Association mapping of yellow pigment in an elite collection of durum wheat cultivars and breeding lines

Genome

Volumn 51, Issue 12, 2008, Pages 1016-1025

  Reimer, S ^a   Pozniak, C J ^a   Clarke, F R ^b   Clarke, J M ^b   Somers, D J ^c   Knox, R E ^b   Singh, A K ^b  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

^b AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^c Cereal Research Centre   (Canada)

Author keywords

Association mapping; Durum wheat; Phytoene synthase; Population structure; Yellow pigment

Indexed keywords

PIGMENT;

ARTICLE; BREEDING; CHROMOSOME MAP; GENE LINKAGE DISEQUILIBRIUM; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; METHODOLOGY; OSMOLARITY; PHYLOGENY; PHYSIOLOGY; PLANT CHROMOSOME; QUANTITATIVE TRAIT LOCUS; WHEAT;

BREEDING; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENETIC VARIATION; LINKAGE DISEQUILIBRIUM; OSMOLAR CONCENTRATION; PHYLOGENY; PIGMENTS, BIOLOGICAL; QUANTITATIVE TRAIT LOCI; SELECTION (GENETICS); TRITICUM;

TRITICUM AESTIVUM; TRITICUM TURGIDUM; TRITICUM TURGIDUM SUBSP. DURUM;

EID: 57149099609     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G08-083     Document Type: Article

References (41)

