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Volumn 99, Issue 4, 2008, Pages 382-389

Nucleotide diversity and linkage disequilibrium in wild avocado (Persea americana Mill.)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AVOCADO; BARLEY; CELL NUCLEUS; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; MAIZE; NONHUMAN; OUTCROSSING; PRIORITY JOURNAL;

EID: 49949086331     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esn016     Document Type: Article
Times cited : (42)

References (58)
  • 1
    • 0035151437 scopus 로고    scopus 로고
    • Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes
    • Mol Biol Evol
    • Aguade M. 2001. Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes, in Arabidopsis thaliana. Mol Biol Evol. 18:1-9.
    • (2001) Arabidopsis thaliana , vol.18 , pp. 1-9
    • Aguade, M.1
  • 2
    • 0033828706 scopus 로고    scopus 로고
    • A genome-wide departure from the standard neutral model in natural populations of Drosophila
    • Andolfatto P, Przeworski M. 2000. A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics. 156:257-268.
    • (2000) Genetics , vol.156 , pp. 257-268
    • Andolfatto, P.1    Przeworski, M.2
  • 3
    • 0142126308 scopus 로고    scopus 로고
    • Microsatellite markers in avocado (Persea americana Mill.): Genealogical relationships among cultivated avocado genotypes
    • Ashworth VE, Clegg MT. 2003. Microsatellite markers in avocado (Persea americana Mill.): genealogical relationships among cultivated avocado genotypes. J Hered. 94:407-415.
    • (2003) J Hered , vol.94 , pp. 407-415
    • Ashworth, V.E.1    Clegg, M.T.2
  • 4
    • 49949095124 scopus 로고    scopus 로고
    • Ausubel FM, Brent R, Kingston RE, Moore DD. 1994. Preparation of genomic DNA from plant tissue. Curr Protoc Mol Biol. 1(Suppl 27):2.3.1.
    • Ausubel FM, Brent R, Kingston RE, Moore DD. 1994. Preparation of genomic DNA from plant tissue. Curr Protoc Mol Biol. 1(Suppl 27):2.3.1.
  • 6
    • 0026646769 scopus 로고
    • Molecular cloning, sequence analysis, and in vitro expression of flavanone 3 beta-hydroxylase from Petunia hybrida
    • Britsch L, Ruhnau-Brich B, Forkmann G. 1992. Molecular cloning, sequence analysis, and in vitro expression of flavanone 3 beta-hydroxylase from Petunia hybrida. J Biol Chem. 267:5380-5387.
    • (1992) J Biol Chem , vol.267 , pp. 5380-5387
    • Britsch, L.1    Ruhnau-Brich, B.2    Forkmann, G.3
  • 8
    • 84936916896 scopus 로고
    • Robust locally weighted regression and smoothing scatterplots
    • Cleveland WS. 1979. Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc. 74:829-836.
    • (1979) J Am Stat Assoc , vol.74 , pp. 829-836
    • Cleveland, W.S.1
  • 9
    • 84954964873 scopus 로고
    • LOWESS: A program for smoothing scatterplots by robust locally weighted regression
    • Cleveland WS. 1981. LOWESS: a program for smoothing scatterplots by robust locally weighted regression. Am Stat. 35:54.
    • (1981) Am Stat , vol.35 , pp. 54
    • Cleveland, W.S.1
  • 10
    • 0002890469 scopus 로고
    • Avocado flowering.
    • Davenport TL. 1986. Avocado flowering. Hortic Rev. 8:257-289.
    • (1986) Hortic Rev , vol.8 , pp. 257-289
    • Davenport, T.L.1
  • 11
  • 12
    • 0042330161 scopus 로고    scopus 로고
    • Nucleotide binding site/leucine-rich repeats, Pto-like and receptor-like kinases related to disease resistance in grapevine
    • Di Gaspero G, Cipriani G. 2003. Nucleotide binding site/leucine-rich repeats, Pto-like and receptor-like kinases related to disease resistance in grapevine. Mol Genet Genomics. 269:612-623.
    • (2003) Mol Genet Genomics , vol.269 , pp. 612-623
    • Di Gaspero, G.1    Cipriani, G.2
  • 13
    • 0033976087 scopus 로고    scopus 로고
    • Molecular evolution of the chalcone synthase multigene family in the morning glory genome
    • Durbin ML, McCaig B, Clegg MT. 2000. Molecular evolution of the chalcone synthase multigene family in the morning glory genome. Plant Mol Biol. 42:79-92.
