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Population Genetics
Genomic prediction with parallel computing for slaughter traits in Chinese Simmental beef cattle using high-density genotypes
Jul 20, 2017   PloS One
Guo P, Zhu B, Xu L, Niu H, Wang Z, Guan L, Liang Y, Ni H, Guo Y, Chen Y, Zhang L, Gao X, Gao H, Li J
Genomic prediction with parallel computing for slaughter traits in Chinese Simmental beef cattle using high-density genotypes
Jul 20, 2017
PloS One
Genomic selection has been widely used for complex quantitative trait in farm animals. Estimations of breeding values for slaughter traits are most important to beef cattle industry, and it is worthwhile to investigate prediction accuracies of genomic selection for these traits. In this study, we assessed genomic predictive abilities for average daily gain weight (ADG), live weight (LW), carcass weight (CW), dressing percentage (DP), lean meat percentage (LMP) and retail meat weight (RMW) using Illumina Bovine 770K SNP Beadchip in Chinese Simmental cattle. To evaluate the abilities of prediction, marker effects were estimated using genomic BLUP (GBLUP) and three parallel Bayesian models, including multiple chains parallel BayesA, BayesB and BayesCπ (PBayesA, PBayesB and PBayesCπ). Training set and validation set were divided by random allocation, and the predictive accuracies were evaluated using 5-fold cross validations. We found the accuracies of genomic predictions ranged from 0.195±0.084 (GBLUP for LMP) to 0.424±0.147 (PBayesB for CW). The average accuracies across traits were 0.327±0.085 (GBLUP), 0.335±0.063 (PBayesA), 0.347±0.093 (PBayesB) and 0.334±0.077 (PBayesCπ), respectively. Notably, parallel Bayesian models were more accurate than GBLUP across six traits. Our study suggested that genomic selections with multiple chains parallel Bayesian models are feasible for slaughter traits in Chinese Simmental cattle. The estimations of direct genomic breeding values using parallel Bayesian methods can offer important insights into improving prediction accuracy at young ages and may also help to identify superior candidates in breeding programs.
From positive psychology to psychopathology: the continuum of attention-deficit hyperactivity disorder
Jul 21, 2017   Journal Of Child Psychology And Psychiatry, And Allied Disciplines
Greven CU, Buitelaar JK, Salum GA
From positive psychology to psychopathology: the continuum of attention-deficit hyperactivity disorder
Jul 21, 2017
Journal Of Child Psychology And Psychiatry, And Allied Disciplines
Integration of positive psychology into clinical research and treatment has been slow. This integration can be facilitated by the conceptualisation of mental disorders as the high, symptomatic extreme of continuous normal variation. This assumes that there is also a low, positive extreme, which is, however, unchartered territory. This study aims to examine how well current measures capture the low extreme of mental disorder continua, using attention-deficit hyperactivity disorder (ADHD) as an example. The ability of three validated scales to capture ADHD as a continuous trait was examined using Item Response Theory in a sample of 9,882 adolescents from the UK population-representative Twins Early Development Study. These scales were: the Strengths and Weakness of ADHD Symptoms and Normal behaviour scale (SWAN), Strength and Difficulties Questionnaire (SDQ - hyperactivity subscale), and Conners' Parent Rating Scale (Conners). Only the SWAN reliably differentiated interindividual differences between participants lying at any level of the continuous ADHD latent trait, including the extreme low, positive end (z-scores from -3 to +3). The SDQ showed low reliability across the ADHD latent trait. In contrast, the Conners performed best at differentiating individuals scoring at or above the mean to the high symptomatic range (z-scores from 0 to +3). The SWAN was the only measure to provide indicators of 'positive mental health', endorsed in the presence of particularly good attentive abilities. Scales such as the SWAN that reliably capture ADHD as a continuous trait, including the positive end, are important for not missing meaningful variation in population-based studies. Indicators of positive mental health may be helpful in clinical practice, as positive attributes have been shown to directly influence as well as buffer negative effects of psychiatric symptoms. © 2017 Association for Child and Adolescent Mental Health.
Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances
Jul 24, 2017   Animal Genetics
Li X, Yang S, Dong K, Tang Z, Li K, Fan B, Wang Z, Liu B
Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances
Jul 24, 2017
Animal Genetics
Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5-56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study. © 2017 Stichting International Foundation for Animal Genetics.
Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements
Jul 24, 2017   American Journal Of Human Genetics
Zepeda-Mendoza CJ, Ibn-Salem J, Kammin T, Harris DJ, Rita D,   . . . . . .   , Ordulu Z, Talkowski ME, Andrade-Navarro MA, Robinson PN, Morton CC
Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements
Jul 24, 2017
American Journal Of Human Genetics
Interpretation of variants of uncertain significance, especially chromosomal rearrangements in non-coding regions of the human genome, remains one of the biggest challenges in modern molecular diagnosis. To improve our understanding and interpretation of such variants, we used high-resolution three-dimensional chromosomal structural data and transcriptional regulatory information to predict position effects and their association with pathogenic phenotypes in 17 subjects with apparently balanced chromosomal abnormalities. We found that the rearrangements predict disruption of long-range chromatin interactions between several enhancers and genes whose annotated clinical features are strongly associated with the subjects' phenotypes. We confirm gene-expression changes for a couple of candidate genes to exemplify the utility of our analysis of position effect. These results highlight the important interplay between chromosomal structure and disease and demonstrate the need to utilize chromatin conformational data for the prediction of position effects in the clinical interpretation of non-coding chromosomal rearrangements. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel
Jul 24, 2017   Animal : An International Journal Of Animal Bioscience
Pérez-Pardal L, Chen S, Costa V, Liu X, Carvalheira J, Beja-Pereira A
Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel
Jul 24, 2017
Animal : An International Journal Of Animal Bioscience
Buffalo (Bubalus bubalis) is an important livestock species in many tropical and subtropical regions. In recent decades, the interest in buffalo's milk have expanded and intensive buffalo farms start to emerge. However, breeding programs and population genetics information for this species is scarce or inexistent. The present study aims to test the suitability of the commercial high-density single nucleotide polymorphisms (SNP) genotyping panel, the Illumina BovineHD BeadChip, to estimate population genetics parameters, pedigree control and identification of common variants in major production candidate genes. From a total of 777 962 SNPs included in the panel, 20 479 were polymorphic in water buffalo at a call rate of 86% and an average expected heterozygosity (HE) of 0.306. From these, 357 were mapped within or around the flanking regions of several major candidate genes. A principal components analysis identified three different clusters, each representing pure swamp buffalo type, pure river buffalo type and admixed river buffalo. The hybrids between swamp and river buffalo were clearly identified as an intermediary cluster. The suitability of these SNPs data set for parentage and identity testing demonstrated that the combination of just 30 to 50 SNPs were enough to attain high probabilities of parentage exclusion (0.9999) in both types and identity (2.3×10-5 and 2.0×10-7) for river and swamp buffalo, respectively. Our analysis confirms the suitability of the BovineHD BeadChip to assess population structure, hybridization and identity of the water buffalo populations.
Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells
Jul 23, 2017   Functional & Integrative Genomics
Xie FF, Deng FY, Wu LF, Mo XB, Zhu H,   . . . . . .   , He P, Bing PF, Lu X, Zhang YH, Lei SF
Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells
Jul 23, 2017
Functional & Integrative Genomics
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P  0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.
Pathogen richness and abundance predict patterns of adaptive MHC variation in insular amphibians
Jul 22, 2017   Molecular Ecology
Wang S, Liu C, Wilson AB, Zhao N, Li X, Zhu W, Gao X, Liu X, Li Y
Pathogen richness and abundance predict patterns of adaptive MHC variation in insular amphibians
Jul 22, 2017
Molecular Ecology
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process, and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and 3 nearby mainland sites. We found a high proportion of private MHC alleles in mainland and insular populations, corresponding to 32 distinct functional supertypes, and strong positive selection on MHC antigen-binding sites in all populations. Viral pathogen diversity and abundance was reduced at island sites relative to the mainland, and islands housed distinctive viral communities. Standardized MHC diversity at island sites exceeded that found at neutral microsatellites, and the representation of key functional supertypes was positively correlated with the abundance of specific viruses in the environment (Frog virus 3 and Ambystoma tigrinum virus). These results indicate that pathogen-driven diversifying selection can play an important role in maintaining functionally-important MHC variation following island isolation, highlighting the importance of considering functionally important genetic variation and host-pathogen associations in conservation planning and management. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.)
Jul 22, 2017   Molecular Genetics And Genomics : MGG
Liu X, Teng Z, Wang J, Wu T, Zhang Z, Deng X, Fang X, Tan Z, Ali I, Liu D, Zhang J, Liu D, Liu F, Zhang Z
Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.)
