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      Identification of Candidate Genes for Reactivity in Guzerat ( Bos indicus) Cattle: A Genome-Wide Association Study

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          Abstract

          Temperament is fundamental to animal production due to its direct influence on the animal-herdsman relationship. When compared to calm animals, the aggressive, anxious or fearful ones exhibit less weight gain, lower reproductive efficiency, decreased milk production and higher herd maintenance costs, all of which contribute to reduced profits. However, temperament is a trait that is complex and difficult to assess. Recently, a new quantitative system, REATEST ®, for assessing reactivity, a phenotype of temperament, was developed. Herein, we describe the results of a Genome-wide association study for reactivity, assessed using REATEST ® with a sample of 754 females from five dual-purpose (milk and meat production) Guzerat ( Bos indicus) herds. Genotyping was performed using a 50k SNP chip and a two-step mixed model approach (Grammar-Gamma) with a one-by-one marker regression was used to identify QTLs. QTLs for reactivity were identified on chromosomes BTA1, BTA5, BTA14, and BTA25. Five intronic and two intergenic markers were significantly associated with reactivity. POU1F1, DRD3, VWA3A, ZBTB20, EPHA6, SNRPF and NTN4 were identified as candidate genes. Previous QTL reports for temperament traits, covering areas surrounding the SNPs/genes identified here, further corroborate these associations. The seven genes identified in the present study explain 20.5% of reactivity variance and give a better understanding of temperament biology.

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          Regional dissociations within the hippocampus--memory and anxiety.

          The amnestic effects of hippocampal lesions are well documented, leading to numerous memory-based theories of hippocampal function. It is debatable, however, whether any one of these theories can satisfactorily account for all the consequences of hippocampal damage: Hippocampal lesions also result in behavioural disinhibition and reduced anxiety. A growing number of studies now suggest that these diverse behavioural effects may be associated with different hippocampal subregions. There is evidence for at least two distinct functional domains, although recent neuroanatomical studies suggest this may be an underestimate. Selective lesion studies show that the hippocampus is functionally subdivided along the septotemporal axis into dorsal and ventral regions, each associated with a distinct set of behaviours. Dorsal hippocampus has a preferential role in certain forms of learning and memory, notably spatial learning, but ventral hippocampus may have a preferential role in brain processes associated with anxiety-related behaviours. The latter's role in emotional processing is also distinct from that of the amygdala, which is associated specifically with fear. Gray and McNaughton's theory can in principle incorporate these apparently distinct hippocampal functions, and provides a plausible unitary account for the multiple facets of hippocampal function.
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            ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

            With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have arisen. However, novel tools and strategies are required to accommodate this large volume of genomic information and to facilitate the transfer of predictions generated by comparative sequence alignment to researchers focused on experimental annotation of genome function. Here, we present the ECR Browser, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.
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              Developmental progress and current status of the Animal QTLdb

              The Animal QTL Database (QTLdb; http://www.animalgenome.org/QTLdb) has undergone dramatic growth in recent years in terms of new data curated, data downloads and new functions and tools. We have focused our development efforts to cope with challenges arising from rapid growth of newly published data and end users’ data demands, and to optimize data retrieval and analysis to facilitate users’ research. Evidenced by the 27 releases in the past 11 years, the growth of the QTLdb has been phenomenal. Here we report our recent progress which is highlighted by addition of one new species, four new data types, four new user tools, a new API tool set, numerous new functions and capabilities added to the curator tool set, expansion of our data alliance partners and more than 20 other improvements. In this paper we present a summary of our progress to date and an outlook regarding future directions.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                26 January 2017
                2017
                : 12
                : 1
                : e0169163
                Affiliations
                [1 ]Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
                [2 ]Embrapa Gado de Leite, Juiz de Fora, Brazil
                [3 ]Center for Genetic Improvement of Livestock, University of Guelph, Guelph, Canada
                [4 ]Beef Improvement Opportunities, Guelph, Canada
                Universita degli Studi di Bologna, ITALY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: FCS MGCDP PASF MFAP RVV ICR FATB MRSC.

                • Data curation: FCS MGCDP.

                • Formal analysis: FCS PASF MGCDP FATB RVV.

                • Funding acquisition: MGCDP MRSC.

                • Investigation: FCS PASF MRSC ICR.

                • Methodology: FCS MGCDP PASF RVV FATB MRSC.

                • Project administration: MGCDP MRSC.

                • Resources: MGCDP MFAP MRSC MAM.

                • Software: FCS RVV.

                • Supervision: MRSC MGCDP.

                • Validation: FCS PASF MGCDP MRSC RVV.

                • Visualization: FCS.

                • Writing – original draft: FCS MGCDP MRSC.

                • Writing – review & editing: FCS MGCDP PASF MFAP RVV ICR FATB MRSC MAM.

                Article
                PONE-D-16-28097
                10.1371/journal.pone.0169163
                5268462
                28125592
                1e0154bb-f7b6-45b8-bb21-1ee65b0eb714
                © 2017 dos Santos et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 14 July 2016
                : 13 December 2016
                Page count
                Figures: 1, Tables: 2, Pages: 15
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100004901, Fundação de Amparo à Pesquisa do Estado de Minas Gerais;
                Award ID: CVZ APQ 01353
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004901, Fundação de Amparo à Pesquisa do Estado de Minas Gerais;
                Award ID: CVZ APQ 3182-5.04/07
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award ID: 307975/2010-0
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award ID: 312068/2015-8
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award ID: 481018/2008-5
                Award Recipient :
                This study was supported by Fundação de Amparo à Pesquisa de Minas Gerais (FAPEMIG), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Maria Gabriela Campolina Diniz Peixoto was supported by the Fapemig - CVZ APQ 01353 e CVZ APQ 3182-5.04/07. MRSC has a fellowship from the CNPq – 307975/2010-0 and was supported by CNPq – 312068/2015-8 and 481018/2008-5 projects. MGCDP, RVV, and MAM have fellowships from FAPEMIG. PASF has CNPq fellowship. FCS and ICR have CAPES fellowships.
                Categories
                Research Article
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
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                Genetic Loci
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