    • (2000) Plant Mol Biol , vol.42 , pp. 79-92
    • Durbin, M.L.1    McCaig, B.2    Clegg, M.T.3
  • 14
    • 0036149896 scopus 로고    scopus 로고
    • Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris
    • Dvornyk V, Sirvio A, Mikkonen M, Savolainen O. 2002. Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Mol Biol Evol. 19:179-188.
    • (2002) Mol Biol Evol , vol.19 , pp. 179-188
    • Dvornyk, V.1    Sirvio, A.2    Mikkonen, M.3    Savolainen, O.4
  • 15
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 16
    • 0018946505 scopus 로고
    • Genetic control of chalcone isomerase activity in flowers of Dianthus caryophyllus
    • Forkmann G, Dangelmayr B. 1980. Genetic control of chalcone isomerase activity in flowers of Dianthus caryophyllus. Biochem Genet. 18:519-527.
    • (1980) Biochem Genet , vol.18 , pp. 519-527
    • Forkmann, G.1    Dangelmayr, B.2
  • 17
    • 0038788126 scopus 로고    scopus 로고
    • Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris
    • Garcia-Gil MR, Mikkonen M, Savolainen O. 2003. Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol Ecol. 12:1195-1206.
    • (2003) Mol Ecol , vol.12 , pp. 1195-1206
    • Garcia-Gil, M.R.1    Mikkonen, M.2    Savolainen, O.3
  • 19
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 20
    • 22344444998 scopus 로고    scopus 로고
    • Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
    • Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P. 2005. Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15:790-799.
    • (2005) Genome Res , vol.15 , pp. 790-799
    • Haddrill, P.R.1    Thornton, K.R.2    Charlesworth, B.3    Andolfatto, P.4
  • 21
    • 0031034399 scopus 로고    scopus 로고
    • Allozyme diversity in cultivated crops. (Germplasm regeneration: Developments in population genetics and their implications)
    • Hamrick J, Godt M. 1997. Allozyme diversity in cultivated crops. (Germplasm regeneration: Developments in population genetics and their implications). Crop Sci. 37:26-31.
    • (1997) Crop Sci , vol.37 , pp. 26-31
    • Hamrick, J.1    Godt, M.2
  • 22
    • 0023612034 scopus 로고
    • Estimating the recombination parameter of a finite population model without selection
    • Hudson RR. 1987. Estimating the recombination parameter of a finite population model without selection. Genet Res. 50:245-250.
    • (1987) Genet Res , vol.50 , pp. 245-250
    • Hudson, R.R.1
  • 23
    • 0035692320 scopus 로고    scopus 로고
    • Two-locus sampling distributions and their application
    • Hudson RR. 2001. Two-locus sampling distributions and their application. Genetics. 159:1805-1817.
    • (2001) Genetics , vol.159 , pp. 1805-1817
    • Hudson, R.R.1
  • 24
    • 0022211482 scopus 로고
    • Statistical properties of the number of recombination events in the history of a sample of DNA sequences
    • Hudson RR, Kaplan NL. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 111:147-164.
    • (1985) Genetics , vol.111 , pp. 147-164
    • Hudson, R.R.1    Kaplan, N.L.2
  • 25
    • 15544362769 scopus 로고    scopus 로고
    • Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae)
    • Ingvarsson PK. 2005. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics. 169:945-953.
    • (2005) Genetics , vol.169 , pp. 945-953
    • Ingvarsson, P.K.1
  • 26
    • 0041817580 scopus 로고    scopus 로고
    • DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato)
    • Kado T, Yoshimaru H, Tsumura Y, Tachida H. 2003. DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics. 164:1547-1559.
    • (2003) Genetics , vol.164 , pp. 1547-1559
    • Kado, T.1    Yoshimaru, H.2    Tsumura, Y.3    Tachida, H.4
  • 28
    • 0033824633 scopus 로고    scopus 로고
    • Quantitative analysis of avocado outcrossing and yield in California using RAPD markers
    • Kobayashi M, Lin JZ, Davis J, Francis L, Clegg MT. 2000. Quantitative analysis of avocado outcrossing and yield in California using RAPD markers. Sci Hortic. 86:135-149.
    • (2000) Sci Hortic , vol.86 , pp. 135-149
    • Kobayashi, M.1    Lin, J.Z.2    Davis, J.3    Francis, L.4    Clegg, M.T.5
  • 29
    • 12244278248 scopus 로고    scopus 로고
    • The influence of linkage and inbreeding on patterns of nucleotide sequence diversity at duplicate alcohol dehydrogenase loci in wild barley (Hordeum vulgare ssp. spontaneum)
    • Lin JZ, Morrell PL, Clegg MT. 2002. The influence of linkage and inbreeding on patterns of nucleotide sequence diversity at duplicate alcohol dehydrogenase loci in wild barley (Hordeum vulgare ssp. spontaneum). Genetics. 162:2007-2015.
