메뉴 건너뛰기




Volumn 14, Issue , 2013, Pages

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

Author keywords

Effective population size; Genetic diversity; Iberian Peninsula; Local breeds; Pig; Population genetics; SNP

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; BREED DIFFERENCE; CONSERVATION GENETICS; CROSS BREEDING; DEMOGRAPHY; DOMESTIC PIG; EFFECTIVE POPULATION SIZE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC DIFFERENCE; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HOMOZYGOSITY; INBREEDING; MOLECULAR PHYLOGENY; NEAR EXTINCT SPECIES; NONHUMAN; POPULATION STRUCTURE; PORTUGAL; SINGLE NUCLEOTIDE POLYMORPHISM; SPAIN; WILD BOAR;

EID: 84887380604     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-14-106     Document Type: Article
Times cited : (91)

References (65)
  • 2
    • 84888063847 scopus 로고    scopus 로고
    • Building on gender agrobiodiversity and local knowledge
    • FAO
    • FAO Building on gender agrobiodiversity and local knowledge. Food Agr Organ Unit Nation 2006, 1:1-5. FAO.
    • (2006) Food Agr Organ Unit Nation , vol.1 , pp. 1-5
  • 3
    • 68949100366 scopus 로고    scopus 로고
    • Prey and prey-age preference by the iberian wolf canis lupus signatus in a multiple-prey ecosystem
    • Barja I. Prey and prey-age preference by the iberian wolf canis lupus signatus in a multiple-prey ecosystem. Wildl Biol 2009, 15:147-154.
    • (2009) Wildl Biol , vol.15 , pp. 147-154
    • Barja, I.1
  • 4
    • 84864962162 scopus 로고    scopus 로고
    • Progress in oral vaccination against tuberculosis in its main wildlife reservoir in Iberia, the Eurasian wild boar
    • 3400400, 22848869
    • Beltrán-Beck B, Ballesteros C, Vicente J, De la Fuente J, Gortázar C. Progress in oral vaccination against tuberculosis in its main wildlife reservoir in Iberia, the Eurasian wild boar. Vet Med Int 2012, 2012:978501. 3400400, 22848869.
    • (2012) Vet Med Int , vol.2012 , pp. 978501
    • Beltrán-Beck, B.1    Ballesteros, C.2    Vicente, J.3    De la Fuente, J.4    Gortázar, C.5
  • 5
    • 37349111572 scopus 로고    scopus 로고
    • Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication
    • 2674914, 18096118
    • Megens HH-J, Crooijmans RPMA, San Cristobal M, Hui X, Li N, Groenen MAM, Magali SC, Xiao H, Ning L, Martien AMG. Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genet Sel Evol 2008, 40:103-128. 2674914, 18096118.
    • (2008) Genet Sel Evol , vol.40 , pp. 103-128
    • Megens, H.H.-J.1    Crooijmans, R.P.M.A.2    San Cristobal, M.3    Hui, X.4    Li, N.5    Groenen, M.A.M.6    Magali, S.C.7    Xiao, H.8    Ning, L.9    Martien, A.M.G.10
  • 6
    • 84982058358 scopus 로고
    • The increased population of the wild boar (Sus scrofa L.) in Europe
    • Sáez-Royuela C, Telleria JL. The increased population of the wild boar (Sus scrofa L.) in Europe. Mamm Rev 1986, 16:97-101.
    • (1986) Mamm Rev , vol.16 , pp. 97-101
    • Sáez-Royuela, C.1    Telleria, J.L.2
  • 7
    • 34248345430 scopus 로고    scopus 로고
    • Inference of hidden population substructure of the Iberian pig breed using multilocus microsatellite data
    • Alves E, Fernández AI, Barragán C, Ovilo C, Rodríguez C, Silió L. Inference of hidden population substructure of the Iberian pig breed using multilocus microsatellite data. Spanish J Agr Res 2006, 4:37-46.
