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      Genome-wide association study of the backfat thickness trait in two pig populations

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          Abstract

          Backfat thickness is a good predictor of carcass lean content, an economically important trait, and a main breeding target in pig improvement. In this study, the candidate genes and genomic regions associated with the tenth rib backfat thickness trait were identified in two independent pig populations, using a genome-wide association study of porcine 60K SNP genotype data applying the compressed mixed linear model (CMLM) statistical method. For each population, 30 most significant single-nucleotide polymorphisms (SNPs) were selected and SNP annotation implemented using Sus scrofa Build 10.2. In the first population, 25 significant SNPs were distributed on seven chromosomes, and SNPs on SSC1 and SSC7 showed great significance for fat deposition. The most significant SNP (ALGA0006623) was located on SSC1, upstream of the MC4R gene. In the second population, 27 significant SNPs were recognized by annotation, and 12 SNPs on SSC12 were related to fat deposition. Two haplotype blocks, M1GA0016251-MARC0075799 and ALGA0065251-MARC0014203-M1GA0016298-ALGA0065308, were detected in significant regions where the PIPNC1 and GH1 genes were identified as contributing to fat metabolism. The results indicated that genetic mechanism regulating backfat thickness is complex, and that genome-wide associations can be affected by populations with different genetic backgrounds.

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          Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

          Background The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.
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            Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs

            Background The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs. Methodology/Principal Findings Using Illumina's PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body size and several FL structure traits), and some HOXA family genes (for overall leg action). The candidate regions responsible for body conformation and FL structure soundness did not overlap greatly which implied that these traits were controlled by different genes. Functional clustering analyses classified the genes into categories related to bone and cartilage development, muscle growth and development or the insulin pathway suggesting the traits are regulated by common pathways or gene networks that exert roles at different spatial and temporal stages. Conclusions/Significance This study is one of the earliest GWA reports on important quantitative traits in pigs, and the findings will contribute to the further biological function analysis of the identified candidate genes and potential utilization of them in marker assisted selection.
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              An atlas of DNA methylomes in porcine adipose and muscle tissues

              It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DNA immunoprecipitation libraries, and provide a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth.
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                Author and article information

                Journal
                Front. Agr. Sci. Eng.
                FASE
                CN10-1204/S
                Frontiers of Agricultural Science and Engineering
                Higher Education Press (4 Huixin Dongjie, Chaoyang District, Beijing 100029, China )
                2095-7505
                2014
                : 1
                : 2
                : 91-95
                Affiliations
                [1]1. Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
                [2]2. Department of Animal Science, Iowa State University, Ames, IA 50011, USA
                [3]3. Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
                Author notes
                fanbin@mail.hzau.edu.cn
                Article
                10.15302/J-FASE-2014005
                9ea0b889-829d-4899-bc68-67af69050943
                Copyright @ 2014

                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
                : 15 March 2014
                : 30 March 2014
                Categories
                LETTER

                backfat thickness,SNP chip,genome-wide association study,compressed mixed linear model,pig

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