Jul 22, 2017
Molecular Genetics And Genomics : MGG
Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.
Population genetic analysis of a 21-plex DIP panel in seven Chinese ethnic populations
Jul 22, 2017   International Journal Of Legal Medicine
Jiang Y, He W, Wang H, Chen D, Bai X, Li J, Liang W, Zhang L
Population genetic analysis of a 21-plex DIP panel in seven Chinese ethnic populations
Jul 22, 2017
International Journal Of Legal Medicine
A 21-plex DIP (deletion and insertion polymorphism) panel has a good performance in analyzing biogeographic ancestry in three main global population groups (European, African, and Asian). This panel was used to investigate 450 unrelated individuals in seven Chinese ethnic groups (Han, Dong, Miao, Zhuang, Uyghur, Tibetan, and Mongolian). Allele frequencies were calculated. Mho (mean value of observed heterozygosity) ranged from 0.3019 to 0.4367, MHe (mean value of expected heterozygosity) ranged from 0.31175 to 0.38341, CMP (combined matching probability) ranged from 3.5834E-07 to 2.5985E-06, CDP (combined power of discrimination) ranged from 0.99999740150 to 0.99999964166, and CPE (combined power of paternity exclusion) ranged from 0.85884504 to 0.97949131. The results suggested the potential of the panel for individual identification and paternity testing in Chinese populations. Pairwise genetic differences Fst values (-0.00091 to 0.05873) and the analysis by STRUCTURE indicated that Chinese populations have good internal consistency.
A drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure
Jul 21, 2017   PLoS Genetics
Zhou S, Luoma SE, St Armour GE, Thakkar E, Mackay TFC, Anholt RRH
A drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure
Jul 21, 2017
PLoS Genetics
The genetic factors that give rise to variation in susceptibility to environmental toxins remain largely unexplored. Studies on genetic variation in susceptibility to environmental toxins are challenging in human populations, due to the variety of clinical symptoms and difficulty in determining which symptoms causally result from toxic exposure; uncontrolled environments, often with exposure to multiple toxicants; and difficulty in relating phenotypic effect size to toxic dose, especially when symptoms become manifest with a substantial time lag. Drosophila melanogaster is a powerful model that enables genome-wide studies for the identification of allelic variants that contribute to variation in susceptibility to environmental toxins, since the genetic background, environmental rearing conditions and toxic exposure can be precisely controlled. Here, we used extreme QTL mapping in an outbred population derived from the D. melanogaster Genetic Reference Panel to identify alleles associated with resistance to lead and/or cadmium, two ubiquitous environmental toxins that present serious health risks. We identified single nucleotide polymorphisms (SNPs) associated with variation in resistance to both heavy metals as well as SNPs associated with resistance specific to each of them. The effects of these SNPs were largely sex-specific. We applied mutational and RNAi analyses to 33 candidate genes and functionally validated 28 of them. We constructed networks of candidate genes as blueprints for orthologous networks of human genes. The latter not only provided functional contexts for known human targets of heavy metal toxicity, but also implicated novel candidate susceptibility genes. These studies validate Drosophila as a translational toxicogenomics gene discovery system.
The role of a FADS1 polymorphism in the association of fatty acid blood levels, BMI and blood pressure in young children-Analyses based on path models
Jul 21, 2017   PloS One
Wolters M, Dering C, Siani A, Russo P, Kaprio J,   . . . . . .   , Pitsiladis Y, Galli C, Foraita R, Börnhorst C, IDEFICS and I. Family consortia
The role of a FADS1 polymorphism in the association of fatty acid blood levels, BMI and blood pressure in young children-Analyses based on path models
Jul 21, 2017
PloS One
The recent obesity epidemic in children also showed an increase in the prevalence of hypertension. As blood pressure (BP) is associated with (long-chain) polyunsaturated fatty acids (LC PUFA), genetic variation in desaturase enzymes being involved in the synthesis of LC PUFA may be associated with BP. This study aimed to investigate the direct effects (independent of mediating variables) and indirect effects (mediated through intermediate variables) of a common variant in the FADS1 gene, rs174546, known to affect delta-5 desaturase (D5D) activity on PUFA level, body mass index (BMI) and BP. A subsample of the IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) baseline survey including 520 children aged 2 to
Genome-scale data reveals that endemic Poecilia populations from small sulfidic springs display no evidence of inbreeding
Jul 21, 2017   Molecular Ecology
Brown AP, Greenway R, Morgan S, Quackenbush CR, Giordani L, Arias-Rodriguez L, Tobler M, Kelley JL
Genome-scale data reveals that endemic Poecilia populations from small sulfidic springs display no evidence of inbreeding
Jul 21, 2017
Molecular Ecology
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulfide rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of P. sulphuraria and one population of P. thermalis. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. The genetic data was also used to infer the demographic history of these populations to obtain estimates for effective population sizes and migration rates. Effective population sizes were large given the small habitats of these populations. Our results imply that these three endemic extremophile populations should each be considered separately for conservation purposes. Additionally, this study suggests that populations in naturally small habitats may generally have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated. We caution, however, that the inferred lack of inbreeding and the large effective population sizes could potentially be a result of colonization by genetically diverse ancestors. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Molecular Mapping of Flowering Time Major Genes and QTLs in Chickpea (Cicer arietinum L.)