    • (2002) Genetics , vol.162 , pp. 2007-2015
    • Lin, J.Z.1    Morrell, P.L.2    Clegg, M.T.3
  • 30
    • 0032827782 scopus 로고    scopus 로고
    • The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits
    • Long AD, Langley CH. 1999. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res. 9:720-731.
    • (1999) Genome Res , vol.9 , pp. 720-731
    • Long, A.D.1    Langley, C.H.2
  • 31
    • 0141480023 scopus 로고    scopus 로고
    • Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration
    • Morrell PL, Lundy KE, Clegg MT. 2003. Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proc Natl Acad Sci USA. 100:10812-10817.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 10812-10817
    • Morrell, P.L.1    Lundy, K.E.2    Clegg, M.T.3
  • 32
    • 14044276992 scopus 로고    scopus 로고
    • Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization
    • Morrell PL, Toleno DM, Lundy KE, Clegg MT. 2005. Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA. 102:2442-2447.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 2442-2447
    • Morrell, P.L.1    Toleno, D.M.2    Lundy, K.E.3    Clegg, M.T.4
  • 33
    • 33746464543 scopus 로고    scopus 로고
    • Estimating the contribution of mutation, recombination and gene conversion in the genetation of haplotypic diversity
    • Morrell PL, Toleno DM, Lundy KE, Clegg MT. 2006. Estimating the contribution of mutation, recombination and gene conversion in the genetation of haplotypic diversity. Genetics. 173:1705-1723.
    • (2006) Genetics , vol.173 , pp. 1705-1723
    • Morrell, P.L.1    Toleno, D.M.2    Lundy, K.E.3    Clegg, M.T.4
  • 34
    • 0024605518 scopus 로고
    • Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS), amplification refractory mutation system (ARMS)
    • Newton C, Graham A, Heptinstall L. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS), amplification refractory mutation system (ARMS). Nucleic Acids Res. 17:2503-2516.
    • (1989) Nucleic Acids Res , vol.17 , pp. 2503-2516
    • Newton, C.1    Graham, A.2    Heptinstall, L.3
  • 35
    • 0030872838 scopus 로고    scopus 로고
    • PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
    • Nickerson DA, Tobe VO, Taylor SL. 1997. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25:2745-2751.
    • (1997) Nucleic Acids Res , vol.25 , pp. 2745-2751
    • Nickerson, D.A.1    Tobe, V.O.2    Taylor, S.L.3
  • 36
    • 0033962299 scopus 로고    scopus 로고
    • Linkage disequilibrium, gene trees and selfing: An ancestral recombination graph with partial self-fertilization
    • Nordborg M. 2000. Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics. 154:923-929.
    • (2000) Genetics , vol.154 , pp. 923-929
    • Nordborg, M.1
  • 38
    • 33750464822 scopus 로고    scopus 로고
    • History and structure of sub-Saharan populations of Drosophila melanogaster
    • Pool JE, Aquadro CF. 2006. History and structure of sub-Saharan populations of Drosophila melanogaster. Genetics. 174:915-929.
    • (2006) Genetics , vol.174 , pp. 915-929
    • Pool, J.E.1    Aquadro, C.F.2
  • 39
    • 1642274061 scopus 로고    scopus 로고
    • Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata
    • Ramos-Onsins SE, Stranger BE, Mitchell-Olds T, Aguade M. 2004. Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata. Genetics. 166:373-388.
    • (2004) Genetics , vol.166 , pp. 373-388
    • Ramos-Onsins, S.E.1    Stranger, B.E.2    Mitchell-Olds, T.3    Aguade, M.4
  • 41
    • 34447276219 scopus 로고    scopus 로고
    • Plant domestication, a unique opportunity to identify the genetic basis of adaptation
    • Ross-Ibarra J, Morrell PL, Gaut BS. 2007. Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci USA. 104(Suppl 1):8641-8648.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.SUPPL. 1 , pp. 8641-8648
    • Ross-Ibarra, J.1    Morrell, P.L.2    Gaut, B.S.3
  • 42
    • 51249187371 scopus 로고
    • The component triacylglycerols of avocado fruit-coat
    • Sharma CB, Martinez GC. 1972. The component triacylglycerols of avocado fruit-coat. J Am Oil Chem Soc. 49:229-232.
    • (1972) J Am Oil Chem Soc , vol.49 , pp. 229-232
    • Sharma, C.B.1    Martinez, G.C.2
  • 43
    • 0021066244 scopus 로고
    • Evolutionary relationship of DNA sequences in finite populations
    • Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics. 105:437-460.