    • (2006) Spanish J Agr Res , vol.4 , pp. 37-46
    • Alves, E.1    Fernández, A.I.2    Barragán, C.3    Ovilo, C.4    Rodríguez, C.5    Silió, L.6
  • 11
    • 79953297263 scopus 로고    scopus 로고
    • Integrating expression profiling and whole-genome association for dissection of fat traits in a porcine model
    • 10.1194/jlr.M013342, 3284160, 21289033
    • Ponsuksili S, Murani E, Brand B, Schwerin M, Wimmers K. Integrating expression profiling and whole-genome association for dissection of fat traits in a porcine model. J Lipid Res 2011, 52:668-678. 10.1194/jlr.M013342, 3284160, 21289033.
    • (2011) J Lipid Res , vol.52 , pp. 668-678
    • Ponsuksili, S.1    Murani, E.2    Brand, B.3    Schwerin, M.4    Wimmers, K.5
  • 13
    • 84869031473 scopus 로고    scopus 로고
    • Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape
    • 10.1371/journal.pgen.1003100, 3510040, 23209444
    • Bosse M, Megens H-J, Madsen O, Paudel Y, Frantz LAF, Schook LB, Crooijmans RPMA, Groenen MAM. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet 2012, 8:e1003100. 10.1371/journal.pgen.1003100, 3510040, 23209444.
    • (2012) PLoS Genet , vol.8
    • Bosse, M.1    Megens, H.-J.2    Madsen, O.3    Paudel, Y.4    Frantz, L.A.F.5    Schook, L.B.6    Crooijmans, R.P.M.A.7    Groenen, M.A.M.8
  • 14
    • 0242500969 scopus 로고    scopus 로고
    • Novel multilocus measure of linkage disequilibrium to estimate past effective population size
    • 10.1101/gr.387103, 430161, 12654718
    • Hayes BJ, Visscher PM, McPartlan HC, Goddard ME. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 2003, 13:635-643. 10.1101/gr.387103, 430161, 12654718.
    • (2003) Genome Res , vol.13 , pp. 635-643
    • Hayes, B.J.1    Visscher, P.M.2    McPartlan, H.C.3    Goddard, M.E.4
  • 15
    • 52049096371 scopus 로고    scopus 로고
    • Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle
    • 10.1534/genetics.107.084301, 2475750, 18622038
    • PW D, Hayes BJ, Spelman RJ, Goddard ME. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics 2008, 179:1503-1512. 10.1534/genetics.107.084301, 2475750, 18622038.
    • (2008) Genetics , vol.179 , pp. 1503-1512
    • PW, D.1    Hayes, B.J.2    Spelman, R.J.3    Goddard, M.E.4
  • 16
    • 84864954190 scopus 로고    scopus 로고
    • Runs of homozygosity and population history in cattle
    • 3502433, 22888858
    • Purfield DC, Berry DP, McParland S, Bradley DG. Runs of homozygosity and population history in cattle. BMC Genet 2012, 13:70. 3502433, 22888858.
    • (2012) BMC Genet , vol.13 , pp. 70
    • Purfield, D.C.1    Berry, D.P.2    McParland, S.3    Bradley, D.G.4
  • 19
    • 52049099430 scopus 로고    scopus 로고
    • Linkage disequilibrium decay and haplotype block structure in the pig
    • 10.1534/genetics.107.084277, 2390633, 18493072
    • Amaral AJ, Megens H-J, Crooijmans RPMA, Heuven HCM, Groenen MAM. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 2008, 179:569-579. 10.1534/genetics.107.084277, 2390633, 18493072.
    • (2008) Genetics , vol.179 , pp. 569-579
    • Amaral, A.J.1    Megens, H.-J.2    Crooijmans, R.P.M.A.3    Heuven, H.C.M.4    Groenen, M.A.M.5
  • 22
    • 80255122614 scopus 로고    scopus 로고
    • Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing
    • 10.1111/j.1365-2052.2011.02198.x, 22035002
    • Ramos AM, Megens HJ, Crooijmans RPMA, Schook LB, Groenen MAM. Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing. Anim Genet 2011, 42:613-620. 10.1111/j.1365-2052.2011.02198.x, 22035002.
