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Genetic variation

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https://www.readbyqxmd.com/read/29036657/genomic-admixture-between-locally-adapted-populations-of-arabidopsis-thaliana-mouse-ear-cress-evidence-of-optimal-genetic-outcrossing-distance
#1
Kattia Palacio-Lopez, Stephen R Keller, Jane Molofsky
Admixture can break up divergent genetic architectures between populations, resulting in phenotypic novelty and generating raw material for environmental selection. The contribution of admixture to progeny trait variation and fitness varies based on the degree of genetic isolation between the parental populations, for which most studies have used geographic distance as a proxy. A novel approach is to estimate optimal crossing distance using the adaptive genetic distance between mates estimated from loci that contribute directly to local adaptation...
September 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036523/stress-dependent-association-between-polygenic-risk-for-schizophrenia-and-schizotypal-traits-in-young-army-recruits
#2
Alex Hatzimanolis, Dimitrios Avramopoulos, Dan E Arking, Anna Moes, Pallav Bhatnagar, Todd Lencz, Anil K Malhotra, Stella G Giakoumaki, Panos Roussos, Nikolaos Smyrnis, Panos Bitsios, Nicholas C Stefanis
Schizotypal personality traits may increase proneness to psychosis and likely index familial vulnerability to schizophrenia (SZ), implying shared genetic determinants with SZ. Here, we sought to investigate the contribution of common genetic risk variation for SZ on self-reported schizotypy in 2 ethnically homogeneous cohorts of healthy young males during compulsory military service, enrolled in the Athens Study of Proneness and Incidence of Schizophrenia (ASPIS, N = 875) and the Learning on Genetics of Schizophrenia Spectrum study (LOGOS, N = 690)...
June 13, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29036466/insights-into-epigenome-evolution-from-animal-and-plant-methylomes
#3
Soojin V Yi
Evolutionary studies of DNA methylation begin to provide insights into the underlying forces governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the contents of repetitive sequences, while the underlying driver of this correlation is less clear in animal genomes...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036451/genetic-mapping-and-phylogenetic-analysis-reveal-intraspecific-variation-in-sex-chromosomes-of-the-virginian-strawberry
#4
Na Wei, Rajanikanth Govindarajulu, Jacob A Tennessen, Aaron Liston, Tia-Lynn Ashman
With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted sequence capture for the subdioecious western Fragaria virginiana ssp...
September 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036328/phylogeography-and-population-genetic-analyses-in-the-iberian-toothcarp-aphanius-iberus-valenciennes-1846-at-different-time-scales
#5
Elena G Gonzalez, Carina Cunha, Hamid R Ghanavi, Francisco J Oliva-Paterna, Mar Torralva, Ignacio Doadrio
Secondary freshwater fish species inhabiting fluctuating and extreme environments are susceptible to changes in dispersion, effective population size, and genetic structure. The Iberian toothcarp Aphanius iberus is an endemic cyprinodontid of the Iberian Peninsula restricted to brackish water of salt marshes and coastal lagoons on the eastern Spanish Mediterranean coast. In this study we analysed mitochondrial cytochrome b DNA and microsatellite variation to evaluate ways in which the processes of extinction, dispersal, and colonization of A...
September 22, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29035683/mapping-of-quantitative-trait-loci-associated-with-size-shape-and-parr-mark-traits-using-first-and-second-generation-backcrosses-between-european-and-north-american-atlantic-salmon-i-salmo-salar-i
#6
Stephanie Pedersen, Lei Liu, Brian Glebe, Steven Leadbeater, Sigbjørn Lien, Elizabeth G Boulding
Little is known about the genetic architecture of traits important for salmonid restoration ecology. We mapped quantitative trait loci (QTL) using single nucleotide polymorphisms (SNPs) for juvenile body length, weight, shape, and vertical skin pigmentation patterns (parr marks) within three hybrid backcross families between European and North American subspecies of Atlantic salmon. Amounts of variation in skin colour and pattern quantified in the two second-generation transAtlantic families exceeded the ranges seen in purebred populations...
October 16, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29035139/novel-17-bp-deletion-in-kdm1b-gene-is-significantly-associated-with-testis-weight-in-male-piglet
#7
Yang Cui, Tao Hu, Rui Chen, Shuai Yu, Wuzi Dong, Xiaoyan Lv, Chuanying Pan
Lysine-specific demethylase 1B (KDM1B) which plays a crucial role in regulating methylation status at lysine 4 of histone 3 is important for male fertility. The aim of this study was to explore the KDM1B mRNA expression profiles and to identify novel genetic variants of the pig KDM1B gene, as well as to determine the association between these variants and testis measurement traits in male piglets. The KDM1B mRNA expression profiles indicated that this gene widely expressed in all tested organs. In addition, a novel 17-bp deletion (NC_010449...
