Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum L.) germplasm representing different market classes

Crop Science

Volumn 47, Issue 3, 2007, Pages 1018-1030

  Chao, Shiaoman ^a   Zhang, Wenjun ^b   Dubcovsky, Jorge ^b   Sorrells, Mark ^c  

^a USDA ARS Red River Valley Agricultural Research Center   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRITICUM AESTIVUM;

EID: 34548181796     PISSN: 0011183X     EISSN: None     Source Type: Journal    
DOI: 10.2135/cropsci2006.06.0434     Document Type: Article

References (61)

1. Akhunov, E., A.W. Goodyear, S. Geng, L. Qi, B. Echalier, B.S. Gill, Miftahudin, J.P. Gustafson, G. Lazo, S. Chao, O.D. Anderson, A.M. Linkiewicz, J. Dubcovsky, M. La Rota, M.E. Sorrells, D. Zhang, H. Nguyen, V. Kalavacharla, K. Hossain, S.F. Kianian, J. Peng, N.L.V. Lapitan, J.L. Gonzalez-Hernandez, J.A. Anderson, D. Choi, T.J. Close, M. Dilbirligi, K.S. Gill, M.K. Walker-Simmons, C. Steber, P.E. McGuire, C.O. Qualset, and J. Dvorak. 2003. The organization and rate of evolution of the wheat genomes are correlated with recombination rates along chromosome arms. Genome Res. 13:753-763.
2. Ardlie, K.G., L. Kruglyak, and M. Seielstad. 2002. Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3:299-309.
3. Barrett, B.A., and K.K. Kidwell. 1998. AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Sci. 38:1261-1271.
4. Barrett, B.A., K.K. Kidwell, and P.N. Fox. 1998. Comparison of AFLP and pedigree-based genetic diversity assessment methods using wheat cultivars from the Pacific Northwest. Crop Sci. 38:1271-1278.
5. Botstein, D., R.L. White, M. Skolnick, and R.W. Davis. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32:314-331.
6. Breseghello, F., and M.E. Sorrells. 2006. Association mapping of kernel size and milling quality in wheat (Tritkum aestivum L.) cultivars. Genetics 172:1165-1177.
7. Brown, G.R., G.P. Gill, R.J. Kuntz, C.H. Langley, and D.B. Neale. 2004. Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. USA 101:15255-15260.
8. Buckler, E.S., B.S. Gaut, and M.D. McMullen. 2006. Molecular and functional diversity of maize. Curr. Opin. Plant Biol. 9:172-176.
9. Buckler, E.S., IV, and J.M. Thornsberry. 2002. Plant molecular diversity and applications of genomics. Curr. Opin. Plant Biol. 5:107-111.
10. Caldwell, K.S., J. Russell, P. Langridge, and W. Powell. 2006. Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172:557-567.
11. Chen, H.B., J.M. Martin, M. Lavin, and L.E. Talbert. 1994. Genetic diversity in hard red spring wheat based on sequence-tagged-site PCR markers. Crop Sci. 34:1628-1632.
12. Cox, T.S., J.P. Murphy, and D.M. Rodgers. 1986. Changes in genetic diversity in the red winter wheat regions of the United States. Proc. Natl. Acad. Sci. USA 83:5583-5586.
13. Diwan, N., and P.B. Cregan. 1997. Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean. Theor. Appl. Genet. 95:723-733.
14. Dreisigacker, S., P. Zhang, M.L. Warburton, M. Van Ginkel, D. Hoisington, and A.E. Melchinger. 2004. SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments. Crop Sci. 44:381-388.
15. Dvorak, J., P.E. McGuire, and B. Cassidy. 1988. Apparent sources of the A genomes of wheats inferred from the polymorphism in abundance and restriction fragment length of repeated nucleotide sequences. Genome 30:680-689.
16. Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol. Bioinformatics Online 1:4750.
17. Falush, D., M. Stephens, and J.K. Pritchard. 2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164:1567-1587.
18. Fu, D., P. Szucs, L. Yan, M. Helguera, J. Skinner, P. Hayes, and J. Dubcovsky. 2005. Large deletions in the first intron of the Vrn-1 gene are associated with spring growth habit in barley and polyploidy wheat. Mol. Genet. Gen. 273:54-65.
