Genetic variation articles within Nature Communications

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  • Article
    | Open Access

    Sex-specific meiotic crossover (CO) landscapes have been identified in multiple species. Here, the authors show that male and female meioses in maize have similar CO landscapes, and differences between COs in the two sexes only exists in their location relative to transcription start sites and some chromatin marks.

    • Penny M. A. Kianian
    • , Minghui Wang
    •  & Wojciech P. Pawlowski

  • Article
    | Open Access

    Mating-type switching enables self-compatible reproduction in fungi, but switching ability is variable even within species. Here, the authors find de novo evolution of switching genotypes in experimentally evolved fission yeast populations and show a trade-off between mating success and growth.

    • Bart P. S. Nieuwenhuis
    • , Sergio Tusso
    •  & Simone Immler

  • Article
    | Open Access

    Pulmonary arterial hypertension (PAH) is a rare lung disorder characterised by narrowing and obliteration of small pulmonary arteries ultimately leading to right heart failure. Here, the authors sequence whole genomes of over 1000 PAH patients and identify likely causal variants in GDF2, ATP13A3, AQP1 and SOX17.

    • Stefan Gräf
    • , Matthias Haimel
    •  & Nicholas W. Morrell

  • Article
    | Open Access

    Somatic cells can accumulate structural variations such as deletions. Here, Møller et al. show that normal human cells generate large extrachromosomal circular DNAs (eccDNAs), most likely the products of excised DNA, that can be transcriptionally active and, thus, may have phenotypic consequences.

    • Henrik Devitt Møller
    • , Marghoob Mohiyuddin
    •  & Birgitte Regenberg

  • Article
    | Open Access

    The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.

    • Florian J. Alberto
    • , Frédéric Boyer
    •  & François Pompanon

  • Article
    | Open Access

    Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.

    • Todd P. Michael
    • , Florian Jupe
    •  & Joseph R. Ecker

  • Article
    | Open Access

    The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.

    • Sean P. Gordon
    • , Bruno Contreras-Moreira
    •  & John P. Vogel

  • Article
    | Open Access

    African populations show a high level of genetic diversity and extensive regional admixture. Here, the authors sequence the whole genomes of 24 South African individuals of different ethnolinguistic origin and find substantive genomic divergence between two southeastern Bantu-speaking groups.

    • Ananyo Choudhury
    • , Michèle Ramsay
    •  & Michael S. Pepper

  • Article
    | Open Access

    Africanized honey bees (AHB) are notoriously aggressive, but in Puerto Rico they have a ‘gentle’ phenotype. Here, Avalos et al. show that there has been a soft selective sweep at several loci in the Puerto Rican AHB population and suggest a role in the rapid evolution of gentle behaviour.

    • Arian Avalos
    • , Hailin Pan
    •  & Guojie Zhang

  • Article
    | Open Access

    Breeding has increased crop productivity, but whether it has also changed phenotypic plasticity is unclear. Here, the authors find maize genomic regions selected for high productivity show reduced contribution to genotype by environment variation and provide evidence for regulatory control of phenotypic stability.

    • Joseph L. Gage
    • , Diego Jarquin
    •  & Natalia de Leon

  • Article
    | Open Access

    Expression quantitative trait loci (eQTL) are widely studied, yet the mechanisms by which they exert their effects are largely unknown. Here, performing CAGE-seq on 154 lymphoblastoid cell lines, the authors map regulatory variants associated with promoter usage (puQTLs) and enhancer activity (eaQTLs).

    • Marco Garieri
    • , Olivier Delaneau
    •  & Alexandre Fort

  • Article
    | Open Access

    The detection of structural variants can be difficult with short-read sequencing technology, especially when variants are highly complex. Here, the authors use a MinION nanopore sequencer to analyse two patient genomes and develop NanoSV to map known and novel structural variants in long read data.

    • Mircea Cretu Stancu
    • , Markus J. van Roosmalen
    •  & Wigard P. Kloosterman

  • Article
    | Open Access

    Nematodes use a characteristic set of movements, called nictation, to hitchhike on more mobile animals. Here, Lee et al. identify a genetic locus in the nematode Caenorhabditis elegans that underlies nictation and contributes to successful hitchhiking, but at expense of reduced offspring production.

