메뉴 건너뛰기




Volumn 12, Issue 4, 2012, Pages 753-770

The design and cross-population application of a genome-wide SNP chip for the great tit Parus major

Author keywords

Marker development; Next generation sequencing; NGS; Population genetics

Indexed keywords

ANIMAL; ARTICLE; DNA MICROARRAY; DNA SEQUENCE; GENE FREQUENCY; GENETICS; GENOMICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; PHENOTYPE; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; SONGBIRD;

EID: 84862157418     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2012.03141.x     Document Type: Article
Times cited : (46)

References (46)
  • 2
  • 3
    • 78349241341 scopus 로고    scopus 로고
    • A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes
    • 647.
    • Aslam ML, Bastiaansen JWM, Crooijmans RPMA et al. (2010) A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes. BMC Genomics, 11, 647.
    • (2010) BMC Genomics , vol.11
    • Aslam, M.L.1    Bastiaansen, J.W.M.2    Crooijmans, R.P.M.A.3
  • 4
    • 0002027027 scopus 로고
    • A comparative study of the breeding ecology of the Great Tit Parus major in different habitats
    • van Balen JH (1973) A comparative study of the breeding ecology of the Great Tit Parus major in different habitats. Ardea, 61, 1-93.
    • (1973) Ardea , vol.61 , pp. 1-93
    • van Balen, J.H.1
  • 5
    • 77949787771 scopus 로고    scopus 로고
    • A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)
    • 218.
    • Ball AD, Stapley J, Dawson DA et al. (2010) A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics, 11, 218.
    • (2010) BMC Genomics , vol.11
    • Ball, A.D.1    Stapley, J.2    Dawson, D.A.3
  • 7
    • 77749324529 scopus 로고    scopus 로고
    • Genome-wide SNP detection in the great tit Parus major using high throughput sequencing
    • van Bers NEM, van Oers K, Kerstens HHD et al. (2010) Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Molecular Ecology, 19 (Suppl 1), 89-99.
    • (2010) Molecular Ecology , vol.19 , Issue.SUPPL 1 , pp. 89-99
    • van Bers, N.E.M.1    van Oers, K.2    Kerstens, H.H.D.3
  • 8
    • 77956652292 scopus 로고    scopus 로고
    • Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology
    • Clutton-Brock T, Sheldon BC (2010) Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology. Trends in Ecology and Evolution, 25, 562-573.
    • (2010) Trends in Ecology and Evolution , vol.25 , pp. 562-573
    • Clutton-Brock, T.1    Sheldon, B.C.2
  • 9
    • 77957903598 scopus 로고    scopus 로고
    • Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): genome assembly and analysis
    • Dalloul RA, Long JA, Zimin AV et al. (2010) Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology, 8, e1000475.
    • (2010) PLoS Biology , vol.8
    • Dalloul, R.A.1    Long, J.A.2    Zimin, A.V.3
  • 10
    • 79959435199 scopus 로고    scopus 로고
    • Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    • Davey JW, Hohenlohe PA, Etter PD et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
    • (2011) Nature Reviews Genetics , vol.12 , pp. 499-510
    • Davey, J.W.1    Hohenlohe, P.A.2    Etter, P.D.3
  • 12
    • 41149166756 scopus 로고    scopus 로고
    • Sequencing goes 454 and takes large-scale genomics into the wild
    • Ellegren H (2008) Sequencing goes 454 and takes large-scale genomics into the wild. Molecular Ecology, 17, 1629-1631.
    • (2008) Molecular Ecology , vol.17 , pp. 1629-1631
    • Ellegren, H.1
  • 13
    • 40749097777 scopus 로고    scopus 로고
    • Genetic basis of fitness differences in natural populations
    • Ellegren H, Sheldon BC (2008) Genetic basis of fitness differences in natural populations. Nature, 452, 169-175.
    • (2008) Nature , vol.452 , pp. 169-175
    • Ellegren, H.1    Sheldon, B.C.2
  • 14
    • 33846689706 scopus 로고    scopus 로고
    • Using GOstats to test gene lists for GO term association
    • Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257-258.
    • (2007) Bioinformatics , vol.23 , pp. 257-258
    • Falcon, S.1    Gentleman, R.2
  • 16
    • 34248231212 scopus 로고    scopus 로고
    • The evolution of the avian genome as revealed by comparative molecular cytogenetics