Jul 21, 2017   Frontiers In Plant Science
Mallikarjuna BP, Samineni S, Thudi M, Sajja SB, Khan AW, Patil A, Viswanatha KP, Varshney RK, Gaur PM
Molecular Mapping of Flowering Time Major Genes and QTLs in Chickpea (Cicer arietinum L.)
Jul 21, 2017
Frontiers In Plant Science
Flowering time is an important trait for adaptation and productivity of chickpea in the arid and the semi-arid environments. This study was conducted for molecular mapping of genes/quantitative trait loci (QTLs) controlling flowering time in chickpea using F2 populations derived from four crosses (ICCV 96029 × CDC Frontier, ICC 5810 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier). Genetic studies revealed monogenic control of flowering time in the crosses ICCV 96029 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier, while digenic control with complementary gene action in ICC 5810 × CDC Frontier. The intraspecific genetic maps developed from these crosses consisted 75, 75, 68 and 67 markers spanning 248.8 cM, 331.4 cM, 311.1 cM and 385.1 cM, respectively. A consensus map spanning 363.8 cM with 109 loci was constructed by integrating four genetic maps. Major QTLs corresponding to flowering time genes efl-1 from ICCV 96029, efl-3 from BGD 132 and efl-4 from ICC 16641 were mapped on CaLG04, CaLG08 and CaLG06, respectively. The QTLs and linked markers identified in this study can be used in marker-assisted breeding for developing early maturing chickpea.
Time-averaged disease activity fits better joint destruction in rheumatoid arthritis
Jul 20, 2017   Scientific Reports
Tsuji H, Yano K, Furu M, Yamakawa N, Ikari K,   . . . . . .   , Matsuda F, Allaart CF, Yamanaka H, Mimori T, Terao C
Time-averaged disease activity fits better joint destruction in rheumatoid arthritis
Jul 20, 2017
Scientific Reports
Disease activity of rheumatoid arthritis (RA), evaluated as Disease Activity Score (DAS), is associated with joint destruction. Since joint destruction reflects the history of disease activities, we hypothesized that time-averaged disease activity would better correlate with joint destruction than one-time disease activity. We recruited RA patients in IORRA (n = 557) and KURAMA (n = 204) cohorts, and calculated time-averaged DAS28 to model a modified Sharp/van der Heijde score (SHS). We evaluated the fitting of the model using time-averaged DAS28 among 1000 models in which we randomly picked up one-time DAS28. We also used clinical disease activity index (CDAI) or data in the BeSt study (European population). After conditioning on autoantibody and disease duration, time-averaged DAS28 showed significant improvement of model fitting compared with one-time DAS28 in both cohorts (p = 0.001 and 0.034, respectively). Time-averaged CDAI also showed a better fit. Integration of multiple DAS fit SHS better in the BeSt study. A good fit of time-averaged DAS could be observed using five to six time points of DAS. In conclusion, time-averaged disease activity fits the joint destruction model better than one-time disease activity. Usage of time-averaged disease activity as a covariate would increase the power of studies to identify novel correlates of joint destruction.