1. AACC International. 2000. Approved methods of the American Association of Cereal Chemists. 10th ed. AACC International, St. Paul, Minn.
2. Agrama, H.A., Eizenga, G.C., and Yan, W. 2007. Association mapping of yield and its components in rice cultivars. Mol. Breed. 19: 341-356. doi:10.1007/s11032-006-9066-6.
3. Akhunov, E.D., Goodyear, A.W., Geng, S., Qi, L.L., Echalier, B., Gill, B.S., et al. 2003. The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res. 13: 753-763. doi:10.1101/gr.808603. PMID:12695326.
4. Botstein, D., White, R.L., Skolnick, M., and Davis, R.W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331. PMID:6247908.
5. Breseghello, F., and Sorrells, M.E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 172: 1165-1177. doi:10.1534/genetics.105.044586. PMID:16079235.
6. Buckler, E.S., IV, and Thornsberry, J.M. 2002. Plant molecular diversity and applications to genomics. Curr. Opin. Plant Biol. 5: 107-111. doi:10.1016/S1369-5266(02)00238-8. PMID:11856604.
7. Cervigni, G., Zhang, W., Picca, A., Carrera, A., Helguera, M., Manthey, F., et al. 2007. QTL mapping for LOX activity and quality traits in durum wheat Triticum turgidum L. var. durum. In Proceedings of the 7th International Wheat Conference: Wheat Production in Stressed Environments, Mar del Plata, Argentina, 27 November - 2 December 2005. Edited by H.T. Buck, J.E. Nisi, and N. Salomón. Springer, the Netherlands.
8. Chao, S., Zhang, W., Dubcovsky, J., and Sorrells, M. 2007. Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci. 47: 1018-1030. doi:10.2135/cropsci2006.06.0434.
9. Clarke, F.R., Yates, S.M., Clarke, J.M., DePauw, R.M., and McLaren, C.G. 2003. The international crop information system: a useful tool for wheat breeding programs. In Proceedings of the 10th International Wheat Genetics Symposium, Paestum, Italy, 1-6 September 2003. Vol. 2. Edited by N.E. Pogna, M. Romano, E.A. Pogna, and G. Galterio. S.I.M.I., Rome. pp. 684-686.
10. Clarke, J.M., McLeod, J.G., McCaig, T.N., DePauw, R.M., Knox, R.E., and Fernandez, M.R. 1998. AC Avonlea durum wheat. Can. J. Plant Sci. 78: 621-623.
11. Clarke, J.M., McLeod, J.G., DePauw, R.M., Marchylo, B.A., McCaig, T.N., Knox, R.E., et al. 2000. AC Pathfinder durum wheat. Can. J. Plant Sci. 80: 347-349.
12. Clarke, J.M., McCaig, T.N., DePauw, R.M., Knox, R.E., Ames, N.P., Clarke, F.R., et al. 2005a. Commander durum wheat. Can. J. Plant Sci. 85: 901-904.
13. Clarke, J.M., McCaig, T.N., DePauw, R.M., Knox, R.E., Clarke, F.R., Fernandez, M.R., and Ames, N.P. 2005b. Strongfield durum wheat. Can. J. Plant Sci. 85: 651-654.
14. Crossa, J., Burgueño, J., Dreisigacker, S., Vargas, M., Herrera-Foessel, S.A., Lillemo, M., et al. 2007. Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics, 177(3): 1889-1913. doi:10.1534/genetics.107.078659. PMID:17947425.
15. Elouafi, I., Nachit, M.M., and Martin, L.M. 2001. Identification of a microsatellite on chromosome 7B showing a strong linkage with yellow pigment in durum wheat (Triticum turgidum L. var. durum). Hereditas, 135: 255-261. doi:10.1111/j.1601-5223.2001.t01-1-00255.x. PMID:12152344.
16. Flint-Garcia, S.A., Thornsberry, J.M., and Buckler, E.S., IV. 2003. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54: 357-374. doi:10.1146/annurev.arplant.54.031902.134907. PMID:14502995.
17. Gaut, B.S., and Long, A.D. 2003. The lowdown on linkage disequilibrium. Plant Cell, 15: 1502-1506. doi:10.1105/tpc.150730. PMID:12837942.
18. Hessler, T.G., Thomson, M.J., Benscher, D., Nachit, M.M., and Sorrells, M.E. 2002. Association of a lipoxygenase locus, Lpx-B1, with variation in lipoxygenase activity in durum wheat seeds. Crop Sci. 42: 1695-1700.
19. Kim, H.S., and Ward, R.W. 1997. Genetic diversity in eastern U.S. soft winter wheat (Triticum aestivum L. em. Thell.) based on RFLPs and coefficients of parentage. Theor. Appl. Genet. 94: 472-479. doi:10.1007/s001220050439.
20. Littell, R.C., Milliken, G.A., Stroup, W.W., and Wolfinger, R.D. 1996. SAS system for mixed models. SAS Institute Inc., Cary, N.C. Liu, K., and Muse, S.V. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 21: 2128-2129. doi:10.1093/bioinformatics/ bti282. PMID:15705655.
21. Maccaferri, M., Sanguineti, M.C., Donini, P., and Tuberosa, R. 2003. Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theor. Appl. Genet. 107: 783-797. doi:10.1007/s00122-003-1319-8. PMID:12845433.
22. Mares, D.J., and Campbell, A.W. 2001. Mapping components of flour and noodle colour in Australian wheat. Aust. J. Agric. Res. 52: 1297-1309. doi:10.1071/AR01048.
23. Neter, J., Kutner, M.H., Nachtshein, C.J., and Wasserman, W. 1996. Applied linear statistical models. McGraw-Hill, New York.
24. Page, R. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12: 357-358.
25. Parker, G.D., Chalmers, K.J., Rathjen, A.J., and Langridge, P. 1998. Mapping loci associated with flour colour in wheat (Triticum aestivum L.). Theor. Appl. Genet. 97: 238-245. doi:10.1007/s001220050891.
26. Patil, R.M., Oak, M.D., Tamhankar, S.A., Sourdille, P., and Rao, V.S. 2008. Mapping and validation of a major QTL for yellow pigment content on 7AL in durum wheat (Triticum turgidum L. ssp. durum). Mol. Breed. 21: 485-496. doi:10.1007/s11032-007-9147-1.
27. Pozniak, C.J., Knox, R.E., Clarke, F.R., and Clarke, J.M. 2007. Identification of QTL and association of a phytoene synthase gene with endosperm colour in durum wheat. Theor. Appl. Genet. 114: 525-537. doi:10.1007/s00122-006-0453-5. PMID:17131106.
28. Pritchard, J.K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. PMID:10835412.
29. Remington, D.L., Thornsberry, J.M., Matsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., et al. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. U.S.A. 98: 11479-11484. doi:10.1073/pnas.201394398. PMID:11562485.
30. Rogers, J.S. 1972. Measures of genetic similarity and genetic distance. Studies in genetics. VII. University of Texas Publ. 7213: 145-153.
31. Rostoks, N., Ramsay, L., MacKenzie, K., Cardle, L., Bhat, P.R., Roose, M.L., et al. 2006. Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc. Natl. Acad. Sci. U.S.A. 103: 18656-18661. doi:10.1073/pnas.0606133103. PMID:17085595.
32. Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18: 233-234. doi:10. 1038/72708. PMID:10657137.
33. Somers, D.J., Isaac, P., and Edwards, K. 2004. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 109: 1105-1114. doi:10.1007/s00122-004-1740-7. PMID:15490101.
34. Somers, D.J., Banks, T., DePauw, R., Fox, S., Clarke, J., Pozniak, C., and McCartney, C. 2007. Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome, 50: 557-567. doi:10.1139/G07-031. PMID:17632577.
35. Spielmeyer, W., Moullet, O., Laroche, A., and Lagudah, E.S. 2000. Highly recombinogenic regions at seed storage protein loci on chromosome IDS of Aegilops tauschii, the D- genome donor of wheat. Genetics, 155: 361-367. PMID:10790409.
36. Tenaillon, M.I., Sawkins, M.C., Long, A.D., Gaut, R.L., Doebley, J.F., and Gaut, B.S. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. U.S.A. 98: 9161-9166. doi:10.1073/pnas.151244298. PMID:11470895.
37. Tommasini, L., Schnurbusch, T., Fossati, D., Mascher, F., and Keller, B. 2007. Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor. Appl. Genet. 115: 697-708. doi:10.1007/s00122-007-0601-6. PMID:17634916.
38. Townley-Smith, T.F., DePauw, R.M., Lendrum, C.W.B., McCrystal, G.E., and Patterson, L.A. 1987. Kyle durum wheat. Can. J. Plant Sci. 67: 225-227.
39. Weir, B.S. 1996. Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates Inc., Sunderland, Mass.
40. Yu, J., and Buckler, E.S. 2006. Genetic association mapping and genome organization of maize. Curr. Opin. Biotechnol. 17: 155-160. PMID:16504497.
41. Zhang, W., and Dubcovsky, J. 2008. Association between allelic variation at the phytoene synthase 1 gene and yellow pigment content in the wheat grain. Theor. Appl. Genet. 116: 635-645. doi:10.1007/s00122-007-0697-8. PMID:18193186.