    • Griffin D, Robertson L, Tempest H, Skinner B (2007) The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenetic and Genome Research, 117, 64-77.
    • (2007) Cytogenetic and Genome Research , vol.117 , pp. 64-77
    • Griffin, D.1    Robertson, L.2    Tempest, H.3    Skinner, B.4
  • 17
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • Harismendy O, Ng PC, Strausberg RL et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biology, 10, R32.
    • (2009) Genome Biology , vol.10
    • Harismendy, O.1    Ng, P.C.2    Strausberg, R.L.3
  • 18
    • 10644283823 scopus 로고    scopus 로고
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • ICGSC
    • ICGSC (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
    • (2004) Nature , vol.432 , pp. 695-716
  • 19
    • 77952734936 scopus 로고    scopus 로고
    • High-throughput DNA sequencing - concepts and limitations
    • Kircher M, Kelso J (2010) High-throughput DNA sequencing - concepts and limitations. BioEssays, 32, 524-536.
    • (2010) BioEssays , vol.32 , pp. 524-536
    • Kircher, M.1    Kelso, J.2
  • 20
    • 0342302204 scopus 로고
    • A long term study of the great tit (Parus major)
    • Lack D (1964) A long term study of the great tit (Parus major). Journal of Animal Ecology, 33, 159-173.
    • (1964) Journal of Animal Ecology , vol.33 , pp. 159-173
    • Lack, D.1
  • 21
    • 0028877463 scopus 로고
    • Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results
    • Lander E, Kruglyak L (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genetics, 11, 241-247.
    • (1995) Nature Genetics , vol.11 , pp. 241-247
    • Lander, E.1    Kruglyak, L.2
  • 22
    • 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 Research, 18, 1851-1858.
    • (2008) Genome Research , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 23
    • 79959829720 scopus 로고    scopus 로고
    • Widespread RNA and DNA sequence differences in the human transcriptome
    • Li M, Wang IX, Li Y et al. (2011) Widespread RNA and DNA sequence differences in the human transcriptome. Science, 333, 53-58.
    • (2011) Science , vol.333 , pp. 53-58
    • Li, M.1    Wang, I.X.2    Li, Y.3
  • 24
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends in Genetics, 24, 133-141.
    • (2008) Trends in Genetics , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 25
    • 67651107321 scopus 로고    scopus 로고
    • Development and characterization of a high density SNP genotyping assay for cattle
    • Matukumalli LK, Lawley CT, Schnabel RD et al. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE, 4, e5350.
    • (2009) PLoS ONE , vol.4
    • Matukumalli, L.K.1    Lawley, C.T.2    Schnabel, R.D.3
  • 26
    • 74049086779 scopus 로고    scopus 로고
    • Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken
    • Megens HJ, Crooijmans RPMA, Bastiaansen JWM et al. (2009) Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genetics, 10, 86.
    • (2009) BMC Genetics , vol.10 , pp. 86
    • Megens, H.J.1    Crooijmans, R.P.M.A.2    Bastiaansen, J.W.M.3
  • 27
    • 72749113546 scopus 로고    scopus 로고
    • Applied conservation genetics and the need for quality control and reporting of genetic data used in fisheries and wildlife management
    • Morin PA, Martien KK, Archer FI et al. (2010) Applied conservation genetics and the need for quality control and reporting of genetic data used in fisheries and wildlife management. Journal of Heredity, 101, 1-10.
    • (2010) Journal of Heredity , vol.101 , pp. 1-10
    • Morin, P.A.1    Martien, K.K.2    Archer, F.I.3
  • 28
    • 29444452921 scopus 로고    scopus 로고
    • Molecular signatures of natural selection
    • Nielsen R (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197-218.
    • (2005) Annual Review of Genetics , vol.39 , pp. 197-218
    • Nielsen, R.1
  • 29
    • 26844571576 scopus 로고    scopus 로고
    • Evolution: selection on heritable phenotypic plasticity in a wild bird population
    • Nussey DH, Postma E, Gienapp P, Visser ME (2005) Evolution: selection on heritable phenotypic plasticity in a wild bird population. Science, 310, 304-306.
    • (2005) Science , vol.310 , pp. 304-306
    • Nussey, D.H.1    Postma, E.2    Gienapp, P.3    Visser, M.E.4
  • 32
