scholarly journals Genetic and epigenetic signatures associated with the rapid radiation of Aquilegia species

2019 ◽  
Author(s):  
Tianyuan Lu ◽  
Ming-Rui Li ◽  
Ning Ding ◽  
Zhen-Hui Wang ◽  
Li-Zhen Lan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Adaptive Radiation ◽  
North American ◽  
Model System ◽  
Epigenetic Factors ◽  
Epigenetic Variability ◽  
Species Diversification ◽  
Genome Wide ◽  
Cell Reproduction ◽  
Epigenetic Signatures

AbstractElucidating how the diverse evolutionary mechanisms interact to determine species diversification is crucial to understanding the evolution and persistence of biodiversity. The genus Aquilegia (columbine) is a model system to identify genetic and epigenetic signatures underpinning the rapid adaptive radiation. In this study, we surveyed the genomes and DNA methylomes of ten worldwide Aquilegia species to investigate whether specific genomic architectures were associated with rapid species diversification in the Asian, European and North American lineages. The resulting phylogenies and population structure inferences revealed clearly high genetic and DNA methylomic divergence among the three lineages. Genome-wide scanning demonstrated significantly higher positive and purifying selection pressures among the Asian species compared to the European and North American lineages. More importantly, candidate genes identified at the genetic and epigenetic levels are functionally related to diverse adaptation-related traits, such as stress tolerance, photosynthesis and cell reproduction. While a considerable proportion of the candidate genes share hotspots of intra- and inter-lineage divergence, genetic and epigenetic factors were found to act on complementary biological pathways. By assessing the interaction between genetic variations and epigenetic variability, we found that epigenetic variability is a partially independent factor that intertwines with genetic mechanism to facilitate the diversification of the Aquilegia species. Taken together, these findings suggest that specific genetic architectures have been involved in vital biological pathways in response to diverse environmental conditions and epigenetic modifications may play a complementary role in the process of adaptive speciation. Our study provides an exploratory overview of how the established genetic and epigenetic signatures are associated with the rapid species diversification of Aquilegia species.Author SummaryDisentangling the genetic and epigenetic bases underpinning species diversification is crucial to understanding the evolution and persistence of biodiversity. The columbine (genus Aquilegia) is a model system to address biological mechanisms associated with rapid adaptive radiation. We surveyed the genomes and DNA methylomes of ten worldwide columbine species to investigate whether specific genetic and epigenetic architectures were involved in the diversification of Asian, European and North American columbine species. We pinpointed candidate genes featuring rapid adaptive radiation identified at either the genetic or the epigenetic levels. These candidate genes are functionally associated with diverse adaptation-related traits such as cell reproduction, plant growth, and stress tolerance. Such genetic and epigenetic signatures have potential contributed adaptabilities to the columbine species to cope with diverse environmental conditions. In addition, we also showed that epigenetic modifications could act as a complementary factor that intertwined with genetic mechanism to facilitate the diversification of the columbine species. In all, our study provides a genome-wide view of how the genetic and epigenetic factors are associated with the rapid species diversification of the columbine species.

Epigenetic modifications in anorexia nervosa patients and remitters compared to healthy control women

2016 ◽  
Vol 33 (S1) ◽  
pp. S30-S31 ◽  
Author(s):  
N. Ramoz ◽  
J. Clarke ◽  
P. Gorwood
Keyword(s):  
Anorexia Nervosa ◽  
Candidate Genes ◽  
Major Gene ◽  
Small Samples ◽  
Genome Wide ◽  
Limited Effectiveness ◽  
Healthy Control ◽  
High Heritability ◽  
Competing Interest ◽  
Epigenetic Signatures

