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      Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

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          Abstract

          Background

          Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle ( Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs).

          Results

          The most significant SNP (rs133012258, P GC = 1.34 × 10 -9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 ( SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length.

          Conclusions

          This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle ( Bos primigenius taurus) also affect birth weight and size in zebu cattle ( Bos primigenius indicus).

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          Most cited references33

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          Ensembl BioMarts: a hub for data retrieval across taxonomic space

          For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/
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            The genome sequence of taurine cattle: a window to ruminant biology and evolution.

            To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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              Development and Characterization of a High Density SNP Genotyping Assay for Cattle

              The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.
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                Author and article information

                Contributors
                Journal
                BMC Genet
                BMC Genet
                BMC Genetics
                BioMed Central
                1471-2156
                2013
                13 June 2013
                : 14
                : 52
                Affiliations
                [1 ]Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
                [2 ]GenSys Consultores Associados, Porto Alegre, 90680-000, Brazil
                [3 ]Department of Sustainable Agricultural Systems, Division of Livestock Sciences, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
                [4 ]Centre for Reproduction and Genomics, AgResearch, Invermay, Mosgiel, New Zealand
                [5 ]ARS-USDA - Agricultural Research Service - United States Department of Agriculture, Animal Improvement Programs Laboratory, Beltsville, Maryland, 20705, USA
                [6 ]United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland, 20705, USA
                [7 ]Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON N1G2W1, Canada
                [8 ]Bioinformatics and Animal Genomics Laboratory, Embrapa Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
                [9 ]School of Veterinary Sciences, The University of Queensland, Gatton, QLD 4343, Australia
                [10 ]School of Rural and Environmental Science, University of New England, Armidale, NSW 2351, Australia
                [11 ]Faculdade de Medicina Veterinária de Araçatuba, UNESP – Univ Estadual Paulista, Araçatuba, São Paulo, 16050-680, Brazil
                Article
                1471-2156-14-52
                10.1186/1471-2156-14-52
                3683327
                23758625
                cc598670-3e74-4dfe-b675-f7459cccd074
                Copyright © 2013 Utsunomiya et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 19 December 2012
                : 5 June 2013
                Categories
                Research Article

                Genetics
                gwas,birth weight,bos primigenius indicus,nellore cattle,stature
                Genetics
                gwas, birth weight, bos primigenius indicus, nellore cattle, stature

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