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Volumn 107, Issue 3, 2011, Pages 256-264

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

Author keywords

Iberian pig; Next generation sequencing; Nucleotide diversity; Pig

Indexed keywords

ANIMAL; ARTICLE; CHROMOSOME MAP; DNA SEQUENCE; FEMALE; GENETIC VARIABILITY; GENETICS; GENOME; GENOMICS; INBREEDING; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE;

EID: 84856373123     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2011.13     Document Type: Article
Times cited : (15)

References (33)
  • 1
    • 79953706639 scopus 로고    scopus 로고
    • Genome wide footprints of pig domestication revealed through massive parallel sequencing of pooled dna
    • Amaral A, Ferretti L, Megens H-J, Crooijmans R, Nie H, Ramos-Onsins SE et al. (2011). Genome wide footprints of pig domestication revealed through massive parallel sequencing of pooled DNA. Plos One (in press).
    • (2011) Plos One
    • Amaral, A.1    Ferretti, L.2    Megens, H.-J.3    Crooijmans, R.4    Nie, H.5    Ramos-Onsins, S.E.6
  • 2
    • 70349574066 scopus 로고    scopus 로고
    • Application of massive parallel sequencing to whole genome snp discovery in the porcine genome
    • Amaral A, Megens H-J, Kerstens H, Heuven H, Dibbits B, Crooijmans R et al. (2009). Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics 10: 374.
    • (2009) BMC Genomics , vol.10 , pp. 374
    • Amaral, A.1    Megens, H.-J.2    Kerstens, H.3    Heuven, H.4    Dibbits, B.5    Crooijmans, R.6
  • 3
    • 78751664988 scopus 로고    scopus 로고
    • To pool, or not to pool?
    • Cutler DJ, Jensen JD (2010). To pool, or not to pool? Genetics 186: 41-43.
    • (2010) Genetics , vol.186 , pp. 41-43
    • Cutler, D.J.1    Jensen, J.D.2
  • 4
    • 61449135985 scopus 로고    scopus 로고
    • Fast and flexible simulation of dna sequence data
    • Chen GK, Marjoram P, Wall JD (2009). Fast and flexible simulation of DNA sequence data. Genome Res 19: 136-142.
    • (2009) Genome Res , vol.19 , pp. 136-142
    • Chen, G.K.1    Marjoram, P.2    Wall, J.D.3
  • 5
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput dna sequencing
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008). Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: el05.
    • (2008) Nucleic Acids Res , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 7
    • 66449105907 scopus 로고    scopus 로고
    • The different levels of genetic diversity in sex chromosomes and autosomes
    • Ellegren H (2009). The different levels of genetic diversity in sex chromosomes and autosomes. Trends Genet 25: 278-284.
    • (2009) Trends Genet , vol.25 , pp. 278-284
    • Ellegren, H.1
  • 8
    • 77951886445 scopus 로고    scopus 로고
    • Haubold B, Pfaffelhuber P, Lynch M (2010). MlRho-a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Mol Ecol 19(Suppl 1): 277-284.
    • Haubold, B.1    Pfaffelhuber, P.2    Lynch, M.3
  • 10
    • 46449121800 scopus 로고    scopus 로고
    • Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
    • Hellmann I, Mang Y, Gu Z, Li P, de la Vega FM, Clark AG et al.(2008). Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res 18: 1020-1029.
    • (2008) Genome Res , vol.18 , pp. 1020-1029
    • Hellmann, I.1    Mang, Y.2    Gu, Z.3    Li, P.4    De La Vega, F.M.5    Clark, A.G.6
  • 11
    • 50649122770 scopus 로고    scopus 로고
    • Eagle view: A genome assembly viewer for next-generation sequencing technologies
    • Huang W, Marth G (2008). Eagle View: a genome assembly viewer for next-generation sequencing technologies. Genome Res 18: 1538-1543.
    • (2008) Genome Res , vol.18 , pp. 1538-1543
    • Huang, W.1    Marth, G.2
  • 12
    • 0028304617 scopus 로고
    • How can the low levels of dna sequence variation in regions of the drosophila genome with low recombination rates be explained?
    • Hudson RR (1994). How can the low levels of DNA sequence variation in regions of the drosophila genome with low recombination rates be explained? Proc Natl Acad Sci USA 91: 6815-6818.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 6815-6818
    • Hudson, R.R.1
  • 13
    • 0023339852 scopus 로고
    • A test of neutral molecular evolution based on nucleotide data
    • Hudson RR, Kreitman M, Aguade M (1987). A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
    • (1987) Genetics , vol.116 , pp. 153-159
    • Hudson, R.R.1    Kreitman, M.2    Aguade, M.3
  • 14
    • 61549106577 scopus 로고    scopus 로고
    • Population genetic inference from resequencing data
    • Jiang R, Tavare S, Marjoram P (2009). Population genetic inference from resequencing data. Genetics 181: 187-197.
    • (2009) Genetics , vol.181 , pp. 187-197
    • Jiang, R.1    Tavare, S.2    Marjoram, P.3
  • 15
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (G+c)-biased genomes
    • Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ (2009). Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Meth 6: 291-295.
    • (2009) Nat Meth , vol.6 , pp. 291-295
    • Kozarewa, I.1    Ning, Z.2    Quail, M.A.3    Sanders, M.J.4    Berriman, M.5    Turner, D.J.6
  • 16