IntroductionAnorexia nervosa (AN) is the most severe in terms of morbidity psychiatric illness with the highest mortality rate increased by 23 fold. Treatments are limited effectiveness. AN has a strong genetic component with heritability at 70% but despite ∼ 200 studies no major gene was identified. Epigenetics, such as DNA methylation, is another component of heritability that could explain the high heritability. Methylation is poorly studied in AN from small samples, and is focused on few candidate genes among publications. Under publication, a first genome-wide methylation study investigated 10 restrictive type AN patients, 19 binging/purging type of AN patients and 15 normal eaters using DNAs from whole blood (Booij, 2015). Of the 480K CpG sites that can be methylated of Infinium Human Methylation450 BeadChip Kit, authors focused on 24,000 sites located close to genes and they identified candidate genes with a different profile of methylation between AN and controls.ObjectivesOur work is to replicate the results of Booji and also to investigate the AN remitters.AimsOur goal is to identify epigenetic signatures of the AN disorder and the prognostic of remission.MethodsTwenty-four AN patients, 24 AN remitters will be compared to 48 healthy control women for methylation using the Infinium Human Methylation450.ResultsAs Booji et al., we will compare methylation for 24,000 sites located close to genes for 24 AN, 24 remitters and 48 controls.ConclusionsWe expected to replicate the published results of Booji and to identify genes with a methylation signature specific of the AN remission.Disclosure of interestThe authors have not supplied their declaration of competing interest.

scholarly journals Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10993
Author(s):  
Melissa R. Price ◽  
Michael G. Hadfield ◽  
Ingrid S.S. Knapp ◽  
Robert J. Toonen ◽  
Zac H. Forsman
Keyword(s):  
Adaptive Radiation ◽  
Environmental Gradients ◽  
Model System ◽  
Species Level ◽  
Conservation Strategies ◽  
Evolutionary Relationships ◽  
Evolutionary Potential ◽  
Snp Data ◽  
Genome Wide ◽  
In The Wild

Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of capacity to adapt to rapidly changing environmental conditions.

scholarly journals The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

2017 ◽  
Vol 7 (7) ◽  
pp. 2391-2403 ◽  
Author(s):  
Amanda S Lobell ◽  
Rachel R Kaspari ◽  
Yazmin L Serrano Negron ◽  
Susan T Harbison
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Natural Populations ◽  
Direct Role ◽  
Genome Wide ◽  
A Genome ◽  
Fitness Trait ◽  
Sleep Parameters ◽  
Activity Behavior ◽  
Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

scholarly journals Distinct epigenetic signatures between adult-onset and late-onset depression

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hirotaka Yamagata ◽  
Hiroyuki Ogihara ◽  
Koji Matsuo ◽  
Shusaku Uchida ◽  
Ayumi Kobayashi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Clinical Symptoms ◽  
Late Onset ◽  
Adult Onset ◽  
Blood Biomarkers ◽  
Major Depressive ◽  
Genome Wide ◽  
Healthy Control ◽  
Epigenetic Signatures

AbstractThe heterogeneity of major depressive disorder (MDD) is attributed to the fact that diagnostic criteria (e.g., DSM-5) are only based on clinical symptoms. The discovery of blood biomarkers has the potential to change the diagnosis of MDD. The purpose of this study was to identify blood biomarkers of DNA methylation by strategically subtyping patients with MDD by onset age. We analyzed genome-wide DNA methylation of patients with adult-onset depression (AOD; age ≥ 50 years, age at depression onset < 50 years; N = 10) and late-onset depression (LOD; age ≥ 50 years, age at depression onset ≥ 50 years; N = 25) in comparison to that of 30 healthy subjects. The methylation profile of the AOD group was not only different from that of the LOD group but also more homogenous. Six identified methylation CpG sites were validated by pyrosequencing and amplicon bisulfite sequencing as potential markers for AOD in a second set of independent patients with AOD and healthy control subjects (N = 11). The combination of three specific methylation markers achieved the highest accuracy (sensitivity, 64%; specificity, 91%; accuracy, 77%). Taken together, our findings suggest that DNA methylation markers are more suitable for AOD than for LOD patients.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

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