    • (1983) Genetics , vol.105 , pp. 437-460
    • Tajima, F.1
  • 44
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 45
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 46
    • 0344464730 scopus 로고    scopus 로고
    • Libsequence: A C++ class library for evolutionary genetic analysis
    • Thornton K. 2003. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics. 9:2325-2327.
    • (2003) Bioinformatics , vol.9 , pp. 2325-2327
    • Thornton, K.1
  • 47
    • 33644763127 scopus 로고    scopus 로고
    • Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster
    • Thornton K, Andolfatto P. 2006. Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics. 172:1607-1619.
    • (2006) Genetics , vol.172 , pp. 1607-1619
    • Thornton, K.1    Andolfatto, P.2
  • 48
    • 0035007364 scopus 로고    scopus 로고
    • Sequence diversity in the tetraploid Zea perennis and the closely related diploid Z. diploperennis: Insights from four nuclear loci
    • Tiffin P, Gaut BS. 2001a. Sequence diversity in the tetraploid Zea perennis and the closely related diploid Z. diploperennis: insights from four nuclear loci. Genetics. 158:401-412.
    • (2001) Genetics , vol.158 , pp. 401-412
    • Tiffin, P.1    Gaut, B.S.2
  • 49
    • 0034751998 scopus 로고    scopus 로고
    • Molecular evolution of the wound-induced serine protease inhibitor wip1 in Zea and related genera
    • Tiffin P, Gaut BS. 2001b. Molecular evolution of the wound-induced serine protease inhibitor wip1 in Zea and related genera. Mol Biol Evol. 18:2092-2101.
    • (2001) Mol Biol Evol , vol.18 , pp. 2092-2101
    • Tiffin, P.1    Gaut, B.S.2
  • 50
    • 3843128155 scopus 로고    scopus 로고
    • Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea
    • Tiffin P, Hacker R, Gaut BS. 2004. Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea. Genetics. 168:425-434.
    • (2004) Genetics , vol.168 , pp. 425-434
    • Tiffin, P.1    Hacker, R.2    Gaut, B.S.3
  • 51
    • 34547907058 scopus 로고    scopus 로고
    • Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations
    • Toleno DM, Morrell PL, Clegg MT. 2007. Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations. Bioinformatics. 23:1807-1814.
    • (2007) Bioinformatics , vol.23 , pp. 1807-1814
    • Toleno, D.M.1    Morrell, P.L.2    Clegg, M.T.3
  • 52
    • 0001141980 scopus 로고
    • Avocado cellulase: Nucleotide sequence of a putative full-length cDNA clone and evidence for a small gene family
    • Tucker ML, Durbin ML, Clegg MT, Lewis LN. 1987. Avocado cellulase: nucleotide sequence of a putative full-length cDNA clone and evidence for a small gene family. Plant Mol Biol. 9:197-203.
    • (1987) Plant Mol Biol , vol.9 , pp. 197-203
    • Tucker, M.L.1    Durbin, M.L.2    Clegg, M.T.3    Lewis, L.N.4
  • 53
    • 0032884643 scopus 로고    scopus 로고
    • Recombination and the power of statistical tests of neutrality
    • Wall JD. 1999. Recombination and the power of statistical tests of neutrality. Genet Res. 74:65-79.
    • (1999) Genet Res , vol.74 , pp. 65-79
    • Wall, J.D.1
  • 54
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7:256-276.
    • (1975) Theor Popul Biol , vol.7 , pp. 256-276
    • Watterson, G.A.1
  • 55
    • 49949087186 scopus 로고    scopus 로고
    • Weir BS. 1990. Genetic Data Analysis. Sunderland (MA): Sinauer. White SE, Doebley JF. 1999. The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics. 153:1455-1462.
    • Weir BS. 1990. Genetic Data Analysis. Sunderland (MA): Sinauer. White SE, Doebley JF. 1999. The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics. 153:1455-1462.
  • 56
    • 0038075570 scopus 로고    scopus 로고
    • Subdivision and haplotype structure in natural populations of Arabidopsis lyrata
    • Wright SI, Lauga B, Charlesworth D. 2003. Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Mol Ecol. 12:1247-1263.
    • (2003) Mol Ecol , vol.12 , pp. 1247-1263
    • Wright, S.I.1    Lauga, B.2    Charlesworth, D.3
  • 58
    • 33847661877 scopus 로고    scopus 로고
    • Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice
    • Zhu Q, Zheng X, Luo J, Gaut BS, Ge S. 2007. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol. 24:875-888.
    • (2007) Mol Biol Evol , vol.24 , pp. 875-888
    • Zhu, Q.1    Zheng, X.2    Luo, J.3    Gaut, B.S.4    Ge, S.5


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