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short dna sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 17
    • 54149110986 scopus 로고    scopus 로고
    • Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects
    • Lynch M (2008). Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects. Mol Biol Evol 25: 2409-2419.
    • (2008) Mol Biol Evol , vol.25 , pp. 2409-2419
    • Lynch, M.1
  • 19
    • 75449118754 scopus 로고    scopus 로고
    • A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic qtl
    • Noguera JL, Rodriguez C, Varona L, Tomas A, Munoz G, Ramirez O et al. (2009). A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL. BMC Genomics 10: 636.
    • (2009) BMC Genomics , vol.10 , pp. 636
    • Noguera, J.L.1    Rodriguez, C.2    Varona, L.3    Tomas, A.4    Munoz, G.5    Ramirez, O.6
  • 21
    • 33845782399 scopus 로고    scopus 로고
    • Unexpected high polymorphism at the fabp4 gene unveils a complex history for pig populations
    • Ojeda A, Rozas J, Folch JM, Perez-Enciso M (2006). Unexpected High Polymorphism at the FABP4 Gene Unveils a Complex History for Pig Populations. Genetics 174: 2119-2127.
    • (2006) Genetics , vol.174 , pp. 2119-2127
    • Ojeda, A.1    Rozas, J.2    Folch, J.M.3    Perez-Enciso, M.4
  • 22
  • 23
    • 17444453832 scopus 로고    scopus 로고
    • A qtl on pig chromosome 4 affects fatty acid metabolism: Evidence from an iberian by landrace intercross
    • Pérez-Enciso M, Clop A, Noguera JL, Ovilo C, Coll A, Folch JM et al. (2000). A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross. J Anim Sci 78: 2525-2531.
    • (2000) J Anim Sci , vol.78 , pp. 2525-2531
    • Pérez-Enciso, M.1    Clop, A.2    Noguera, J.L.3    Ovilo, C.4    Coll, A.5    Folch, J.M.6
  • 24
    • 77649263292 scopus 로고    scopus 로고
    • Population genetic inference from genomic sequence variation
    • Pool JE, Hellmann I, Jensen JD, Nielsen R (2010). Population genetic inference from genomic sequence variation. Genome Res 20: 291-300.
    • (2010) Genome Res , vol.20 , pp. 291-300
    • Pool, J.E.1    Hellmann, I.2    Jensen, J.D.3    Nielsen, R.4
  • 25
    • 36549065630 scopus 로고    scopus 로고
    • Population size changes reshape genomic patterns of diversity
    • Pool JE, Nielsen R (2007). Population size changes reshape genomic patterns of diversity. Evolution 61: 3001-3006.
    • (2007) Evolution , vol.61 , pp. 3001-3006
    • Pool, J.E.1    Nielsen, R.2
  • 26
    • 57049122389 scopus 로고    scopus 로고
    • Durbin ret al. (2008). A large genome center's improvements to the illumina sequencing system
    • Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin Ret al. (2008). A large genome center's improvements to the Illumina sequencing system. Nat Methods 5:1005-1010.
    • Nat Methods , vol.5 , pp. 1005-1010
    • Quail, M.A.1    Kozarewa, I.2    Smith, F.3    Scally, A.4    Stephens, P.J.5
  • 27
    • 38749091304 scopus 로고    scopus 로고
    • Pyrobayes: An improved base caller for snp discovery in pyrosequences
    • Quinlan AR, Stewart DA, Stromberg MP, Marth GT (2008). Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 5: 179-181.
    • (2008) Nat Methods , vol.5 , pp. 179-181
    • Quinlan, A.R.1    Stewart, D.A.2    Stromberg, M.P.3    Marth, G.T.4
  • 28
    • 68349137618 scopus 로고    scopus 로고
    • Design of a high density snp genotyping assay in the pig using snps identified and characterized by next generation sequencing technology
    • Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE et al. (2009). Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4: e6524.
    • (2009) Plos One , vol.4 , pp. e6524
    • Ramos, A.M.1    Crooijmans, R.P.2    Affara, N.A.3    Amaral, A.J.4    Archibald, A.L.5    Beever, J.E.6
  • 30
    • 75649094779 scopus 로고    scopus 로고
    • Population genomic inferences from sparse high-throughput sequencing of two populations of drosophila melanogaster
    • Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M et al. (2009). Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol 1: 449-465.
    • (2009) Genome Biol Evol , vol.1 , pp. 449-465
    • Sackton, T.B.1    Kulathinal, R.J.2    Bergman, C.M.3    Quinlan, A.R.4    Dopman, E.B.5    Carneiro, M.6
  • 31
    • 0000192787 scopus 로고    scopus 로고
    • A comparison of carcass, meat quality and histochemical characteristics of iberian and landrace pigs
    • Serra X, Gil F, Pérez-Enciso M, Oliver MA, Vazquez JM, Gispert M et al. (1998). A comparison of carcass, meat quality and histochemical characteristics of Iberian and Landrace pigs. LivestProdSci 56: 215-223.
    • (1998) Livestprodsci , vol.56 , pp. 215-223
    • Serra, X.1    Gil, F.2    Pérez-Enciso, M.3    Oliver, M.A.4    Vazquez, J.M.5    Gispert, M.6
  • 32
    • 0034515464 scopus 로고    scopus 로고
    • Genealogical analysis of a closed herd of black hairless iberian pigs
    • Toro M, Rodrigánez J, Silio L, Rodriguez M (2000). Genealogical analysis of a closed herd of black hairless Iberian pigs. Conservation Biol 14: 1843-1851.
    • (2000) Conservation Biol , vol.14 , pp. 1843-1851
    • Toro, M.1    Rodrigánez, J.2    Silio, L.3    Rodriguez, M.4


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