Genetic association mapping and genome organization of maize

Current Opinion in Biotechnology

Volumn 17, Issue 2, 2006, Pages 155-160

  Yu, Jianming ^a   Buckler, Edward S ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; GENETIC ENGINEERING; STATISTICAL METHODS;

GENE ASSOCIATION MAPPING; GENOME ORGANIZATION; MAPPING PANELS;

CROPS;

DNA SEQUENCE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; LINKAGE ANALYSIS; MAIZE; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOME MAP; GENETICS; GENOME; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; STATISTICS;

FARM CROPS; GENES; GENETIC ENGINEERING; STATISTICAL METHODS;

ZEA MAYS;

CHROMOSOME MAPPING; GENOME, PLANT; LINKAGE DISEQUILIBRIUM; QUANTITATIVE TRAIT LOCI; ZEA MAYS;

EID: 33744980661     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2006.02.003     Document Type: Review

References (51)

1. Risch N., and Merikangas K. The future of genetic studies of complex human diseases. Science 273 (1996) 1516-1517
2. Mackay T.F. The genetic architecture of quantitative traits. Annu Rev Genet 35 (2001) 303-339
3. Thornsberry J.M., Goodman M.M., Doebley J., Kresovich S., Nielsen D., and Buckler E.S. Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28 (2001) 286-289
4. Remington D.L., Thornsberry J.M., Matsuoka Y., Wilson L.M., Whitt S.R., Doebley J., Kresovich S., Goodman M.M., and Buckler E.S. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98 (2001) 11479-11484
5. Buckler E.S., and Thornsberry J.M. Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5 (2002) 107-111
6. Flint-Garcia S.A., Thornsberry J.M., and Buckler E.S. Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54 (2003) 357-374
7. Wilson L.M., Whitt S.R., Ibanez A.M., Rocheford T.R., Goodman M.M., and Buckler E.S. Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16 (2004) 2719-2733. An association study of six candidate genes involved in the starch biosynthetic pathway with diverse maize inbred lines. Principle component analysis was applied to summarize the information on the correlated phenotypic traits for kernel composition and starch pasting properties. Good discussion on association mapping versus linkage analysis.
8. Hirschhorn J.N., and Daly M.J. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6 (2005) 95-108. A comprehensive review of genome-wide association studies in humans, including rationale, power, efficiency, approaches, analysis and interpretation.
9. Whitt S.R., and Buckler E.S. Using natural allelic diversity to evaluate gene function. Methods Mol Biol 236 (2003) 123-140
10. Gaut B.S., and Long A.D. The lowdown on linkage disequilibrium. Plant Cell 15 (2003) 1502-1506
11. Tenaillon M.I., Sawkins M.C., Long A.D., Gaut R.L., Doebley J.F., and Gaut B.S. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98 (2001) 9161-9166
12. Ching A., Caldwell K.S., Jung M., Dolan M., Smith O.S., Tingey S., Morgante M., and Rafalski A.J. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3 (2002) 19
13. Palaisa K.A., Morgante M., Williams M., and Rafalski A. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15 (2003) 1795-1806. Maize phytonene synthase Y1 was associated with endosperm color. Nucleotide diversity was found to be equivalent at PSY2, another putative phytonene synthase, but was 19-fold less in yellow maize inbred lines than in white.
14. Palaisa K., Morgante M., Tingey S., and Rafalski A. Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc Natl Acad Sci USA 101 (2004) 9885-9890. A follow-up study on the surrounding region of the Y1 gene, which was previously associated with determining maize endosperm color. This is the largest extension of LD (200 kb upstream and 600 kd downstream of Y1) reported in a maize candidate gene so far, possibly owing to the qualitative nature of the trait, strong selection in short time, and partial isolation.
15. Jung M., Ching A., Bhattramakki D., Dolan M., Tingey S., Morgante M., and Rafalski A. Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm. Theor Appl Genet 109 (2004) 681-689
16. Ingvarsson P.K. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169 (2005) 945-953
17. Brown G.R., Gill G.P., Kuntz R.J., Langley C.H., and Neale D.B. Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc Natl Acad Sci USA 101 (2004) 15255-15260
18. Morrell P.L., Toleno D.M., Lundy K.E., and Clegg M.T. Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 102 (2005) 2442-2447
19. Garris A.J., McCouch S.R., and Kresovich S. Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165 (2003) 759-769
20. Hamblin M.T., Mitchell S.E., White G.M., Gallego J., Kukatla R., Wing R.A., Paterson A.H., and Kresovich S. Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor. Genetics 167 (2004) 471-483
21. Nordborg M., Borevitz J.O., Bergelson J., Berry C.C., Chory J., Hagenblad J., Kreitman M., Maloof J.N., Noyes T., Oefner P.J., et al. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30 (2002) 190-193
22. Nordborg M., Hu T.T., Ishino Y., Jhaveri J., Toomajian C., Zheng H., Bakker E., Calabrese P., Gladstone J., Goyal R., et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3 (2005) e196
23. Messing J., Bharti A.K., Karlowski W.M., Gundlach H., Kim H.R., Yu Y., Wei F., Fuks G., Soderlund C.A., Mayer K.F., et al. Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101 (2004) 14349-14354. A comprehensive sequence analysis of the maize genome. The maize genome was found to contain 59 000 genes, accounting for 7.5% of the genome. All types of repeat elements make up 58% of the genome, and unknown sequences account for the remaining 34.5%. Although one-third of the maize gene is organized in tandem arrays, fewer than half of the genes are present in two orthologous copies.
