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.

scholarly journals On the Use of Blood Samples for Measuring DNA Methylation in Ecological Epigenetic Studies

2020 ◽  
Vol 60 (6) ◽  
pp. 1558-1566 ◽  
Author(s):  
Arild Husby
Keyword(s):  
Dna Methylation ◽  
Phenotypic Variation ◽  
Evolutionary Biology ◽  
Phenotypic Diversity ◽  
Genomic Region ◽  
Epigenetic Mechanism ◽  
Blood Samples ◽  
Reduced Representation ◽  
Bisulfite Treatment ◽  
Methylation Patterns

Synopsis There is increasing interest in understanding the potential for epigenetic factors to contribute to phenotypic diversity in evolutionary biology. One well studied epigenetic mechanism is DNA methylation, the addition of a methyl group to cytosines, which have the potential to alter gene expression depending on the genomic region in which it takes place. Obtaining information about DNA methylation at genome-wide scale has become straightforward with the use of bisulfite treatment in combination with reduced representation or whole-genome sequencing. While it is well recognized that methylation is tissue specific, a frequent limitation for many studies is that sampling-specific tissues may require sacrificing individuals, something which is generally undesirable and sometimes impossible. Instead, information about DNA methylation patterns in the blood is frequently used as a proxy tissue. This can obviously be problematic if methylation patterns in the blood do not reflect that in the relevant tissue. Understanding how, or if, DNA methylation in blood reflect DNA methylation patterns in other tissues is therefore of utmost importance if we are to make inferences about how observed differences in methylation or temporal changes in methylation can contribute to phenotypic variation. The aim of this review is to examine what we know about the potential for using blood samples in ecological epigenetic studies. I briefly outline some methods by which we can measure DNA methylation before I examine studies that have compared DNA methylation patterns across different tissues and, finally, examine how useful blood samples may be for ecological studies of DNA methylation. Ecological epigenetic studies are in their infancy, but it is paramount for the field to move forward to have detailed information about tissue and time dependence relationships in methylation to gain insights into if blood DNA methylation patterns can be a reliable bioindicator for changes in methylation that generate phenotypic variation in ecologically important traits.

scholarly journals Epigenetics and Early Life Stress: Experimental Brood Size Affects DNA Methylation in Great Tits (Parus major)

2021 ◽  
Vol 9 ◽  
Author(s):  
Bernice Sepers ◽  
Jolijn A. M. Erven ◽  
Fleur Gawehns ◽  
Veronika N. Laine ◽  
Kees van Oers
Keyword(s):  
Dna Methylation ◽  
Life Stress ◽  
Early Life ◽  
Brood Size ◽  
Early Life Stress ◽  
Parus Major ◽  
Phenotypic Change ◽  
Phenotypic Traits ◽  
Reduced Representation ◽  
Cpg Sites

Early developmental conditions are known to have life-long effects on an individual’s behavior, physiology and fitness. In altricial birds, a majority of these conditions, such as the number of siblings and the amount of food provisioned, are controlled by the parents. This opens up the potential for parents to adjust the behavior and physiology of their offspring according to local post-natal circumstances. However, the mechanisms underlying such intergenerational regulation remain largely unknown. A mechanism often proposed to possibly explain how parental effects mediate consistent phenotypic change is DNA methylation. To investigate whether early life effects on offspring phenotypes are mediated by DNA methylation, we cross-fostered great tit (Parus major) nestlings and manipulated their brood size in a natural study population. We assessed genome-wide DNA methylation levels of CpG sites in erythrocyte DNA, using Reduced Representation Bisulfite Sequencing (RRBS). By comparing DNA methylation levels between biological siblings raised in enlarged and reduced broods and between biological siblings of control broods, we assessed which CpG sites were differentially methylated due to brood size. We found 32 differentially methylated sites (DMS) between siblings from enlarged and reduced broods, a larger number than in the comparison between siblings from control broods. A considerable number of these DMS were located in or near genes involved in development, growth, metabolism, behavior and cognition. Since the biological functions of these genes line up with previously found effects of brood size and food availability, it is likely that the nestlings in the enlarged broods suffered from nutritional stress. We therefore conclude that early life stress might directly affect epigenetic regulation of genes related to early life conditions. Future studies should link such experimentally induced DNA methylation changes to expression of phenotypic traits and assess whether these effects affect parental fitness to determine if such changes are also adaptive.

