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Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle
Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, Mekki Boussaha, Fabio Pilla, Baldassare Portolano, Salvatore Mastrangelo To cite this version: Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, et al.. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Frontiers in Genetics, Frontiers, 2021, 10.3389/fgene.2021.675569. hal-03210766 HAL Id: hal-03210766 https://hal.inrae.fr/hal-03210766 Submitted on 28 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License ORIGINAL RESEARCH published: 28 April 2021 doi: 10.3389/fgene.2021.675569 Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa 1, Gabriele Senczuk 2, Elena Ciani 3, Roberta -
Novel Mutations Consolidate KCTD7 As a Progressive Myoclonus Epilepsy Gene
Europe PMC Funders Group Author Manuscript J Med Genet. Author manuscript; available in PMC 2013 September 16. Published in final edited form as: J Med Genet. 2012 June ; 49(6): 391–399. doi:10.1136/jmedgenet-2012-100859. Europe PMC Funders Author Manuscripts Novel mutations consolidate KCTD7 as a progressive myoclonus epilepsy gene Maria Kousi1,2, Verneri Anttila3,4, Angela Schulz5, Stella Calafato3, Eveliina Jakkula4, Erik Riesch6, Liisa Myllykangas1,7, Hannu Kalimo7, Meral Topcu8, Sarenur Gokben9, Fusun Alehan10, Johannes R Lemke11, Michael Alber12, Aarno Palotie3,4,13,14, Outi Kopra1,2, and Anna-Elina Lehesjoki1,2 1Folkhälsan Institute of Genetics, Finland 2Haartman Institute, Department of Medical Genetics and Research Program’s Unit, Molecular Medicine, and Neuroscience Center, University of Helsinki, Finland 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK 4Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland 5Children’s Hospital, University Medical Center Hamburg Eppendorf, Hamburg, Germany 6CeGaT GmbH, Tübingen, Germany 7Department of Pathology, University of Helsinki, and Helsinki University Central Hospital, Helsinki, Finland 8Department of Pediatrics, Hacettepe University Faculty of Medicine, Section of Child Neurology, Ankara, Turkey 9Department of Pediatrics, Ege University Medical Faculty, Izmir, Turkey 10Baskent University Faculty of Medicine Division of Child Neurology, Baskent, Turkey 11University Children’s Hospital, Inselspital, Bern, Switzerland 12Department -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
A Systems-Genetics Analyses of Complex Phenotypes
A systems-genetics analyses of complex phenotypes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 David Ashbrook Table of contents Table of contents Table of contents ............................................................................................... 1 Tables and figures ........................................................................................... 10 General abstract ............................................................................................... 14 Declaration ....................................................................................................... 15 Copyright statement ........................................................................................ 15 Acknowledgements.......................................................................................... 16 Chapter 1: General introduction ...................................................................... 17 1.1 Overview................................................................................................... 18 1.2 Linkage, association and gene annotations .............................................. 20 1.3 ‘Big data’ and ‘omics’ ................................................................................ 22 1.4 Systems-genetics ..................................................................................... 24 1.5 Recombinant inbred (RI) lines and the BXD .............................................. 25 Figure 1.1: -
A Genome-Wide Linkage and Association Study of Musical Aptitude Identifies Loci Containing Genes Related to Inner Ear Development and Neurocognitive Functions