A Gene-Based Analysis of Acoustic Startle Latency
Jul 21, 2017   Frontiers In Psychiatry
Smith AK, Jovanovic T, Kilaru V, Lori A, Gensler L, Lee SS, Norrholm SD, Massa N, Cuthbert B, Bradley B, Ressler KJ, Duncan E
A Gene-Based Analysis of Acoustic Startle Latency
Jul 21, 2017
Frontiers In Psychiatry
Latency of the acoustic startle response is the time required from the presentation of startling auditory stimulus until the startle response is elicited and provides an index of neural processing speed. Latency is prolonged in subjects with schizophrenia compared to controls in some but not all studies and is 68-90% heritable in baseline startle trials. In order to determine the genetic association with latency as a potential inroad into genetically based vulnerability to psychosis, we conducted a gene-based study of latency followed by an independent replication study of significant gene findings with a single-nucleotide polymorphism (SNP)-based analysis of schizophrenia and control subjects. 313 subjects from an urban population of low socioeconomic status with mixed psychiatric diagnoses were included in the gene-based study. Startle testing was conducted using a Biopac M150 system according to our published methods. Genotyping was performed with the Omni-Quad 1M or the Omni Express BeadChip. The replication study was conducted on 154 schizophrenia subjects and 123 psychiatric controls. Genetic analyses were conducted with Illumina Human Omni1-Quad and OmniExpress BeadChips. Twenty-nine SNPs were selected from four genes that were significant in the gene-based analysis and also associated with startle and/or schizophrenia in the literature. Linear regressions on latency were conducted, controlling for age, race, and diagnosis as a dichotomous variable. In the gene-based study, 2,870 genes demonstrated the evidence of association after correction for multiple comparisons (false discovery rate 
Evidence of selection on splicing-associated loci in human populations and relevance to disease loci mapping
Jul 21, 2017   Scientific Reports
Gamazon ER, Konkashbaev A, Derks EM, Cox NJ, Lee Y
Evidence of selection on splicing-associated loci in human populations and relevance to disease loci mapping
Jul 21, 2017
Scientific Reports
We performed a whole-genome scan of genetic variants in splicing regulatory elements (SREs) and evaluated the extent to which natural selection has shaped extant patterns of variation in SREs. We investigated the degree of differentiation of single nucleotide polymorphisms (SNPs) in SREs among human populations and applied long-range haplotype- and multilocus allelic differentiation-based methods to detect selection signatures. We describe an approach, sampling a large number of loci across the genome from functional classes and using the consensus from multiple tests, for identifying candidates for selection signals. SRE SNPs in various SNP functional classes show different patterns of population differentiation compared with their non-SRE counterparts. Intronic regions display a greater enrichment for extreme population differentiation among the potentially tissue-dependent transcript ratio quantitative trait loci (trQTLs) than SRE SNPs in general and includ outlier trQTLs for cross-population composite likelihood ratio, suggesting that incorporation of context annotation for regulatory variation may lead to improved detection of signature of selection on these loci. The proportion of extremely rare SNPs disrupting SREs is significantly higher in European than in African samples. The approach developed here will be broadly useful for studies of function and disease-associated variation in the human genome.
Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
Jul 21, 2017   Scientific Reports
Sorkheh K, Dehkordi MK, Ercisli S, Hegedus A, Halász J
Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
Jul 21, 2017
Scientific Reports
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
Genetic differentiation of the Schizothorax species complex (Cyprinidae) in the Nujiang River (upper Salween)
Jul 21, 2017   Scientific Reports
Chen W, Yue X, He S
Genetic differentiation of the Schizothorax species complex (Cyprinidae) in the Nujiang River (upper Salween)
Jul 21, 2017
Scientific Reports
Phenotypically diverse species from recently evolved groups always share allele/haplotype due to insufficient differentiation in the early process. In this study, we performed population genetics analyses using sequences from the mitochondrial cytochrome b gene, and two nuclear genes to investigate the genetic differentiation of the closely related Schizothorax species complex, comprising a group of alpine fish living in the Nujiang River. The results from both mtDNA and nDNA markers revealed relatively low but pronounced genetic differentiation among the three Schizothorax species, i.e., Schizothorax gongshanensis, S. lissolabiatus, and S. nukiangensis. However, haplotype sharing was frequently occurred among the three species. Divergence time estimation suggested the last glaciation on the Tibetan Plateau (0.075-0.01 Ma) might drive the divergence of the species complex. Gene flow might contribute to the haplotype sharing between S. gongshanensis and S. lissolabiatus, and between S. gongshanensis and S. nukiangensis, whereas retention of ancestral polymorphisms seemed to be a better explanation of the haplotype sharing between S. lissolabiatus and S. nukiangensis. In addition, S. lissolabiatus populations should obtain more protection in the future because of their low genetic diversity and habitat fragmentation. In summary, our study assesses genetic differentiation among the three closely related Schizothorax species and explores the possible driving forces for their differentiation.