    • (2011) Anim Genet , vol.42 , pp. 613-620
    • Ramos, A.M.1    Megens, H.J.2    Crooijmans, R.P.M.A.3    Schook, L.B.4    Groenen, M.A.M.5
  • 23
    • 84876459242 scopus 로고    scopus 로고
    • Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed
    • 10.1111/age.12001, 23051150
    • Herrero-Medrano JM, Megens HJ, Crooijmans RP, Abellaneda JM, Ramis G. Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed. Anim Genet 2013, 44:259-266. 10.1111/age.12001, 23051150.
    • (2013) Anim Genet , vol.44 , pp. 259-266
    • Herrero-Medrano, J.M.1    Megens, H.J.2    Crooijmans, R.P.3    Abellaneda, J.M.4    Ramis, G.5
  • 25
    • 79955587949 scopus 로고    scopus 로고
    • Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds
    • 10.2527/jas.2010-3249, 21036932
    • Uimari P, Tapio M. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. J Anim Sci 2011, 89:609-614. 10.2527/jas.2010-3249, 21036932.
    • (2011) J Anim Sci , vol.89 , pp. 609-614
    • Uimari, P.1    Tapio, M.2
  • 26
    • 21244479740 scopus 로고    scopus 로고
    • Detecting the number of clusters of individuals using the software structure: a simulation study
    • 10.1111/j.1365-294X.2005.02553.x, 15969739
    • Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 2005, 14:2611-2620. 10.1111/j.1365-294X.2005.02553.x, 15969739.
    • (2005) Mol Ecol , vol.14 , pp. 2611-2620
    • Evanno, G.1    Regnaut, S.2    Goudet, J.3
  • 27
    • 0015070635 scopus 로고
    • Linkage disequilibrium of chromosome segments
    • Sved JA. Linkage disequilibrium of chromosome segments. Theor Popul Biol 1971, 141:125-141.
    • (1971) Theor Popul Biol , vol.141 , pp. 125-141
    • Sved, J.A.1
  • 30
    • 0036208832 scopus 로고    scopus 로고
    • Patterns of linkage disequilibrium in the human genome
    • 10.1038/nrg777, 11967554
    • Ardlie KG, Kruglyak L, Seielstad M. Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 2002, 3:299-309. 10.1038/nrg777, 11967554.
    • (2002) Nat Rev Genet , vol.3 , pp. 299-309
    • Ardlie, K.G.1    Kruglyak, L.2    Seielstad, M.3
  • 31
    • 34147165220 scopus 로고    scopus 로고
    • Recent human effective population size estimated from linkage disequilibrium
    • 10.1101/gr.6023607, 1832099, 17351134
    • Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM. Recent human effective population size estimated from linkage disequilibrium. Genome Res 2007, 17:520-526. 10.1101/gr.6023607, 1832099, 17351134.
    • (2007) Genome Res , vol.17 , pp. 520-526
    • Tenesa, A.1    Navarro, P.2    Hayes, B.J.3    Duffy, D.L.4    Clarke, G.M.5    Goddard, M.E.6    Visscher, P.M.7
  • 33
    • 77958582819 scopus 로고    scopus 로고
    • Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds
    • 10.1371/journal.pone.0013038, 2948016, 20927341
    • Gautier M, Laloë D, Moazami-Goudarzi K. Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PloS One 2010, 5:e13038. 10.1371/journal.pone.0013038, 2948016, 20927341.
    • (2010) PloS One , vol.5
    • Gautier, M.1    Laloë, D.2    Moazami-Goudarzi, K.3
  • 36
    • 84863593260 scopus 로고    scopus 로고
    • Genetic diversity, population structure and subdivision of local Balkan pig breeds in Austria, Croatia, Serbia and Bosnia-Herzegovina and its practical value in conservation programs
    • 10.1186/1297-9686-44-5, 3311151, 22376364
    • Druml T, Salajpal K, Dikic M, Urosevic M, Grilz-Seger G, Baumung R. Genetic diversity, population structure and subdivision of local Balkan pig breeds in Austria, Croatia, Serbia and Bosnia-Herzegovina and its practical value in conservation programs. Genet Sel Evol 2012, 44:5. 10.1186/1297-9686-44-5, 3311151, 22376364.