    • Daehan Lee
    • , Heeseung Yang
    •  & Junho Lee

  • Article
    | Open Access

    Isolated populations can provide useful information on low-frequency variants for dissecting genetic architecture of complex traits. Here, Zeggini and colleagues show enrichment of rare and low-frequency variants and 8 novel low-frequency variant signals for cardiometabolic traits in two Greek isolated populations

    • Lorraine Southam
    • , Arthur Gilly
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Endometriosis is a major cause of infertility. Molecular mechanisms underlying the disease involve genetic and environmental risk factors. In a meta-analysis of eleven GWA studies, Sapkota and colleagues identify five novel risk loci, implicating steroid sex hormone pathways in the pathogenesis.

    • Yadav Sapkota
    • , Valgerdur Steinthorsdottir
    •  & Dale R. Nyholt

  • Article
    | Open Access

    Detection ofde novo, low frequency mutations is important for characterising heterogeneous cell populations, such as those found in cancer cell populations. Here the authors present o2n-seq, an ultrasensitive method with highly efficient data usage for detection of rare mutations.

    • Kaile Wang
    • , Shujuan Lai
    •  & Jue Ruan

  • Article
    | Open Access

    It is known that males have lower recombination rates than females over much of the genome but little is known about differences at a fine scale. Here the authors combine data from over 100,000 meioses and show that the majority of differences can be explained by variation in hotspot magnitude.

    • Claude Bhérer
    • , Christopher L. Campbell
    •  & Adam Auton

  • Article
    | Open Access

    In ancient cultures without a writing system, it is difficult to infer the basis of status and rank. Here the authors analyse ancient DNA from nine presumed elite individuals buried successively over a 300-year period at Chaco Canyon, and show evidence of matrilineal relationships.

    • Douglas J. Kennett
    • , Stephen Plog
    •  & George H. Perry

  • Article
    | Open Access

    Genetic data has led to great advances in our understanding of human evolution and dispersal, but information on more recent events is limited. Here, the authors analyse genotypes from 770,000 US individuals to map the fine-scale population structure of North America after European settlement.

    • Eunjung Han
    • , Peter Carbonetto
    •  & Catherine A. Ball

  • Article
    | Open Access

    Cooperation can be stabilized against exploitation if cooperators can reliably recognize each other. Here, Gruenheit and colleagues show that different alleles of the Tgr locus of the social amoebaDictyostelium discoideumunderlie the ability of different strains to recognize and cooperate with socially compatible individuals.

    • Nicole Gruenheit
    • , Katie Parkinson
    •  & Christopher R. L. Thompson

  • Article
    | Open Access

    Fission yeastSchizosaccharomyces pombe has diverse traits. Jeffares et al. characterize large copy number variations (CNVs) and rearrangements in S. pombe, and show that CNVs are transient with effects on quantitative traits and gene expression, whereas rearrangements influence intrinsic reproductive isolation.

    • Daniel C. Jeffares
    • , Clemency Jolly
    •  & Fritz J. Sedlazeck

  • Article
    | Open Access

    A First Nation population declined after European contact, likely as a result of infectious disease. Here, researchers partner with indigenous communities to analyse ancient and modern Native American exomes, and find a shift in selection pressure on immune genes, correlated to European-borne epidemics.

    • John Lindo
    • , Emilia Huerta-Sánchez
    •  & Ripan S. Malhi

  • Article
    | Open Access

    Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleraceareference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits

    • Agnieszka A. Golicz
    • , Philipp E. Bayer
    •  & David Edwards

  • Article
    | Open Access

    Currently available methods for phenotype to genetic markers association need to account for population structure. Here, Klasen et al. devise a statistical method called Quantitative Trait Cluster Association Test (QTCAT) that overcomes the need for population structure correction.

    • Jonas R. Klasen
    • , Elke Barbez
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    Dissecting the architecture of complex trait is challenging. Here, Hallin, Märtens et al. devises Phased Outbred Lines (POLs) in order to accurately decompose growth trait variation in diploid yeast across different environments.

    • Johan Hallin
    • , Kaspar Märtens
    •  & Gianni Liti

  • Article
    | Open Access

    The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) aims to better understand population genetics of the African diaspora. Here, it uses deeply sequenced whole-genomes to describe the impact of admixture and potential disease burden of deleterious variants.

    • Rasika Ann Mathias
    • , Margaret A. Taub
    •  & Kathleen C. Barnes

  • Article
    | Open Access

    Several GWAS have identified many common variants associated with blood metabolites. Here, the authors use an exome array to identify low frequency, potentially functional variants that impact human metabolism.

