Corn and humans: Recombination and linkage disequilibrium in two genomes of similar size

Trends in Genetics

Volumn 20, Issue 2, 2004, Pages 103-111

  Rafalski, Antoni ^a   Morgante, Michele ^b  

^a DUPONT COMPANY   (United States)

^b UNIVERSITY OF UDINE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME SIZE; HAPLOTYPE; HUMAN; HUMAN GENOME; LINKAGE ANALYSIS; MAIZE; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; REVIEW; SPECIES DIFFERENCE;

EMBRYOPHYTA; ZEA MAYS;

EID: 1642473027     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2003.12.002     Document Type: Review

References (78)

1. Weiss K.M., Clark A.G. Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 18:2002;19-24.
2. Goldstein D.B., Weale M.E. Linkage disequilibrium holds the key. Current Biology. 11:2001;R576-R579.
3. Nordborg M., Tavare S. Linkage disequilibrium: what history has to tell us. Trends Genet. 18:2002;83-90.
4. Flint-Garcia S.A., et al. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54:2003;357-374.
5. Cardon L.R., Abecasis G.R. Using haplotype blocks to map human complex loci. Trends Genet. 19:2003;135-140.
6. Cardon L.R., Bell J.I. Association study designs for complex diseases. Nat. Rev. Genet. 2:2001;91-99.
7. Jorde L.B. Linkage diseqilibrium as a gene-mapping tool. Am. J. Hum. Genet. 56:1995;11-14.
8. Jorde L.B. Linkage disequilibrium and the search for complex disease genes. Genome Res. 10:2000;1435-1444.
9. Meyers B.C., et al. Abundance, distribution and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11:2001;1660-1676.
10. Buckler E.S., et al. Molecular diversity, structure and domestication of grasses. Genet. Res. 77:2001;213-218.
11. Tishkoff S.A., Verrelli B.C. Patterns of human genetic diversity: implications for human evolutionary history and disease. Annu. Rev. Genomics Hum. Genet. 4:2003;293-340.
12. Marshall H.D., et al. Sequence-repeat polymorphisms exhibit the signature of recombination in lodgepole pine chloroplast DNA. Mol. Biol. Evol. 18:2001;2136-2138.
13. Eyre-Walker A., Awadalla P. Does human mtDNA recombine? J. Mol. Evol. 53:2001;430-435.
14. Shepard K.A., Purugganan M.D. Molecular population genetics of the Arabidopsis CLAVATA2 region. The genomic scale of variation and selection in a selfing species. Genetics. 163:2003;1083-1095.
15. Nordborg M., et al. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30:2002;190-193.
16. Zhu Y.L., et al. Single-nucleotide polymorphisms in soybean. Genetics. 163:2003;1123-1134.
17. Kroymann, J. et al. Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc. Natl. Acad. Sci. U. S. A. (in press).
18. Dvornyk V., et al. Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Mol. Biol. Evol. 19:2002;179-188.
19. Tenaillon M.I., et al. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. U. S. A. 98:2001;9161-9166.
20. Jeffreys A.J., et al. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29:2001;217-222.
21. Olivier M., et al. Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21. Genomics. 78:2001;64-72.
22. Patil N., et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science. 294:2001;1719-1723.
23. Wall J.D., Pritchard J.K. Haplotype blocks and linkage disequilibrium in the human genome. Nat. Rev. Genet. 4:2003;587-597.
24. Wall J.D., Pritchard J.K. Assessing the performance of the haplotype block model of linkage disequilibrium. Am. J. Hum. Genet. 73:2003;502-515.
25. Tenaillon M.I., et al. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays spp. mays L.). Genetics. 162:2002;1401-1413.
26. Dooner H.K., et al. A molecular genetic analysis of insertion mutations in the bronze locus in maize. Mol. Gen. Genet. 200:1985;240-246.
27. Dooner H.K., Martinez-Ferez I.M. Recombination occurs uniformly within the bronze gene, a meiotic recombination hotspot in the maize genome. Plant Cell. 9:1997;1633-1646.
28. Fu H., et al. Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. U. S. A. 99:2002;1082-1087.
29. Brown J., Sundaresan V. A recombination hotspot in the maize A1 intragenic region. Theor. Appl. Genet. 81:1991;185-188.
30. Thuriaux P. Is recombination confined to structural genes on the eukaryotic genome? Nature. 268:1977;460-462.
31. Wang R.-L., et al. The limits of selection during maize domestication. Nature. 398:1999;236-239.
32. Wu D.Y., et al. Allele-specific enzymatic amplification of β-globin genomic DNA for diagnosis of sickle cell anemia. Proc. Natl. Acad. Sci. U. S. A. 86:1989;2757-2760.
33. Bennetzen J.L., et al. Grass genomes. Proc. Natl. Acad. Sci. U. S. A. 95:1998;1975-1978.
34. Song R., et al. Mosaic organization of orthologous sequences in grass genomes. Genome Res. 12:2002;1549-1555.
35. Bhattramakki D., et al. Insertion-deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol. Biol. 48:2002;539-547.
36. Fu H., Dooner H.K. Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. U. S. A. 99:2002;9573-9578.
37. Consortium I.H.G.S. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
