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Zhang C, Plastow G. Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock. Curr Genomics 2011; 12:138-46. [PMID: 21966252 PMCID: PMC3129048 DOI: 10.2174/138920211795564386] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 01/21/2011] [Accepted: 01/22/2011] [Indexed: 11/22/2022] Open
Abstract
We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (F(IS)), population differentiation (F(ST)), and Nei's genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher F(IS), and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies.
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Affiliation(s)
| | - Graham Plastow
- 1400 College Plaza, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8, Canada
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Ramos AM, Crooijmans RPMA, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Churcher C, Clark R, Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TPL, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RT, Schook LB, Groenen MAM. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 2009; 4:e6524. [PMID: 19654876 PMCID: PMC2716536 DOI: 10.1371/journal.pone.0006524] [Citation(s) in RCA: 464] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 06/21/2009] [Indexed: 12/02/2022] Open
Abstract
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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Affiliation(s)
- Antonio M. Ramos
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | | | - Nabeel A. Affara
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andreia J. Amaral
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | - Alan L. Archibald
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Midlothian, United Kingdom
| | - Jonathan E. Beever
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | | | - Carol Churcher
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Richard Clark
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Patrick Dehais
- INRA, Laboratoire de Génétique Cellulaire, Castanet Tolosan, France
| | - Mark S. Hansen
- Illumina, Inc., San Diego, California, United States of America
| | - Jakob Hedegaard
- Aarhus University, Faculty of Agricultural Sciences, Tjele, Denmark
| | - Zhi-Liang Hu
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Hindrik H. Kerstens
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | - Andy S. Law
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Midlothian, United Kingdom
| | - Hendrik-Jan Megens
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | - Denis Milan
- INRA, Laboratoire de Génétique Cellulaire, Castanet Tolosan, France
| | - Danny J. Nonneman
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Gary A. Rohrer
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Max F. Rothschild
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Tim P. L. Smith
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Curt P. Van Tassell
- Bovine Functional Genomics Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, Maryland, United States of America
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Ralph T. Wiedmann
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Lawrence B. Schook
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Martien A. M. Groenen
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
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Vingborg RKK, Gregersen VR, Zhan B, Panitz F, Høj A, Sørensen KK, Madsen LB, Larsen K, Hornshøj H, Wang X, Bendixen C. A robust linkage map of the porcine autosomes based on gene-associated SNPs. BMC Genomics 2009; 10:134. [PMID: 19327136 PMCID: PMC2674067 DOI: 10.1186/1471-2164-10-134] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 03/27/2009] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived from expressed sequence tags (ESTs) and genomic shotgun sequences. RESULTS Linkage maps of all 18 porcine autosomes were constructed based on 456 gene-associated and six porcine EST-based SNPs. The total length of the averaged-sex whole porcine autosome was estimated to 1,711.8 cM resulting in an average SNP spacing of 3.94 cM. The female and male maps were estimated to 2,336.1 and 1,441.5 cM, respectively. The gene order was validated through comparisons to the cytogenetic and/or physical location of 203 genes, linkage to evenly spaced microsatellite markers as well as previously reported conserved synteny. A total of 330 previously unmapped genes and ESTs were mapped to the porcine autosome while ten genes were mapped to unexpected locations. CONCLUSION The linkage map presented here shows high accuracy in gene order. The pedigree family network as well as the large amount of meiotic events provide good reliability and make this map suitable for QTL and association studies. In addition, the linkage to the RH-map of microsatellites makes it suitable for comparison to other QTL studies.
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Affiliation(s)
- Rikke K K Vingborg
- Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark.
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Du HL, Chen J, Zhang YS, Zhang XQ. Molecular cloning, mapping, and polymorphism of the porcine SCG2 gene. Biochem Genet 2008; 46:369-79. [PMID: 18278550 DOI: 10.1007/s10528-008-9153-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 10/12/2007] [Indexed: 10/22/2022]
Abstract
The secretogranin II (SCG2) gene is associated with the synthesis and secretion of follicle-stimulating hormone and luteinizing hormone. In the present study, we have determined the complete cDNA sequence of pig SCG2, which was submitted to GenBank with accession no. AY870646. Its complete open reading frame of 1,851 nucleotides encodes 616 amino acids. The predicted protein shares 80-87% identity with mouse, human, and bovine SCG2 proteins, and all four species share almost complete identity in the secretoneurin and EM66 domains. Pig SCG2 is a protein of 589 amino acids and 68,132 Da, preceded by a signal peptide of 27 residues. It contains nine pairs of dibasic residues, which are used as potential cleavage sites for generation of physiologically active peptides. Analysis of the SCG2 gene across the INRA-Minnesota porcine radiation hybrid panel indicates close linkage with microsatellite marker SW2608, located on Sus scrofa chromosome 15 (SSC15) q25, which harbors several QTL for ovulation rate and meat quality. Comparative sequencing and EST analysis revealed nine SNPs in porcine SCG2 cDNA, including seven SNPs in the coding region and two SNPs in the 3' UTR. Four nonsynonymous SNPs (G622A, G1671T, C1718T, and A1790C) resulted in amino acid substitutions of Ala-->Thr, Glu-->Asp, Pro-->Leu, and Asn-->Thr, respectively.