19. Fufa, H., P.S. Baenziger, B.S. Beecher, I. Dweikat, R.A. Graybosch, and K.M. Eskridge. 2005. Comparison of phenotypic and molecular marker-based classification of hard red winter wheat cultivars. Euphytica 145:133-146.
20. Garris, A.J., S.R. McCouch, and S. Kresovich. 2003. Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759-769.
21. Gaut, B.S., and A.D. Long. 2003. The lowdown on linkage disequilibrium. Plant Cell 15:1502-1506.
22. Glaubitz, J.C. 2004. CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Notes 4:309-310.
23. Gupta, P.K., H.S. Balyan, K.J. Edwards, P. Isaac, V. Korzun, M. Roder, M.-F. Gautier, P. Joudrier, A.R. Schlatter, J. Dubcovsky, R.C. de la Pena, M. Khairallah, G. Penner, M.J. Hayden, P. Sharp, B. Keller, R.C.C. Wang, J.P. Hardouin, P. Jack, and P. Leroy. 2002. Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor. Appl. Genet. 105:413-422.
24. Guyomarc'h, H., P. Sourdille, G. Charmet, K.J. Edwards, and M. Bernard. 2002. Characterization of polymorphic microsatellite markers from Aegilops tauschii and transferability to the D-genome of bread wheat. Theor. Appl. Genet. 104:1164-1172.
25. Hamblin, M.T., S.E. Mitchell, C.M. White, J. Gallego, R. Kukatla, R.A. Wing, A.H. Peterson, and S. Kresovish. 2004. Comparative population genetics of the Panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics 167:471-483.
26. Huang, X.Q., A. Borner, M.S. Roder, and M.W. Ganal. 2002. Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theor. Appl. Genet. 105:699-707.
27. Huttley, G.A., M.W. Smith, M. Carrington, and S.J. O'Brien. 1999. A scan of linkage disequilibrium across the human genome. Genetics 152:1711-1722.
28. Kim, H.S., and R.W. Ward. 1997. Genetic diversity in eastern US soft winter wheat (Triticum aestivum L. Em. Thell.) based on RFLPs and coefficients of parentage. Theor. Appl. Genet. 94:472-479.
29. Kraakman, A.T.W., R.E. Niks, P.M.M.M. Van den Berg, P. Stam, and F.A. Van Eeuwijk. 2004. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435-446.
30. Kraft, T., M. Hansen, and N.-O. Nilsson. 2000. Linkage disequilibrium and fingerprinting in sugar beet. Theor. Appl. Genet. 101:323-326.
31. Liu, K., M. Goodman, S. Muse, J.S. Smith, E. Buckler, and J. Doebley. 2003. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellite. Genetics 165:2117-2128.
32. Liu, K., and S.V. Muse. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
33. Lu, H., M.A. Redus, J.R. Coburn, J.N. Rutger, S.R. McCouch, and T.H. Tai. 2005. Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci. 45:66-76.
34. Maccaferri, M., M.C. Sanguineti, E. Noli, and R. Tuberosa. 2005. Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol. Breed. 15:271-289.
35. Manifesto, M.M., A.R. Schlatter, H.E. Hopp, E.Y. Suarez, and J. Dubcovsky. 2001. Quantitative evaluation of genetic diversity in wheat germplasm using molecular markers. Crop Sci. 41:682-690.
36. Nordborg, M., J.O. Borevitz, J. Bergelson, C.C. Berry, J. Chory, J. Hagenblad, M. Kreitman, J.N. Maloof, T. Noyes, P.J. Oefner, E.A. Stahl, and D. Wiegel. 2002. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30:190-193.
37. Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.
38. Parker, G.D., P.N. Fox, P. Langridge, K. Chalmers, B. Whan, and P.F. Ganter. 2002, Genetic diversity within Australian wheat breeding programs based on molecular and pedigree data. Euphytica 124:293-306.
39. Paull, J.G., K.J. Chalmers, A. Karakousis, J.M. Kretschmer, S. Manning, and P. Langridge. 1998. Genetic diversity in Australian wheat varieties and breeding material based on RFLP data. Theor. Appl. Genet. 96:435-446.