    • 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 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
    • Ramos, A.M.1    Crooijmans, R.P.2    Affara, N.A.3
  • 33
    • 77954210220 scopus 로고    scopus 로고
    • An updated overview on wnt signaling pathways: a prelude for more
    • Rao TP, Kühl M (2010) An updated overview on wnt signaling pathways: a prelude for more. Circulation Research, 106, 1798-1806.
    • (2010) Circulation Research , vol.106 , pp. 1798-1806
    • Rao, T.P.1    Kühl, M.2
  • 34
    • 79957800445 scopus 로고    scopus 로고
    • Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing
    • Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J (2011) Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics, 12, 283.
    • (2011) BMC Genomics , vol.12 , pp. 283
    • Santure, A.W.1    Gratten, J.2    Mossman, J.A.3    Sheldon, B.C.4    Slate, J.5
  • 35
    • 79951766233 scopus 로고    scopus 로고
    • Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms
    • Seeb JE, Carvalho G, Hauser L et al. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11 (Suppl 1), 1-8.
    • (2011) Molecular Ecology Resources , vol.11 , Issue.SUPPL 1 , pp. 1-8
    • Seeb, J.E.1    Carvalho, G.2    Hauser, L.3
  • 36
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: a parallel assembler for short read sequence data
    • Simpson JT, Wong K, Jackman SD et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Research, 19, 1117-1123.
    • (2009) Genome Research , vol.19 , pp. 1117-1123
    • Simpson, J.T.1    Wong, K.2    Jackman, S.D.3
  • 37
    • 77953290833 scopus 로고    scopus 로고
    • Genome mapping in intensively studied wild vertebrate populations
    • Slate J, Santure AW, Feulner PGD et al. (2010) Genome mapping in intensively studied wild vertebrate populations. Trends in Genetics, 26, 275-284.
    • (2010) Trends in Genetics , vol.26 , pp. 275-284
    • Slate, J.1    Santure, A.W.2    Feulner, P.G.D.3
  • 38
    • 77950645759 scopus 로고    scopus 로고
    • Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
    • Stapley J, Birkhead TR, Burke T, Slate J (2010) Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome. Genome Research, 20, 496-502.
    • (2010) Genome Research , vol.20 , pp. 496-502
    • Stapley, J.1    Birkhead, T.R.2    Burke, T.3    Slate, J.4
  • 39
    • 0030616845 scopus 로고    scopus 로고
    • Natal dispersal of great tits in a patchy environment
    • Verhulst S, Perrins CM, Riddington R (1997) Natal dispersal of great tits in a patchy environment. Ecology, 78, 864-872.
    • (1997) Ecology , vol.78 , pp. 864-872
    • Verhulst, S.1    Perrins, C.M.2    Riddington, R.3
  • 40
    • 38849159051 scopus 로고    scopus 로고
    • Keeping up with a warming world; assessing the rate of adaptation to climate change
    • Visser ME (2008) Keeping up with a warming world; assessing the rate of adaptation to climate change. Proceedings of the Royal Society B - Biological Sciences, 275, 649-659.
    • (2008) Proceedings of the Royal Society B - Biological Sciences , vol.275 , pp. 649-659
    • Visser, M.E.1
  • 43
    • 0021566877 scopus 로고
    • Estimating F-statistics for the analysis of population-structure
    • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population-structure. Evolution, 38, 1358-1370.
    • (1984) Evolution , vol.38 , pp. 1358-1370
    • Weir, B.S.1    Cockerham, C.C.2
  • 44
    • 30344469564 scopus 로고    scopus 로고
    • Comparison of microsatellites, single-nucleotide polymorphisms (SNPs) and composite markers derived from SNPs in linkage analysis
    • Xing C, Schumacher FR, Xing G et al. (2005) Comparison of microsatellites, single-nucleotide polymorphisms (SNPs) and composite markers derived from SNPs in linkage analysis. BMC Genetics, 6(Suppl 1), S29.
    • (2005) BMC Genetics , vol.6 , Issue.SUPPL 1
    • Xing, C.1    Schumacher, F.R.2    Xing, G.3
  • 45
    • 0345306317 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
    • Zhang Z, Gerstein M (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Research, 31, 5338-5348.
    • (2003) Nucleic Acids Research , vol.31 , pp. 5338-5348
    • Zhang, Z.1    Gerstein, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.