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Affiliation(s)
- Hong-Li Du
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510640, P.R. China
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5
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LIU DW, ZHANG H, WU ZF, LI JQ, YANG GF, ZHANG XQ. Identification of SNPs and Their Effects on Swine Growth and Carcass Traits for Porcine IGFBP-3 Gene. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1671-2927(08)60062-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhang Y, Du H, Chen J, Yang G, Zhang X. Porcine growth differentiation factor 9 gene polymorphisms and their associations with litter size. J Genet Genomics 2008; 35:163-9. [DOI: 10.1016/s1673-8527(08)60022-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 07/05/2007] [Accepted: 07/09/2007] [Indexed: 12/27/2022]
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7
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Wimmers K, Murani E, Te Pas MFW, Chang KC, Davoli R, Merks JWM, Henne H, Muraniova M, da Costa N, Harlizius B, Schellander K, Böll I, Braglia S, de Wit AAC, Cagnazzo M, Fontanesi L, Prins D, Ponsuksili S. Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition. Anim Genet 2007; 38:474-84. [PMID: 17697135 DOI: 10.1111/j.1365-2052.2007.01639.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain x (Landrace x Large White), Duroc x (Landrace x Large White) as well as in an experimental F(2) population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human-porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of < or = 0.05; PDGFRA revealed no association reaching the P < or = 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical-genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.
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Affiliation(s)
- K Wimmers
- Research Institute for the Biology of Farm Animals (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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8
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Richardson MK, Crooijmans RPMA, Groenen MAM. Sequencing and genomic annotation of the chicken (Gallus gallus) Hox clusters, and mapping of evolutionarily conserved regions. Cytogenet Genome Res 2007; 117:110-9. [PMID: 17675851 DOI: 10.1159/000103171] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 09/29/2006] [Indexed: 11/19/2022] Open
Abstract
Hox genes encode transcription factors that are involved in the regulation of normal development and are mutated in some diseases and malformations. Chicken HOX genes have been extensively studied in the chick limb and other developmental models. To date while the chicken HOXA cluster has been completely sequenced many other chicken HOX genes are known only from partial mRNAs or unfinished genome assemblies. Furthermore, although a finished sequence of the HOXA cluster is available, the sequence has not yet been annotated. We have therefore manually annotated the available HOX sequences and improved the sequences by sequencing PCR fragments that bridge existing gaps in the genome sequences. These sequences complement the published sequences, including the currently incomplete WashUC Gallus_gallus-2.1 build, to give an improved coverage of the cluster. We used phylogenetic footprinting to map the genomic location of 398 Ultra Conserved Regions in the HOX complex 248 of which do not overlap with any known annotated coding exon. These included the hox-related microRNAs miR-10 and miR-196. The chicken HOX clusters appear to be broadly comparable to their human counterparts. A few human orthologues were not recovered from the chicken, presumably because of incomplete sequence.