40. Pestsova, E., M.W. Ganal, and M.S. Roder. 2000. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43:689-697.
41. Plaschke, J., M. Ganal, and M. Roder. 1995. Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor. Appl. Genet. 91:1001-1007.
42. Pritchard, J.K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
43. Reif J.C., A.E. Melchinger, and M. Frisch. 2005. Genetical and mathematical properties of similarity and dissimilarity coefficients applied in plant breeding and seed bank management. Crop Sci. 45:1-7.
44. Remington, D.L., J.M. Thornsberry, Y. Matsuoka, L.M. Wilson, S.R. Whitt, J. Doebley, S. Kresovich, M.M. Goodman, and E.S. Buckler, IV. 2001. Structure of linkage disequilibrium and phenotypic association in the maize genome. Proc. Natl. Acad. Sci. USA 98:11479-11484.
45. Roder, M.S., V. Korzun, K. Wendehake, J. Plaschke, M.-H. Tixier, P. Leroy, and M.W. Ganal. 1998. A microsatellite map of wheat. Genetics 149:2007-2023.
46. Rogers, J.S. 1972. Measures of genetic similarity and genetic distance. p. 145-153. In Studies in genetics VII. University of Texas Publication 7213. Univ. of Texas, Austin.
47. Roussel, V., J. Koenig, M. Beckert, and F. Balfourier. 2004. Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor. Appl. Genet. 108:920-930.
48. Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18:233-234.
49. Simko, I., S. Costanzo, K.G. Haynes, B.J. Chris, and R.W. Jones. 2004. Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato (Solanum tuberosum) through a candidate gene approach. Theor. Appl. Genet. 108:217-224.
50. Skot, L., M.O. Humphreys, I. Armstead, S. Heywood, K.P. Skøt, R. Sanderson, I.D. Thomas, K.H. Chorlton, and N.R.S. Hamilton. 2005. An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Mol. Breed. 15:233-245.
51. Somers, D.J., P. Isaac, and K. Edwards. 2004. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 109:1105-1114.
52. Song, Q.J., E.W. Fickus, and P.B. Cregan. 2002. Characterization of trinucleotide SSR motifs in wheat. Theor. Appl. Genet. 104:286-293.
53. Song, Q.J., J.R. Shi, S. Singh, E.W. Fickus, J.M. Costa, J. Lewis, B.S. Gill, R. Ward, and P.B. Cregan. 2005. Development and mapping of microsatellite (SSR) markers in wheat. Theor. Appl. Genet. 110:550-560.
54. Sourdille, P., S. Singh, T. Cadalen, G.L. Brown-Guedira, G. Gay, L. Qi, B.S. Gill, P. Dufour, A. Murigneux, and M. Bernard. 2004. Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Funct. Integr. Genomics 4:12-25.
55. Sourdille, P., M. Tavaud, G. Charmet, and M. Bernard. 2001. Transferability of wheat microsatellite to diploid Triticeae species carrying the A, B and D genomes. Theor. Appl. Genet. 103:346-352.
56. Stich, B., A.E. Melchinger, M. Frisch, H.P. Maurer, M. Heckenberger, and J.C. Reif 2005. Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor. Appl. Genet. 111:723-730.
57. van Beuningen, L.T., and R.H. Busch. 1997. Genetic diversity among North American spring wheat cultivars: I. Analysis of the coefficient of parentage matrix. Crop Sci. 37:570-579.
58. Weir, B.S. 1996. Genetic data analysis II. Sinauer Associated, Inc., Sunderland, MA.
59. Yan, L., M. Helguera, K. Kato, S. Fukuyama, J. Sherman, and J. Dubcovsky. 2004. Allelic variation at the Vrn-1 promoter region in polyploidy wheat. Theor. Appl. Genet. 109:1677-1686.
60. Yan, L., A. Loukoianov, G. Tranquilli, M. Helguera, T. Fahima, and J. Dubcovsky. 2003. Positional cloning of wheat vernalization gene Vrn1. Proc. Natl. Acad. Sci. USA 100:6263-6268.
61. Yu, J.K., M. La Rota, R.V. Kantety, and M.E. Sorrells. 2004. EST derived SSR markers for comparative mapping in wheat and rice. Mol. Genet. Gen. 271:742-751.