    • (2012) Genet Sel Evol , vol.44 , pp. 5
    • Druml, T.1    Salajpal, K.2    Dikic, M.3    Urosevic, M.4    Grilz-Seger, G.5    Baumung, R.6
  • 39
    • 78649730822 scopus 로고    scopus 로고
    • Genomic runs of homozygosity record population history and consanguinity
    • 10.1371/journal.pone.0013996, 2981575, 21085596
    • Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. Genomic runs of homozygosity record population history and consanguinity. PloS One 2010, 5:e13996. 10.1371/journal.pone.0013996, 2981575, 21085596.
    • (2010) PloS One , vol.5
    • Kirin, M.1    McQuillan, R.2    Franklin, C.S.3    Campbell, H.4    McKeigue, P.M.5    Wilson, J.F.6
  • 40
    • 0032473955 scopus 로고    scopus 로고
    • Conservation biology: inbreeding leads to extinction
    • Frankham R, Ralls K. Conservation biology: inbreeding leads to extinction. Nature 1998, 392:441-442.
    • (1998) Nature , vol.392 , pp. 441-442
    • Frankham, R.1    Ralls, K.2
  • 41
    • 31344454299 scopus 로고    scopus 로고
    • Estimation of effective population sizes from data on genetic markers
    • Wang J. Estimation of effective population sizes from data on genetic markers. Phil Trans Roy Soc Lond B Biol Sci 2005, 360:1395-1409.
    • (2005) Phil Trans Roy Soc Lond B Biol Sci , vol.360 , pp. 1395-1409
    • Wang, J.1
  • 42
    • 0019771734 scopus 로고
    • Estimation of effective population size from data on linkage disequilibrium
    • Hill WG. Estimation of effective population size from data on linkage disequilibrium. Genet Res 1981, 38:209-216.
    • (1981) Genet Res , vol.38 , pp. 209-216
    • Hill, W.G.1
  • 43
    • 84888067114 scopus 로고    scopus 로고
    • Effective population size of current human population
    • Park L. Effective population size of current human population. Genet Res 2011, 31:1-10.
    • (2011) Genet Res , vol.31 , pp. 1-10
    • Park, L.1
  • 44
    • 80053967558 scopus 로고    scopus 로고
    • Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration
    • 10.1534/genetics.111.132233, 3189803, 21840864
    • Waples RS, England PR. Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration. Genetics 2011, 189:633-644. 10.1534/genetics.111.132233, 3189803, 21840864.
    • (2011) Genetics , vol.189 , pp. 633-644
    • Waples, R.S.1    England, P.R.2
  • 45
    • 84864599767 scopus 로고    scopus 로고
    • Genomic patterns of homozygosity in worldwide human populations
    • 10.1016/j.ajhg.2012.06.014, 3415543, 22883143
    • Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet 2012, 91:275-292. 10.1016/j.ajhg.2012.06.014, 3415543, 22883143.
    • (2012) Am J Hum Genet , vol.91 , pp. 275-292
    • Pemberton, T.J.1    Absher, D.2    Feldman, M.W.3    Myers, R.M.4    Rosenberg, N.A.5    Li, J.Z.6
  • 47
    • 78649433120 scopus 로고    scopus 로고
    • Genetic diversity of wild boar populations and domestic pig breeds (Sus scrofa) in South-western Europe
    • Alves PC, Pinheiro I, Godinho R, Vicente J, Gortázar C, Scandura M. Genetic diversity of wild boar populations and domestic pig breeds (Sus scrofa) in South-western Europe. Biol J Linn Soc 2010, 101:797-822.
    • (2010) Biol J Linn Soc , vol.101 , pp. 797-822
    • Alves, P.C.1    Pinheiro, I.2    Godinho, R.3    Vicente, J.4    Gortázar, C.5    Scandura, M.6
  • 49
    • 0344441428 scopus 로고    scopus 로고
    • Estimating recombination rates from population-genetic data
    • 10.1038/nrg1227, 14631356
    • Stumpf MPH, McVean GAT. Estimating recombination rates from population-genetic data. Nat Rev Genet 2003, 4:959-968. 10.1038/nrg1227, 14631356.