    • Eugene P. Rhee
    • , Qiong Yang
    •  & Robert E. Gerszten

  • Article
    | Open Access

    Analysis of cancer genome sequencing data has been used to predict genes associated with the pathogenesis of cancer. Here, the authors propose a new algorithm entitled RUBIC that predicts breaks in DNA as opposed to previously published methods that predict amplifications and deletions of DNA.

    • Ewald van Dyk
    • , Marlous Hoogstraat
    •  & Lodewyk F. A. Wessels

  • Article
    | Open Access

    Copper (Cu) is an essential mineral nutrient but high concentrations in rice grain can cause toxicity. Here the authors provide evidence that natural variation in rice grain Cu concentration is caused by altered sequestration of Cu into root vacuoles due to a single amino acid substitution in the OsHMA4 transporter.

    • Xin-Yuan Huang
    • , Fenglin Deng
    •  & Jian Feng Ma

  • Article
    | Open Access

    It has been increasingly recognised that tumours are not made up of a homogeneous population of cells. Here, the authors show heterogeneous expression of five protein markers in renal cell cancer and demonstrate that the progression of the tumour does not influence the degree of heterogeneity in the tumour.

    • Rouven Hoefflin
    • , Bernd Lahrmann
    •  & Stefan Duensing

  • Article
    | Open Access

    Clinical RNA-seq datasets can predict clinical outcomes. Here, Shen et al. report a statistical method for survival analysis of mRNA isoform variation using clinical RNA-seq datasets, and the identified isoform based survival predictors outperform gene expression based survival predictors using TCGA data on six cancer types.

    • Shihao Shen
    • , Yuanyuan Wang
    •  & Yi Xing

  • Article
    | Open Access

    The T300A substitution in ATG16L is associated with Crohn’s disease risk and disrupts clearance of intracellular pathogens by autophagy. Here the authors show that the mutation impairs interaction of ATG16L with TMEM59 and disrupts unconventional TMEM-induced autophagy, an aspect of innate immunity.

    • Emilio Boada-Romero
    • , Inmaculada Serramito-Gómez
    •  & Felipe X. Pimentel-Muiños

  • Article
    | Open Access

    Deficit in transcription factor Tbx1 causes heart defects in humans and mice. Here the authors show that Tbx1 regulates gene expression by recruiting histone methyltransferases that affect chromatin marks, and that a drug inhibiting histone demethylation ameliorates the cardiovascular phenotype in Tbx1 haploinsufficient or hypomorphic mice.

    • Filomena Gabriella Fulcoli
    • , Monica Franzese
    •  & Antonio Baldini

  • Article
    | Open Access

    Cryptic genetic variants may not individually show discernible phenotypic effects, but collectively, these polymorphisms can lead to unexpected, genetically complex traits that might be relevant to evolution and disease. Here, the authors use large yeast populations to comprehensively dissect the genetic bases of 17 independent occurrences of a phenotype that arises due to combinations of epistatically interacting cryptic variants.

    • Matthew B. Taylor
    • , Joann Phan
    •  & Ian M. Ehrenreich

  • Article
    | Open Access

    Genome-wide association studies have been performed to identify genetic variants that are associated with susceptibility to colorectal cancer. Here, the authors expand on these studies and identify a variant that regulates the expression of ETV6 and find that over-expression of ETV6 blocks cell proliferation in vitro.

    • Meilin Wang
    • , Dongying Gu
    •  & Jinfei Chen

  • Article
    | Open Access

    The variability in patient response to radiation treatment is difficult to predict. Here, using more than 500 cell lines the authors measure response to radiation exposure and a large panel of compounds, and show that response can be predicted by genetic alterations of the cells.

    • Brian D. Yard
    • , Drew J. Adams
    •  & Mohamed E. Abazeed

  • Article
    | Open Access

    Use of general linear mixed models (GLMMs) in genetic variance analysis can quantify the relative contribution of additive effects from genetic variation on a given trait. Here, Jonathan Mosley and colleagues apply GLMM in a phenome-wide analysis and show that genetic variations in the HLA region are associated with 44 phenotypes, 5 phenotypes which were not previously reported in GWASes.

    • Jonathan D. Mosley
    • , John S. Witte
    •  & Joshua C. Denny

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