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Affiliation(s)
- M K Richardson
- Department of Integrative Zoology, Institute of Biology, Leiden University, Leiden, The Netherlands
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9
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Liu D, Zhang Y, Du Y, Yang G, Zhang X. Identification and characterization of single nucleotide polymorphisms in 6 growth-correlated genes in porcine by denaturing high performance liquid chromatography. ACTA ACUST UNITED AC 2007; 18:220-7. [PMID: 17454007 DOI: 10.1080/10425170601150839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The growth-correlated genes that are part of the neuroendocrine growth axis play crucial roles in the regulation of growth and development of pig. The identification of genetic polymorphisms in these genes will enable the scientist to evaluate the biological relevance of such polymorphisms and to gain a better understanding of quantitative traits like growth. In the present study, seven pairs of primers were designed to obtain unknown sequences of growth-correlated genes, and other 25 pairs of primers were designed to identify single nucleotide polymorphisms (SNP) using the denaturing high-performance liquid chromatography (DHPLC) technology in four pig breeds (Duroc, Landrace, Lantang and Wuzhishan), significantly differing in growth and development characteristics. A total of 101 polymorphisms were discovered in 10,707 base pairs (bp) from six genes of the ghrelin (GHRL), leptin (LEP), insulin-like growth factor II (IGF-II), insulin-like growth factor binding protein 2 (IGFBP-2), insulin-like growth factor binding protein 3 (IGFBP-3), and somatostatin (SS). The observed average distances between the SNP in the 5'UTR, coding regions, introns and 3'UTR were 134, 521, 81 and 92 bp, respectively. Four SNPs were found in the coding regions of IGF-II, IGFBP-2 and LEP, respectively. Two synonymous mutations were obtained in IGF-II and LEP genes respectively, and two non-synonymous were found in IGFBP-2 and LEP genes, respectively. Seven other mutations were also observed. Thirty-two PCR-RFLP markers were found among 101 polymorphisms of the six genes. The SNP discovered in this study would provide suitable markers for association studies of candidate genes with growth related traits in pig.
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Affiliation(s)
- Dewu Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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Jungerius BJ, Gu J, Crooijmans RPMA, van der Poel JJ, Groenen MAM, van Oost BA, Te Pas MFW. ESTIMATION OF THE EXTENT OF LINKAGE DISEQUILIBRIUM IN SEVEN REGIONS OF THE PORCINE GENOME. Anim Biotechnol 2007; 16:41-54. [PMID: 28881173 DOI: 10.1081/abio-200053402] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Linkage disequilibrium (LD) refers to the correlation among neighboring alleles, reflecting non-random patterns of association between alleles at (nearby) loci. A better understanding of LD in the porcine genome is of direct relevance for identification of genes and mutations with a certain effect on the traits of interest. Here, 215 SNPs in seven genomic regions were genotyped in individuals of three breeds. Pairwise linkage disequilibrium was calculated for all marker pairs. To estimate the extent of LD, all pairwise LD values were plotted against the distance between the markers. Based on SNP markers in four genomic regions analyzed in three panels from populations of Large White, Dutch Landrace, and Meishan origin, useful LD is estimated to extend for approximately 40 to 60 kb in the porcine genome.
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Affiliation(s)
- Bart J Jungerius
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | - Jingjing Gu
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | | | - Jan J van der Poel
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | - Martien A M Groenen
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | - Bernard A van Oost
- b Department of Laboratory Animal Sciences , Utrecht University , Utrecht , Netherlands
| | - Marinus F W Te Pas
- c Animal Sciences Group , Wageningen University and Research Centre , Lelystad , Netherlands
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Sawera M, Cirera S, Jørgensen CB, Gorodkin J, Fredholm M. Linkage mapping of gene-associated SNPs to pig chromosome 11. Anim Genet 2006; 37:199-204. [PMID: 16734676 DOI: 10.1111/j.1365-2052.2006.01419.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single nucleotide polymorphisms (SNPs) were discovered in porcine expressed sequence tags (ESTs) orthologous to genes from human chromosome 13 (HSA13) and predicted to be located on pig chromosome 11 (SSC11). The SNPs were identified as sequence variants in clusters of EST sequences from pig cDNA libraries constructed in the Sino-Danish pig genome project. In total, 312 human gene sequences from HSA13 were used for similarity searches in our pig EST database. Pig ESTs showing significant similarity with HSA13 genes were clustered and candidate SNPs were identified. Allele frequencies for 26 SNPs were estimated in a group of 80 unrelated pigs from Danish commercial pig breeds: Duroc, Hampshire, Landrace and Large White. Eighteen of the 26 SNPs genotyped in the PiGMaP Reference Families were mapped by linkage analysis to SSC11. The EST-based SNPs published here are new genetic markers useful for linkage and association studies in commercial and experimental pig populations. This study represents the first gene-associated SNP linkage map of pig chromosome 11 and adds new comparative mapping information between SSC11 and HSA13. Furthermore, our data facilitate future studies aimed at the identification of interesting regions on pig chromosome 11, positional cloning and fine mapping of quantitative trait loci in pig.