    • (2003) Nat Rev Genet , vol.4 , pp. 959-968
    • Stumpf, M.P.H.1    McVean, G.A.T.2
  • 50
    • 84954949379 scopus 로고
    • The systematics of the wildboar (Sus scrofa L.) in Italy
    • Apollonio M, Randi E, Toso S. The systematics of the wildboar (Sus scrofa L.) in Italy. Bollettino di Zoologia 1988, 3:213-221.
    • (1988) Bollettino di Zoologia , vol.3 , pp. 213-221
    • Apollonio, M.1    Randi, E.2    Toso, S.3
  • 54
    • 84880514467 scopus 로고    scopus 로고
    • A population genetics view of animal domestication
    • 10.1016/j.tig.2013.01.003, 23415592
    • Larson G, Burger J. A population genetics view of animal domestication. Trends Genet 2013, 29:197-205. 10.1016/j.tig.2013.01.003, 23415592.
    • (2013) Trends Genet , vol.29 , pp. 197-205
    • Larson, G.1    Burger, J.2
  • 56
    • 0141525024 scopus 로고    scopus 로고
    • Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations
    • 10.1046/j.1365-2052.2003.01010.x, 14510666
    • Alves E, Ovilo C, Rodríguez MC, Silió L. Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Anim Genet 2003, 34:319-324. 10.1046/j.1365-2052.2003.01010.x, 14510666.
    • (2003) Anim Genet , vol.34 , pp. 319-324
    • Alves, E.1    Ovilo, C.2    Rodríguez, M.C.3    Silió, L.4
  • 57
    • 84855642252 scopus 로고    scopus 로고
    • Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds
    • 10.1111/j.1365-2052.2011.02222.x, 22221023
    • Van Asch B, Pereira F, Santos LS, Carneiro J, Santos N, Amorim A. Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds. Anim Genet 2012, 43:35-41. 10.1111/j.1365-2052.2011.02222.x, 22221023.
    • (2012) Anim Genet , vol.43 , pp. 35-41
    • Van Asch, B.1    Pereira, F.2    Santos, L.S.3    Carneiro, J.4    Santos, N.5    Amorim, A.6
  • 58
    • 0000655270 scopus 로고
    • Genetic distance between populations
    • Nei M. Genetic distance between populations. Am Nat 1972, 106:283-292.
    • (1972) Am Nat , vol.106 , pp. 283-292
    • Nei, M.1
  • 59
    • 18744382780 scopus 로고    scopus 로고
    • PowerMarker: an integrated analysis environment for genetic marker analysis
    • 10.1093/bioinformatics/bti282, 15705655
    • Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 2005, 21:2128-2129. 10.1093/bioinformatics/bti282, 15705655.
    • (2005) Bioinformatics , vol.21 , pp. 2128-2129
    • Liu, K.1    Muse, S.V.2
  • 60
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
    • 10.1093/molbev/msm092, 17488738
    • Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 61
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • 1461096, 10835412
    • Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959. 1461096, 10835412.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 62
    • 84882759440 scopus 로고    scopus 로고
    • Structure harvester: a website and program for visualizing structure output and implementing the Evanno method
    • Earl DA, vonHoldt BM. Structure harvester: a website and program for visualizing structure output and implementing the Evanno method. Conservat Genet Resour 2011, 4:359-361.
    • (2011) Conservat Genet Resour , vol.4 , pp. 359-361
    • Earl, D.A.1    vonHoldt, B.M.2
  • 63
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • 10.1038/ng1847, 16862161
    • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006, 38:904-909. 10.1038/ng1847, 16862161.
    • (2006) Nat Genet , vol.38 , pp. 904-909
    • Price, A.L.1    Patterson, N.J.2    Plenge, R.M.3    Weinblatt, M.E.4    Shadick, N.A.5    Reich, D.6
  • 65
    • 13444269543 scopus 로고    scopus 로고
    • Haploview: analysis and visualization of LD and haplotype maps
    • 10.1093/bioinformatics/bth457, 15297300
    • Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21:263-265. 10.1093/bioinformatics/bth457, 15297300.
    • (2005) Bioinformatics , vol.21 , pp. 263-265
    • Barrett, J.C.1    Fry, B.2    Maller, J.3    Daly, M.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.