Detection of quantitative trait loci for wood strength in Cryptomeria japonica

2000 ◽  
Vol 30 (10) ◽  
pp. 1525-1533 ◽  
Author(s):  
Noritsugu Kuramoto ◽  
Teiji Kondo ◽  
Yoshitake Fujisawa ◽  
Ryogo Nakata ◽  
Eiji Hayashi ◽  
...  
Keyword(s):  
Cryptomeria Japonica ◽  
Rapd Markers ◽  
Forest Tree ◽  
Phenotypic Traits ◽  
Phenotypic Variance ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Important Indicator ◽  
Wood Strength ◽  
Map Distance

Cryptomeria japonica D. Don (sugi) is one of the most important forest tree species in Japan. The progeny of a cross between the cultivars Iwao-sugi and Boka-sugi were analyzed using RAPD markers, with the pseudo-test-cross strategy, to construct linkage maps of the parental cultivars. A total of 355 segregating loci were detected among 72 offspring: 200 and 155 markers being distributed in Iwao-sugi and Boka-sugi, respectively. In Iwao-sugi, 119 markers with confirmed map positions were assigned to 21 linkage groups covering 1756.4 cM. In Boka-sugi, 84 markers with confirmed map positions were assigned to 14 linkage groups covering 1111.9 cM. The framework map distance in Iwao-sugi and Boka-sugi provides about 62 and 40% coverage, respectively, of the total genome, estimated to be approximately 2800 cM in length. Using genetic linkage maps constructed in this study, 15 QTLs were detected that are associated with the modulus of elasticity (MOE), an important indicator of wood strength. The QTLs for MOE explained about 45% of its total phenotypic variance. Some QTLs associated with different phenotypic traits were located on the same linkage groups. Some of the QTLs for MOE measured by two different methods (the hanging method and the tapping method) were located independently on the different linkage groups.

scholarly journals Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon

2018 ◽  
Vol 285 (1883) ◽  
pp. 20180935 ◽  
Author(s):  
Shawn R. Narum ◽  
Alex Di Genova ◽  
Steven J. Micheletti ◽  
Alejandro Maass
Keyword(s):  
Life History ◽  
Association Mapping ◽  
Chinook Salmon ◽  
Phenotypic Variation ◽  
Life History Traits ◽  
Phenotypic Diversity ◽  
Genomic Variation ◽  
Phenotypic Traits ◽  
Life History Variation ◽  
Phylogenetic Lineages

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon ( Oncorhynchus tshawytscha ; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.

scholarly journals Contributions of source population and incubation temperature to phenotypic variation of hatchling Chinese skinks

2020 ◽  
Author(s):  
Hong-Liang Lu ◽  
Yan-Fu Qu ◽  
Hong Li ◽  
Xiang Ji
Keyword(s):  
Body Mass ◽  
Phenotypic Variation ◽  
Incubation Temperature ◽  
Tail Length ◽  
Population Variation ◽  
Phenotypic Traits ◽  
Source Population ◽  
Relative Importance ◽  
The Difference ◽  
Hatchling Size

Abstract Phenotypic plasticity and local adaptation are viewed as the main factors that result in between-population variation in phenotypic traits, but contributions of these factors to phenotypic variation vary between traits and between species and have only been explored in a few species of reptiles. Here, we incubated eggs of the Chinese skink (Plestiodon chinensis) from 7 geographically separated populations in Southeast China at 3 constant temperatures (24, 28, and 32 °C) to evaluate the combined effects of clutch origin, source population, and incubation temperature on hatchling traits. The relative importance of these factors varied between traits. Nearly all examined hatchling traits, including body mass, snout–vent length (SVL), tail length, head size, limb length, tympanum diameter, and locomotor speed, varied among populations and were affected by incubation temperature. Measures for hatchling size (body mass and SVL) varied considerably among clutches. Source population explained much of the variation in hatchling body mass, whereas incubation temperature explained much of the variation in other examined traits. Our results indicate that between-population variation in hatchling traits of P. chinensis likely reflects the difference in natural incubation conditions and genetic divergence.