October 16, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29035135/draft-de-novo-genome-sequence-of-agapornis-roseicollis-for-application-in-avian-breeding
#8
Henriëtte van der Zwan, Francois van der Westhuizen, Carina Visser, Rencia van der Sluis
In aviculture, lovebirds are considered one of the most popular birds to keep. This African parakeet is known for its range of plumage colors and ease to tame. Plumage variation is the most important price-determining trait of these birds, and also the main selection criterion for breeders. Currently, no genetic screening tests for traits of economic importance or to confirm pedigree data are available for any of the nine lovebird species. As a starting point to develop these tests, the de novo genome of Agapornis roseicollis (rosy-faced lovebird) was sequenced, assembled, and annotated...
October 16, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29034956/homoeologous-exchanges-cause-extensive-dosage-dependent-gene-expression-changes-in-an-allopolyploid-crop
#9
Andrew Lloyd, Aurélien Blary, Delphine Charif, Catherine Charpentier, Joseph Tran, Sandrine Balzergue, Etienne Delannoy, Guillem Rigaill, Eric Jenczewski
Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined. Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop. We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs...
October 16, 2017: New Phytologist
https://www.readbyqxmd.com/read/29034898/generation-of-induced-pluripotent-stem-cells-ipsc-from-an-atrial-fibrillation-patient-carrying-a-pitx2-p-m200v-mutation
#10
Cristina Mora, Marialaura Serzanti, Alessio Giacomelli, Silvia Beltramone, Eleonora Marchina, Valeria Bertini, Giovanna Piovani, Lena Refsgaard, Morten Salling Olesen, Venusia Cortellini, Patrizia Dell'Era
Atrial fibrillation (AF) is the most common sustained arrhythmia associated with several cardiac risk factors, but increasing evidences indicated a genetic component. Indeed, genetic variations of the specific PITX2 gene have been identified in patients with early-onset AF. To investigate the molecular mechanisms underlying AF, we reprogrammed to pluripotency polymorphonucleated leukocytes isolated from the blood of a patient carrying a PITX2 p.M200V mutation, using a commercially available non-integrating expression system...
October 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29034891/generation-of-induced-pluripotent-stem-cells-ipsc-from-an-atrial-fibrillation-patient-carrying-a-kcna5-p-d322h-mutation
#11
Cristina Mora, Marialaura Serzanti, Alessio Giacomelli, Valentina Turco, Eleonora Marchina, Valeria Bertini, Giovanna Piovani, Giulia Savio, Lena Refsgaard, Morten Salling Olesen, Venusia Cortellini, Patrizia Dell'Era
Atrial fibrillation (AF) is the most common sustained arrhythmia associated with several cardiac risk factors, but increasing evidences indicated a genetic component. Indeed, genetic variations of the atrial specific KCNA5 gene have been identified in patients with early-onset lone AF. To investigate the molecular mechanisms underlying AF, we reprogrammed to pluripotency polymorphonucleated leukocytes isolated from the blood of a patient carrying a KCNA5 p.D322H mutation, using a commercially available non-integrating system...
October 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29034850/pseudomonas-aeruginosa-variants-obtained-from-veterinary-clinical-samples-reveal-a-role-for-cyclic-di-gmp-in-biofilm-formation-and-colony-morphology
#12
Maria T Brock, Galya C Fedderly, Grace I Borlee, Michael M Russell, Liliana K Filipowska, Doreene R Hyatt, Ryan A Ferris, Bradley R Borlee
Overuse of antibiotics is contributing to an emerging antimicrobial resistance crisis. To better understand how bacteria adapt tolerance and resist antibiotic treatment, Pseudomonas aeruginosa isolates obtained from infection sites sampled from companion animals were collected and evaluated for phenotypic differences. Selected pairs of clonal isolates were obtained from individual infection samples and were assessed for antibiotic susceptibility, cyclic di-GMP levels, biofilm production, motility and genetic-relatedness...
October 16, 2017: Microbiology
https://www.readbyqxmd.com/read/29034771/genome-wide-analysis-of-epstein-barr-virus-identifies-variants-and-genes-associated-with-gastric-carcinoma-and-population-structure
#13
Youyuan Yao, Miao Xu, Liming Liang, Haojiong Zhang, Ruihua Xu, Qisheng Feng, Lin Feng, Bing Luo, Yi-Xin Zeng
Epstein-Barr virus is a ubiquitous virus and is associated with several human malignances, including the significant subset of gastric carcinoma, Epstein-Barr virus-associated gastric carcinoma. Some Epstein-Barr virus-associated diseases are uniquely prevalent in populations with different geographic origins. However, the features of the disease and geographically associated Epstein-Barr virus genetic variation as well as the roles that the variation plays in carcinogenesis and evolution remain unclear. Therefore, in this study, we sequenced 95 geographically distinct Epstein-Barr virus isolates from Epstein-Barr virus-associated gastric carcinoma biopsies and saliva of healthy donors to detect variants and genes associated with gastric carcinoma and population structure from a genome-wide spectrum...