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Affiliation(s)
- M Sawera
- Division of Genetics, IBHV, The Royal Veterinary and Agricultural University, Frederiksberg C, 1870, Denmark
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12
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Ponsuksili S, Chomdej S, Murani E, Bläser U, Schreinemachers HJ, Schellander K, Wimmers K. SNP detection and genetic mapping of porcine genes encoding enzymes in hepatic metabolic pathways and evaluation of linkage with carcass traits. Anim Genet 2006; 36:477-83. [PMID: 16293120 DOI: 10.1111/j.1365-2052.2005.01351.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have previously identified and mapped porcine expressed sequence tags (ESTs) derived from genes that are preferentially expressed in liver. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in porcine genes encoding enzymes in hepatic metabolic pathways and use the SNPs for mapping. Furthermore, these genes, which are involved in utilization and partitioning of nutrients, were examined for their effects on carcass and meat quality traits by linkage analyses. In total, 100 ESTs were screened for SNPs by single strand conformation polymorphism analyses across a diverse panel of animals with a 36% success rate. Twelve of 36 polymorphic loci segregated in a three-generation Duroc x Berlin Miniature Pig (F2) resource population, the DUMI resource population, and were genetically mapped. Interval mapping of the corresponding chromosomes was performed to verify mapping of the genes within quantitative trait loci (QTL) regions detected in this resource population. QTL with genome-wide significance were detected in the vicinity of GNMT, ESTL147 and HGD. These loci therefore are positional candidate genes.
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Affiliation(s)
- S Ponsuksili
- Institute of Animal Breeding and Genetics, University of Bonn, 53115 Bonn, Germany
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13
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Nie Q, Sun B, Zhang D, Luo C, Ishag NA, Lei M, Yang G, Zhang X. High Diversity of the Chicken Growth Hormone Gene and Effects on Growth and Carcass Traits. J Hered 2005; 96:698-703. [PMID: 16267170 DOI: 10.1093/jhered/esi114] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The chicken growth hormone (cGH) gene plays a crucial role in controlling growth and metabolism, leading to potential correlations between cGH polymorphisms and economic traits. In this study, DNA from four divergent chicken breeds were screened for single nucleotide polymorphisms (SNPs) in the cGH gene using denaturing high-performance liquid chromatography and sequencing. A total of 46 SNPs were identified, of which 4 were in the 5' untranslated region, 1 in the 3' untranslated region, 5 in exons (two of which are nonsynonymous), with the remaining 36 in introns. The nucleotide diversity in the cGH gene ( theta = 2.7 x 10(-3)) was higher than that reported for other chicken genes, even within the same breeds. The associations of five of these SNPs and their haplotypes with chicken growth and carcass traits were determined using polymerase chain reaction-restriction fragment length polymorphism analysis in a F2 resource population cross of two of the four chicken breeds (White Recessive Rock and Xinghua). This analysis shows that, among other correlations, G+1705A was significantly associated with body weight at all ages measured, shank length at three of four ages measured, and average daily gain within weeks 0 to 4. Thus, this cGH polymorphism, or another polymorphism that is in linkage disequilibrium with G+1705A, appears to correspond to a significant growth-related quantitative trait locus difference between the two breeds used to construct the resource population.
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Affiliation(s)
- Q Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
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14
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Goffaux F, China B, Dams L, Clinquart A, Daube G. Development of a genetic traceability test in pig based on single nucleotide polymorphism detection. Forensic Sci Int 2005; 151:239-47. [PMID: 15939158 DOI: 10.1016/j.forsciint.2005.02.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 02/22/2005] [Accepted: 02/22/2005] [Indexed: 11/16/2022]
Abstract
In order to assure traceability along the meat transformation process, a powerful system is required. The administrative traceability shows limits that the use of genetic markers could overcome. The individual genomes contain sequence differences, basis of the genetic polymorphism of which the genetic markers are the witnesses. Among them, two classes seem to dominate on the traceability field: the microsatellites and the single nucleotide polymorphisms (SNP). The aim of this work was to develop a genetic traceability test in pig based on SNPs mainly located in 5' and 3' untranslated regions (UTRs). A set of 21 SNP markers including new SNPs identified in this study and SNPs previously described was selected. A genotyping assay was performed on 96 individuals representing the major crossbred of the pig population in Belgium. Results showed that all individuals tested presented a different genotype. This genotyping method might help the administrative system to guarantee the traceability of pork meat along the transformation process.
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Affiliation(s)
- F Goffaux
- Department of Food Sciences, Faculty of Veterinary Medicine, University of Liège, Boulevard de Colonster, 20/B43bis, 4000 Liege, Belgium
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Current Research Status for Economically Important and Disease Related Genes in Major Livestock Species. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2005. [DOI: 10.5187/jast.2005.47.3.325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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