scholarly journals Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections

2021 ◽  
Vol 9 (7) ◽  
pp. 1416
Author(s):  
Karen Leth Nielsen ◽  
Marc Stegger ◽  
Kristoffer Kiil ◽  
Berit Lilje ◽  
Karen Ejrnæs ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Genomic Variation ◽  
Whole Genome Sequencing Data ◽  
Phenotypic Traits ◽  
Recurrent Infections ◽  
Single Nucleotide ◽  
Recurrent Urinary Tract Infections ◽  
Tract Infections

Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.

scholarly journals DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing

2018 ◽  
Vol 19 (11) ◽  
pp. 3542 ◽  
Author(s):  
Ángela Prudencio ◽  
Olaf Werner ◽  
Pedro Martínez-García ◽  
Federico Dicenta ◽  
Rosa Ros ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Prunus Persica ◽  
Prolonged Exposure ◽  
Genotyping By Sequencing ◽  
Fruit Trees ◽  
Prunus Dulcis ◽  
Dormancy Release ◽  
Release Process ◽  
Cold Temperatures ◽  
Reduced Representation

DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.

scholarly journals Umbilical Cord Blood DNA Methylation in Children Who Later Develop Type 1 Diabetes

2021 ◽  
Author(s):  
Essi Laajala ◽  
Ubaid Ullah ◽  
Toni Grönroos ◽  
Omid Rasool ◽  
Viivi Halla-aho ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Type 1 Diabetes ◽  
Cord Blood ◽  
Umbilical Cord ◽  
Umbilical Cord Blood ◽  
Reduced Representation ◽  
Prediction And Prevention ◽  
Develop Type ◽  
Methylation Patterns

Distinct DNA methylation patterns have recently been observed to precede type 1 diabetes in whole blood collected from young children. Our aim was to determine, whether perinatal DNA methylation could be associated with later progression to type 1 diabetes. Reduced representation bisulfite sequencing (RRBS) analysis was performed on umbilical cord blood samples collected within the Type 1 Diabetes Prediction and Prevention (DIPP) study. Children later diagnosed with type 1 diabetes and/or testing positive for multiple islet autoantibodies (N=43) were compared to control individuals (N=79), who remained autoantibody-negative throughout the DIPP follow-up until 15 years of age. Potential confounding factors related to the pregnancy and the mother were included in the analysis. No differences in the cord blood methylation patterns were observed between these cases and controls.

scholarly journals Identification of quantitative trait loci for leaf traits in rice

Genetika ◽  
2016 ◽  
Vol 48 (2) ◽  
pp. 643-652 ◽  
Author(s):  
Baoyan Jia ◽  
Xinhua Zhao ◽  
Yang Qin ◽  
Muhammad Irfan ◽  
Tae-Heon Kim ◽  
...  
Keyword(s):  
Recombinant Inbred Lines ◽  
Leaf Traits ◽  
Rice Cultivar ◽  
Interval Mapping ◽  
Mapping Method ◽  
Japonica Rice ◽  
Phenotypic Variance ◽  
Simple Sequence ◽  
Variance Explained ◽  
Map Distance

A recombinant inbred lines (RILs) population of 90 lines were developed from a subspecies cross between an indica type cultivar, ?Cheongcheong?, and a japonica rice cultivar, ?Nagdong? was evaluated for leaf traits in 2009. A genetic linkage map consisting of 154 simple sequence repeat (SSR) markers was constructed, covering 1973.6 cM of 12 chromosomes with an average map distance of 13.9 cM between markers. By composite interval mapping method a total of 19 QTLs were identified for the leaf traits on 5 chromosomes (Chr.1, Chr.3, Chr.6, Chr.8 and Chr.11). The percentage of phenotypic variance explained by each QTL varied from 8.1% to 29.4%. Five pleiotropic effects loci were identified on chromosomes 1,6.

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