Evaluation of ATM heterozygous mutations underlying individual differences in radiosensitivity using genome editing in human cultured cells
Jul 21, 2017   Scientific Reports
Royba E, Miyamoto T, Natsuko Akutsu S, Hosoba K, Tauchi H, Kudo Y, Tashiro S, Yamamoto T, Matsuura S
Evaluation of ATM heterozygous mutations underlying individual differences in radiosensitivity using genome editing in human cultured cells
Jul 21, 2017
Scientific Reports
Ionizing radiation (IR) induces DNA double-strand breaks (DSBs), which are an initial step towards chromosomal aberrations and cell death. It has been suggested that there are individual differences in radiosensitivity within human populations, and that the variations in DNA repair genes might determine this heterogeneity. However, it is difficult to quantify the effect of genetic variants on the individual differences in radiosensitivity, since confounding factors such as smoking and the diverse genetic backgrounds within human populations affect radiosensitivity. To precisely quantify the effect of a genetic variation on radiosensitivity, we here used the CRISPR-ObLiGaRe (Obligate Ligation-Gated Recombination) method combined with the CRISPR/Cas9 system and a nonhomologous end joining (NHEJ)-mediated knock-in technique in human cultured cells with a uniform genetic background. We generated ATM heterozygous knock-out (ATM +/-) cell clones as a carrier model of a radiation-hypersensitive autosomal-recessive disorder, ataxia-telangiectasia (A-T). Cytokinesis-blocked micronucleus assay and chromosome aberration assay showed that the radiosensitivity of ATM +/- cell clones was significantly higher than that of ATM +/+ cells, suggesting that ATM gene variants are indeed involved in determining individual radiosensitivity. Importantly, the differences in radiosensitivity among the same genotype clones were small, unlike the individual differences in fibroblasts derived from A-T-affected family members.
Genome-wide association studies and meta-analysis reveal novel quantitative trait loci and pleiotropic loci for swine head-related traits
Jul 20, 2017   Journal Of Animal Science
Chen H, Huang T, Zhang Z, Yang B, Jiang C,   . . . . . .   , Zhang M, Chen C, Ren J, Ai H, Huang L
Genome-wide association studies and meta-analysis reveal novel quantitative trait loci and pleiotropic loci for swine head-related traits
Jul 20, 2017
Journal Of Animal Science
The pig is an important domestic animal that provides a larger amount of meat and serves as a biomedical animal model for human. Head and facial features are closely linked to identity recognition in mammal communication. To uncover the genetic architecture of swine head and facial features, we constructed 5 experimental pig populations and accurately measured 10 traits related to head and facial features, for which genome-wide association studies and meta-analysis were later carried out. As a result, we identified a total of 24 loci harboring 437 SNP on 8 swine chromosomes (SSC) that surpassed suggestively significant levels, of which 17 loci on 6 chromosomes exceeded the 5% genome-wide significance thresholds. To our knowledge, this is the first report of QTL for the distance from the low corner of the eye to the snout end (DES) and to the mouth corner (DEM), the size of extra mouth cleft (EMC), lip thickness, head length, and tongue weight and length in pigs. Notably, 3 pleiotropic loci were detected, including the loci at 298.1 Mb on SSC1 for head length and DES, at about 80.0 Mb on SSC4 for head weight, tongue weight and length, and at 34.8 Mb on SSC7 for head weight, EMC, and lip thickness. Several positional candidate genes at the identified loci might play roles in craniofacial development or have been implicated in syndromes affecting human head and facial features, including glutamate metabotropic receptor 4 (), high mobility group AT-hook 1 (), high mobility group AT-hook 2 (), serum/glucocorticoid regulated kinase family member 3 (), pleiomorphic adenoma gene 1 (), proto-oncogene serine/threonine-protein kinase mos () and DENN (differentially expressed in normal and neoplastic cells) domain containing 1A (). These findings will contribute to further detection of the causal mutations underlying these QTL for head and facial features in pigs and provide insights into the genetic basis of head and facial characteristics in human or other mammals.
Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in Sinonovacula constricta
Jul 20, 2017   Marine Biotechnology (New York, N.Y.)
Niu D, Du Y, Wang Z, Xie S, Nguyen H, Dong Z, Shen H, Li J
Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in Sinonovacula constricta
Jul 20, 2017
Marine Biotechnology (New York, N.Y.)
The razor clam (Sinonovacula constricta) is an important aquaculture species, for which a high-density genetic linkage map would play an important role in marker-assisted selection (MAS). In this study, we constructed a high-density genetic map and detected quantitative trait loci (QTLs) for Sinonovacula constricta with an F1 cross population by using the specific locus amplified fragment sequencing (SLAF-seq) method. A total of 315,553 SLAF markers out of 467.71 Mreads were developed. The final linkage map was composed of 7516 SLAFs (156.60-fold in the parents and 20.80-fold in each F1 population on average). The total distance of the linkage map was 2383.85 cM, covering 19 linkage groups with an average inter-marker distance of 0.32 cM. The proportion of gaps less than 5.0 cM was on average 96.90%. A total of 16 suggestive QTLs for five growth-related traits (five QTLs for shell height, six QTLs for shell length, three QTLs for shell width, one QTL for total body weight, and one QTL for soft body weight) were identified. These QTLs were distributed on five linkage groups, and the regions showed overlapping on LG9 and LG13. In conclusion, the high-density genetic map and QTLs for S. constricta provide a valuable genetic resource and a basis for MAS.
The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)
Jul 20, 2017   Ecology And Evolution
Martin MD, Olsen MT, Samaniego JA, Zimmer EA, Gilbert MTP
The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)
Jul 20, 2017
Ecology And Evolution
Common ragweed (Ambrosia artemisiifolia L.) is an invasive, wind-pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, and Australia. Phenotypic divergence between European and native-range populations has been described as rapid evolution. However, a recent study demonstrated major human-mediated shifts in ragweed genetic structure before introduction to Europe and suggested that native-range genetic structure and local adaptation might fully explain accelerated growth and other invasive characteristics of introduced populations. Genomic differentiation that potentially influenced this structure has not yet been investigated, and it remains unclear whether substantial admixture during historical disturbance of the native range contributed to the development of invasiveness in introduced European ragweed populations. To investigate fine-scale population genetic structure across the species' native range, we characterized diallelic SNP loci via a reduced-representation genotyping-by-sequencing (GBS) approach. We corroborate phylogeographic domains previously discovered using traditional sequencing methods, while demonstrating increased power to resolve weak genetic structure in this highly admixed plant species. By identifying exome polymorphisms underlying genetic differentiation, we suggest that geographic differentiation of this important invasive species has occurred more often within pathways that regulate growth and response to defense and stress, which may be associated with survival in North America's diverse climatic regions.
Common shared genetic variation behind decreased risk of breast cancer in celiac disease
Jul 20, 2017   Scientific Reports
Ugalde-Morales E, Li J, Humphreys K, Ludvigsson JF, Yang H, Hall P, Czene K
Common shared genetic variation behind decreased risk of breast cancer in celiac disease
Jul 20, 2017
Scientific Reports
There is epidemiologic evidence showing that women with celiac disease have reduced risk of later developing breast cancer, however, the etiology of this association is unclear. Here, we assess the extent of genetic overlap between the two diseases. Through analyses of summary statistics on densely genotyped immunogenic regions, we show a significant genetic correlation (r = -0.17, s.e. 0.05, P 
Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Jul 20, 2017   Nature Communications
Zillikens MC, Demissie S, Hsu YH, Yerges-Armstrong LM, Chou WC,   . . . . . .   , Loos RJF, Karasik D, Harris TB, Ohlsson C, Kiel DP
Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Jul 20, 2017
Nature Communications
Zillikens MC, Demissie S, Hsu YH, Yerges-Armstrong LM, Chou WC, Stolk L, Livshits G, Broer L, Johnson T, Koller DL, Kutalik Z, Luan J, Malkin I, Ried JS, Smith AV, Thorleifsson G, Vandenput L, Hua Zhao J, Zhang W, Aghdassi A, Åkesson K, Amin N, Baier LJ, Barroso I, Bennett DA, Bertram L, Biffar R, Bochud M, Boehnke M, Borecki IB, Buchman AS, Byberg L, Campbell H, Campos Obanda N, Cauley JA, Cawthon PM, Cederberg H, Chen Z, Cho NH, Jin Choi H, Claussnitzer M, Collins F, Cummings SR, De Jager PL, Demuth I, Dhonukshe-Rutten RAM, Diatchenko L, Eiriksdottir G, Enneman AW, Erdos M, Eriksson JG, Eriksson J, Estrada K, Evans DS, Feitosa MF, Fu M, Garcia M, Gieger C, Girke T, Glazer NL, Grallert H, Grewal J, Han BG, Hanson RL, Hayward C, Hofman A, Hoffman EP, Homuth G, Hsueh WC, Hubal MJ, Hubbard A, Huffman KM, Husted LB, Illig T, Ingelsson E, Ittermann T, Jansson JO, Jordan JM, Jula A, Karlsson M, Khaw KT, Kilpeläinen TO, Klopp N, Kloth JSL, Koistinen HA, Kraus WE, Kritchevsky S, Kuulasmaa T, Kuusisto J, Laakso M, Lahti J, Lang T, Langdahl BL, Launer LJ, Lee JY, Lerch MM, Lewis JR, Lind L, Lindgren C, Liu Y, Liu T, Liu Y, Ljunggren Ö, Lorentzon M, Luben RN, Maixner W, McGuigan FE, Medina-Gomez C, Meitinger T, Melhus H, Mellström D, Melov S, Michaëlsson K, Mitchell BD, Morris AP, Mosekilde L, Newman A, Nielson CM, O'Connell JR, Oostra BA, Orwoll ES, Palotie A, Parker S, Peacock M, Perola M, Peters A, Polasek O, Prince RL, Räikkönen K, Ralston SH, Ripatti S, Robbins JA, Rotter JI, Rudan I, Salomaa V, Satterfield S, Schadt EE, Schipf S, Scott L, Sehmi J, Shen J, Soo Shin C, Sigurdsson G, Smith S, Soranzo N, Stančáková A, Steinhagen-Thiessen E, Streeten EA, Styrkarsdottir U, Swart KMA, Tan ST, Tarnopolsky MA, Thompson P, Thomson CA, Thorsteinsdottir U, Tikkanen E, Tranah GJ, Tuomilehto J, van Schoor NM, Verma A, Vollenweider P, Völzke H, Wactawski-Wende J, Walker M, Weedon MN, Welch R, Wichman HE, Widen E, Williams FMK, Wilson JF, Wright NC, Xie W, Yu L, Zhou Y, Chambers JC, Döring A, van Duijn CM, Econs MJ, Gudnason V, Kooner JS, Psaty BM, Spector TD, Stefansson K, Rivadeneira F, Uitterlinden AG, Wareham NJ, Ossowski V, Waterworth D, Loos RJF, Karasik D, Harris TB, Ohlsson C, Kiel DP
Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p 
Consequences of severe habitat fragmentation on density, genetics, and spatial capture-recapture analysis of a small bear population
Jul 24, 2017   PloS One
Murphy SM, Augustine BC, Ulrey WA, Guthrie JM, Scheick BK, McCown JW, Cox JJ
Consequences of severe habitat fragmentation on density, genetics, and spatial capture-recapture analysis of a small bear population
Jul 24, 2017
PloS One
Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the degree of contemporary habitat fragmentation and investigate the consequences of habitat fragmentation on population density and genetics of the HGS. Remaining natural habitats sustaining the HGS were significantly more fragmented and patchier than those supporting Florida's largest black bear subpopulation. Genetic diversity was low (AR = 3.57; HE = 0.49) and effective population size was small (NE = 25 bears), both of which remained unchanged over a period spanning one bear generation despite evidence of some immigration. Subpopulation density (0.054 bear/km2) was among the lowest reported for black bears, was significantly female-biased, and corresponded to a subpopulation size of 98 bears in available habitat. Conserving remaining natural habitats in the area occupied by the small, genetically depauperate HGS, possibly through conservation easements and government land acquisition, is likely the most important immediate step to ensuring continued persistence of bears in this area. Our study also provides evidence that preferentially placing detectors (e.g., hair traps or cameras) primarily in quality habitat across fragmented landscapes poses a challenge to estimating density-habitat covariate relationships using spatial capture-recapture models. Because habitat fragmentation and loss are likely to increase in severity globally, further investigation of the influence of habitat fragmentation and detector placement on estimation of this relationship is warranted.

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