (T2D). Using Illumina HumanMethylation450 BeadChip arrays, we tested for association of DNA methylation at 446 356 sites with age, sex and phenotypic traits related to T2D in 850 pedigreed Mexican-American individuals. Robust statistical analyses showed that (i) 15% of the methylome is significantly heritable, with a median heritability of 0.14; (ii) DNA methylation at 14% of CpG sites is associated with nearby sequence variants; (iii) 22% and 3% of the autosomal CpG sites are associated with age and sex, respectively; (iv) 53 CpG sites were significantly associated with liability to T2D, fasting blood glucose and insulin resistance; (v) DNA methylation levels at five CpG sites, mapping to three well-characterized genes (TXNIP, ABCG1 and SAMD12) independently explained 7.8% of the heritability of T2D (vi) methylation at these five sites was unlikely to be influenced by neighboring DNA sequence variation. Our study has identified novel epigenetic indicators of T2D risk in Mexican Americans who have increased risk for this disease. These results provide new insights into potential treatment targets of T2D.

scholarly journals Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 569
Author(s):  
Luke Browne ◽  
Brandon MacDonald ◽  
Sorel Fitz-Gibbon ◽  
Jessica W. Wright ◽  
Victoria L. Sork
Keyword(s):  
Dna Methylation ◽  
Phenotypic Variation ◽  
Leaf Traits ◽  
Forest Tree ◽  
Genomic Variation ◽  
Causal Mechanism ◽  
Phenotypic Traits ◽  
Phenotypic Variance ◽  
Reduced Representation ◽  
Valley Oak

Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species.

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