38. Ching A., et al. SNP frequency and haplotype structure of 18 maize genes. BMC Genet. 3:2002;19.
39. Gaut B.S., Clegg M.T. Molecular evolution of the Adh1 locus in the genus Zea. Proc. Natl. Acad. Sci. U. S. A. 90:1993;5095-5099.
40. White S.E., Doebley J.F. The molecular evolution of terminal ear 1, a regulatory gene in the genus Zea. Genetics. 153:1999;1455-1462.
41. Song R., Messing J. Gene expression of a gene family in maize based on noncollinear haplotypes. Proc. Natl. Acad. Sci. U. S. A. 100:2003;9055-9060.
42. Feng Q., et al. Sequence and analysis of rice chromosome 4. Nature. 420:2002;316-320.
43. Sasaki T., et al. The genome sequence and structure of rice chromosome 1. Nature. 420:2002;312-316.
44. Matsuoka Y., et al. A single domestication for maize shown by multilocus microsatellite genotyping. Proc. Natl. Acad. Sci. U. S. A. 99:2002;6080-6084.
45. Zhang L., et al. Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays spp. mays L.) and its wild ancestor (Zea mays spp. parviglumis). Genetics. 162:2002;851-860.
46. Matsuoka Y., et al. Microsatellites in Zea - variability, patterns of mutations, and use for evolutionary studies. Theor. Appl. Genet. 104:2002;436-450.
47. Morgante M., et al. Genetic-mapping and variability of 7 soybean simple sequence repeat loci. Genome. 37:1994;763-769.
48. Powell W., et al. Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics. 144:1996;793-803.
49. Golubinoff P., et al. Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archeological specimens. Proc. Natl. Acad. Sci. U. S. A. 90:1993;1997-2001.
50. Barton N.H., Keightley P.D. Understanding quantitative genetic variation. Nat. Rev. Genet. 3:2002;11-21.
51. Filatov D.A., Charlesworth D. DNA polymorphism, haplotype structure and balancing selection in the Leavenworthia PgiC locus. Genetics. 153:1999;1423-1434.
52. Mead S., et al. Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics. Science. 300:2003;640-643.
53. Noonan J.P., et al. Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster. Am. J. Hum. Genet. 72:2003;621-635.
54. Verrelli B.C., et al. Evidence for balancing selection from nucleotide sequence analyses of human G6PD. Am. J. Hum. Genet. 71:2002;1112-1128.
55. Birchler J.A., et al. In search of the molecular basis of heterosis. Plant Cell. 15:2003;2236-2239.
56. Schneider K., et al. SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Mol. Breed. 8:2001;63-74.
57. Palaisa K., et al. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell. 15:2003;1795-1806.
58. Vigouroux Y., et al. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc. Natl. Acad. Sci. U. S. A. 99:2002;9650-9655.
59. Wootton J.C., et al. Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum. Nature. 418:2002;320-323.
60. Saez A.G., et al. Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep. Proc. Natl. Acad. Sci. U. S. A. 100:2003;1793-1798.
61. Reich D.E., et al. Linkage disequilibrium in the human genome. Nature. 411:2001;199-204.
62. Wall J.D. Estimating ancestral population sizes and divergence times. Genetics. 163:2003;395-404.
63. Vigouroux Y., et al. Rate and pattern of mutation at microsatellite loci in maize. Mol. Biol. Evol. 19:2002;1251-1260.
64. Remington D.L., et al. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. U. S. A. 98:2001;11479-11484.
65. Eyre-Walker A., et al. Investigation of the bottleneck leading to the domestication of maize. Proc. Natl. Acad. Sci. U. S. A. 95:1998;4441-4446.
66. Pritchard J.K., et al. Inference of population structure using multilocus genotype data. Genetics. 155:2000;945-959.
67. Mott R., et al. A method for fine mapping quantitative trait loci in outbred animal stocks. Proc. Natl. Acad. Sci. U. S. A. 97:2000;12649-12654.
68. Paran I., Zamir D. Quantitative traits in plants: beyond the QTL. Trends Genet. 19:2003;303-306.
69. Tautz D. Evolution of transcriptional regulation. Curr. Opin. Genet. Dev. 10:2000;575-579.
70. Cowles C., et al. Detection of regulatory variation in mouse genes. Nat. Genet. 32:2002;432-437.
71. Rockman M.V., Wray G.A. Abundant raw material for cis-regulatory evolution in humans. Mol. Biol. Evol. 19:2002;1991-2004.
72. Lo H.S., et al. Allelic variation in gene expression is common in the human genome. Genome Res. 13:2003;1855-1862.
73. Whitney A.R., et al. Individuality and variation in gene expression patterns in human blood. Proc. Natl. Acad. Sci. U. S. A. 100:2003;1896-1901.
74. Schadt E.E., et al. Genetics of gene expression surveyed in maize, mouse and man. Nature. 422:2003;297-302.
75. Stam M., et al. The regulatory regions required for B′ paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics. 162:2002;917-930.
76. Levine M., Tjian R. Transcription regulation and animal diversity. Nature. 424:2003;147-151.
77. Farnir F., et al. Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 10:2000;220-227.
78. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408:2000;796-815.