24. Wright S.I., Bi I.V., Schroeder S.G., Yamasaki M., Doebley J.F., McMullen M.D., and Gaut B.S. The effects of artificial selection on the maize genome. Science 308 (2005) 1310-1314
25. Fu H., and Dooner H.K. Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99 (2002) 9573-9578
26. Brunner S., Fengler K., Morgante M., Tingey S., and Rafalski A. Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17 (2005) 343-360. A large-scale examination of sequence nonhomology among maize inbred lines. From 2.8 Mb of sequence studied, more than half was found to be noncollinear between two maize inbred lines, B73 and Mo17, owing to the insertion of large numbers of long-terminal repeat (LTR) retrotransposons. The ratio between shared and nonshared LTR retroelements was 27:62 and that of genes was 45:27.
27. Lai J., Ma J., Swigonova Z., Ramakrishna W., Linton E., Llaca V., Tanyolac B., Park Y.J., Jeong O.Y., Bennetzen J.L., et al. Gene loss and movement in the maize genome. Genome Res 14 (2004) 1924-1931
28. Lai J., Li Y., Messing J., and Dooner H.K. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci USA 102 (2005) 9068-9073
29. Morgante M., Brunner S., Pea G., Fengler K., Zuccolo A., and Rafalski A. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37 (2005) 997-1002. A genome-wide comparison of gene content in two maize inbred lines, B73 and Mo17. Among 20 656 genes and gene fragments examined in allelic bacterial artificial chromosome (BAC) contigs, 20.6% were not shared between the two lines. Eight of nine genic insertion sites examined appeared to be mediated by helitron with an unknown mechanism.
30. Brunner S., Pea G., and Rafalski A. Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize. Plant J 43 (2005) 799-810
31. Liu K., Goodman M., Muse S., Smith J.S., Buckler E., and Doebley J. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165 (2003) 2117-2128
32. Flint-Garcia S.A., Thuillet A., Yu J., Pressoir G., Romero S.M., Mitchell S.E., Doebley J.F., Kresovich S., Goodman M.M., and Buckler E.S. Maize association population: A high resolution platform for QTL dissection. Plant J 44 (2005) 1054-1064. A systematic description of a maize association mapping panel of 302 diverse inbred lines. Population structure estimates of the whole set, and heritability estimates for 60 traits based on replicated measurement from a subset, are presented.
33. Camus-Kulandaivelu L, Veyrieras J-B, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A: Maize adaptation to temperate climate: relationship with population structure and polymorphism in the Dwarf8 gene. Genetics 2006; published ahead of print doi: 10.1534/genetics.105.048603.
34. Yu J., Pressoir G., Briggs W.H., Vroh Bi I., Yamasaki M., Doebley J.F., McMullen M.D., Gaut B.S., Nielsen D.M., Holland J.B., et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38 (2006) 203-208. Reports new statistical methods for association mapping that simultaneously account for both population structure and familial relatedness within a sample. Marker-based relative kinship and population structure were simultaneously introduced into the traditional mix-model framework. The method crosses the boundary between family-based and mixed association samples and is demonstrated with maize quantitative traits and human gene expression examples.
35. Garris A.J., Tai T.H., Coburn J., Kresovich S., and McCouch S. Genetic structure and diversity in Oryza sativa L. Genetics 169 (2005) 1631-1638
36. Andersen J.R., Schrag T., Melchinger A.E., Zein I., and Lubberstedt T. Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111 (2005) 206-217
37. Devlin B., and Roeder K. Genomic control for association studies. Biometrics 55 (1999) 997-1004
38. Pritchard J.K., and Rosenberg N.A. Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65 (1999) 220-228
39. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
40. Falush D., Stephens M., and Pritchard J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164 (2003) 1567-1587
41. Pritchard J.K. Deconstructing maize population structure. Nat Genet 28 (2001) 203-204
42. Whitt S.R., Wilson L.M., Tenaillon M.I., Gaut B.S., and Buckler E.S. Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci USA 99 (2002) 12959-12962
43. Szalma S.J., Buckler E.S., Snook M.E., and McMullen M.D. Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110 (2005) 1324-1333
44. Wong J.C., Lambert R.J., Wurtzel E.T., and Rocheford T.R. QTL and candidate genes phytoene synthase and zeta-carotene desaturase associated with the accumulation of carotenoids in maize. Theor Appl Genet 108 (2004) 349-359
45. Laurie C.C., Chasalow S.D., LeDeaux J.R., McCarroll R., Bush D., Hauge B., Lai C., Clark D., Rocheford T.R., and Dudley J.W. The genetic architecture of response to long-term artificial selection for oil concentration in the maize kernel. Genetics 168 (2004) 2141-2155
46. Chardon F., Virlon B., Moreau L., Falque M., Joets J., Decousset L., Murigneux A., and Charcosset A. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168 (2004) 2169-2185
47. Parisseaux B., and Bernardo R. In silico mapping of quantitative trait loci in maize. Theor Appl Genet 109 (2004) 508-514
48. Zhang Y.M., Mao Y., Xie C., Smith H., Luo L., and Xu S. Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.). Genetics 169 (2005) 2267-2275
49. Yu J., Arbelbide M., and Bernardo R. Power of in silico QTL mapping from phenotypic, pedigree, and marker data in a hybrid breeding program. Theor Appl Genet 110 (2005) 1061-1067
50. Stich B., Melchinger A.E., Frisch M., Maurer H.P., Heckenberger M., and Reif J.C. Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111 (2005) 723-730
51. Martienssen R.A., Rabinowicz P.D., O'Shaughnessy A., and McCombie W.R. Sequencing the maize genome. Curr Opin Plant Biol 7 (2004) 102-107