Molecular Psychiatry (2015) 20, 275–282 © 2015 Macmillan Publishers Limited All rights reserved 1359-4184/15 www.nature.com/mp ORIGINAL ARTICLE A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions J Oikkonen1,2, Y Huang3, P Onkamo2, L Ukkola-Vuoti1, P Raijas4, K Karma4, VJ Vieland3 and I Järvelä1 Humans have developed the perception, production and processing of sounds into the art of music. A genetic contribution to these skills of musical aptitude has long been suggested. We performed a genome-wide scan in 76 pedigrees (767 individuals) characterized for the ability to discriminate pitch (SP), duration (ST) and sound patterns (KMT), which are primary capacities for music perception. Using the Bayesian linkage and association approach implemented in program package KELVIN, especially designed for complex pedigrees, several single nucleotide polymorphisms (SNPs) near genes affecting the functions of the auditory pathway and neurocognitive processes were identified. The strongest association was found at 3q21.3 (rs9854612) with combined SP, ST and KMT test scores (COMB). This region is located a few dozen kilobases upstream of the GATA binding protein 2 (GATA2) gene. GATA2 regulates the development of cochlear hair cells and the inferior colliculus (IC), which are important in tonotopic mapping. The highest probability of linkage was obtained for phenotype SP at 4p14, located next to the region harboring the protocadherin 7 gene, PCDH7. Two SNPs rs13146789 and rs13109270 of PCDH7 showed strong association. PCDH7 has been suggested to play a role in cochlear and amygdaloid complexes. Functional class analysis showed that inner ear and schizophrenia- related genes were enriched inside the linked regions. -
Variation in Protein Coding Genes Identifies Information Flow
bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number. -
Chromosomal Microarray Analysis As a First-Tier Clinical Diagnostic Test
Original Article Diagnostic Genetics CROSSMARK_logo_3_Test 1 / 1 Ann Lab Med 2019;39:299-310 https://doi.org/10.3343/alm.2019.39.3.299 ISSN 2234-3806 • eISSN 2234-3814 https://crossmark-cdn.crossref.org/widget/v2.0/logos/CROSSMARK_Color_square.svg 2017-03-16 Chromosomal Microarray Analysis as a First-Tier Clinical Diagnostic Test in Patients With Developmental Delay/Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies: A Prospective Multicenter Study in Korea Woori Jang, M.D.1,2, Yonggoo Kim, M.D.1,2, Eunhee Han, M.D.1,2, Joonhong Park, M.D.1,2, Hyojin Chae, M.D.1,2, Ahlm Kwon, M.T.2, Hayoung Choi, M.T.2, Jiyeon Kim, M.T.2, Jung-Ok Son, M.T.2, Sang-Jee Lee, M.D.3, Bo Young Hong, M.D.4, Dae-Hyun Jang, M.D.5, Ji Yoon Han, M.D.6, Jung Hyun Lee, M.D.7, So Young Kim, M.D.8, In Goo Lee, M.D.6, In Kyung Sung, M.D.6, Yeonsook Moon, M.D.9, Myungshin Kim , M.D.1,2, and Joo Hyun Park, M.D.10 1Department of Laboratory Medicine and 2Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea; 3Department of Rehabilitation Medicine, Daejeon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Korea; 4Department of Rehabilitation Medicine, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea; 5Department of Rehabilitation Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea; 6Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea; 7Department of Pediatrics, St. -
Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production
Copyright Ó 2010 by the Genetics Society of America DOI: 10.1534/genetics.110.116111 Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production Alessandra Stella,* Paolo Ajmone-Marsan,† Barbara Lazzari‡ and Paul Boettcher§,1 *Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, 20133 Milan, Italy, †Istituto di Zootecnica, Universita` Cattolica del Sacro Cuore, 29100 Piacenza, Italy, ‡Parco Tecnologico Padano, 26900 Lodi, Italy and §Joint Food and Agriculture Organization of the United Nations–International Atomic Energy Agency Division for Nuclear Applications to Food and Agriculture, International Atomic Energy Agency, A-1400 Vienna, Austria Manuscript received February 27, 2010 Accepted for publication May 4, 2010 ABSTRACT The genomics revolution has spurred the undertaking of HapMap studies of numerous species, allowing for population genomics to increase the understanding of how selection has created genetic differences between subspecies populations. The objectives of this study were to (1) develop an approach to detect signatures of selection in subsets of phenotypically similar breeds of livestock by comparing single nucleotide polymorphism (SNP) diversity between the subset and a larger population, (2) verify this method in breeds selected for simply inherited traits, and (3) apply this method to the dairy breeds in the International Bovine HapMap (IBHM) study. The data consisted of genotypes for 32,689 SNPs of 497 animals from 19 breeds. For a given subset of breeds, the test statistic was the parametric composite log likelihood (CLL) of the differences in allelic frequencies between the subset and the IBHM for a sliding window of SNPs. The null distribution was obtained by calculating CLL for 50,000 random subsets (per chromosome) of individuals.