October 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29034632/-research-progress-and-stress-induced-variation-of-dna-methylation-in-plants
#14
Zhen Yang, Xuanming Peng, Yiyan Zhang, Yuanhai Zhang, Yong Zhang
Chemical modification of DNA bases in recent years has been one of the hot areas of life science research. DNA methylation is a common epigenetic phenomenon and can change the genetic performance without changing the DNA sequence. Various stress factors can induce the variation of DNA methylation in plants, but the response mechanism is still unknown. In this paper, the progress of DNA methylation in plants was reviewed. In combination with the researchconclusions of our own research group, the DNA methylation variation induced by 7Li ion beam and gamma ray was reported to provide a basis for DNA methylation, which may be involved in the phenotypic plasticity of plants...
December 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29033977/the-empirical-distribution-of-singletons-for-geographic-samples-of-dna-sequences
#15
Philippe Cubry, Yves Vigouroux, Olivier François
Rare variants are important for drawing inference about past demographic events in a species history. A singleton is a rare variant for which genetic variation is carried by a unique chromosome in a sample. How singletons are distributed across geographic space provides a local measure of genetic diversity that can be measured at the individual level. Here, we define the empirical distribution of singletons in a sample of chromosomes as the proportion of the total number of singletons that each chromosome carries, and we present a theoretical background for studying this distribution...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29033955/multilevel-regulation-of-abiotic-stress-responses-in-plants
#16
REVIEW
David C Haak, Takeshi Fukao, Ruth Grene, Zhihua Hua, Rumen Ivanov, Giorgio Perrella, Song Li
The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29033455/genetic-variation-birds-of-a-feather-genetic-mapping-of-yellow-pigmentation
#17
Ross Cloney
No abstract text is available yet for this article.
October 16, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29033291/controversies-in-poland-syndrome-alternative-diagnoses-in-patients-with-congenital-pectoral-muscle-deficiency
#18
Martijn Baas, Elise B Burger, Dimitri Sneiders, Robert-Jan H Galjaard, Steven E R Hovius, Christianne A van Nieuwenhoven
PURPOSE: Poland syndrome was first described as a deficiency of the pectoral muscle with ipsilateral symbrachydactyly. Currently, numerous case reports describe variations of Poland syndrome in which pectoral muscle deficiency is often used as the only defining criterion. However, more syndromes can present with pectoral muscle deficiency. The aim of this review is to illustrate the diversity of the phenotypic spectrum of Poland syndrome and to create more awareness for alternative diagnoses in pectoral muscle deficiency...
October 13, 2017: Journal of Hand Surgery
https://www.readbyqxmd.com/read/29032825/line-1-retrotransposon-mediated-dna-transductions-in-endometriosis-associated-ovarian-cancers
#19
Zhouchunyang Xia, Dawn R Cochrane, Michael S Anglesio, Yi Kan Wang, Tayyebeh Nazeran, Basile Tessier-Cloutier, Melissa K McConechy, Janine Senz, Amy Lum, Ali Bashashati, Sohrab P Shah, David G Huntsman
OBJECTIVE: Endometrioid (ENOC) and clear cell ovarian carcinoma (CCOC) share a common precursor lesion, endometriosis, hence the designation endometriosis associated ovarian cancers (EAOC). Long interspersed nuclear element 1 (LINE-1 or L1), is a family of mobile genetic elements activated in many cancers capable of moving neighboring DNA through 3' transductions. Here we investigated the involvement of specific L1-mediated transductions in EAOCs. METHODS: Through whole genome sequencing, we identified active L1-mediated transductions originating within the TTC28 gene in 34% (10/29) of ENOC and 31% (11/35) of CCOC cases...
October 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29032502/gut-microbiota-changes-in-the-extreme-decades-of-human-life-a-focus-on-centenarians
#20
REVIEW
Aurelia Santoro, Rita Ostan, Marco Candela, Elena Biagi, Patrizia Brigidi, Miriam Capri, Claudio Franceschi
The gut microbiota (GM) is a complex, evolutionarily molded ecological system, which contributes to a variety of physiological functions. The GM is highly dynamic, being sensitive to environmental stimuli, and its composition changes over the host's entire lifespan. However, the basic question of how much these changes may be ascribed to variables such as population, diet, genetics and gender, and/or to the aging process per se is still largely unanswered. We argue that comparison among studies on centenarians-the best model of healthy aging and longevity-recruited from different geographical areas/populations (different genetics and dietary habits) can help to disentangle the contribution of aging and non-aging-related variables to GM remodeling with age...
October 14, 2017: Cellular and Molecular Life Sciences: CMLS
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