Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa

Genome

Volumn 50, Issue 10, 2007, Pages 963-973

  Zhao, Jianjun ^a,b   Paulo, Maria João ^a,c   Jamar, Diaan ^a   Lou, Ping ^a   Van Eeuwijk, Fred ^a   Bonnema, Guusje ^a   Vreugdenhil, Dick ^a   Koornneef, Maarten ^a,c  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b AGRICULTURAL UNIVERSITY OF HEBEI   (China)

^c MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

Author keywords

Association mapping; Brassica rapa; Genetic variation; Phytate

Indexed keywords

PHYTIC ACID;

ARTICLE; CHEMISTRY; FLOWER; GENETIC LINKAGE; GENETIC MARKER; GENETICS; GROWTH, DEVELOPMENT AND AGING; PLANT LEAF; QUANTITATIVE TRAIT LOCUS; TURNIP;

BRASSICA RAPA; FLOWERS; GENETIC MARKERS; LINKAGE (GENETICS); PHYTIC ACID; PLANT LEAVES; QUANTITATIVE TRAIT LOCI;

BRASSICA RAPA; BRASSICA RAPA SUBSP. RAPA;

EID: 36349037129     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G07-078     Document Type: Article

References (37)

1. Aranzana, M.J., Kim, S., Zhao, K., Bakker, E., Horton, M., Jakob, K., et al. 2005. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet. 1(5): e60. doi:10.1371/journal.pgen.0010060.
2. Benjamini, Y., and Yekutieli, D. 2005. Quantitative trait loci analysis using the false discovery rate. Genetics, 171: 783-790. doi:10.1534/genetics.104.036699.
3. Bentsink, L., Yuan, K., Koornneef, M., and Vreugdenhil, D. 2003. The genetics of phytate and phosphate accumulation in seeds and leaves of Arabidopsis thaliana using natural variation. Theor. Appl. Genet. 106: 1234-1243.
4. 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.
5. Dobson, A.J. 2002. An introduction to generalized linear models. 2nd ed. Chapman & Hall/CRC, Boca Raton, Fla.
6. Falush, D., Stephens, M., and Pritchard, J.K. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164: 1567-1587.
7. Farnir, F., Coppieters, W., Arranz, J.J., Berzi, P., Cambisano, N., Grisart, B., et al. 2000. Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 10: 220-227. doi:10.1101/gr.10.2.220.
8. Fisher, R.A. 1954. Statistical methods for research workers. 12th ed. Hafner Publishing Company Inc., New York.
9. Flint-Garcia, S.A., Thornsberry, J.M., and Buckler, E.S. 2003. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54: 357-374. doi:10.1146/annurev.arplant.54.031902.134907.
10. Garris, A.J., McCouch, S.R., and Kresovich, S. 2003. Population structure and its effect on haplotype diversity and linkage dise-quilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics, 165: 759-769.
11. Gupta, P.K., Rustgi, S., and Kulwal, P.L. 2005. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Biol. 57: 461-485. doi:10.1007/s11103-005-0257-z.
12. Jorde, L.B. 2000. Linkage disequilibrium and the search for complex disease genes. Genome Res. 10: 1435-1444. doi:10.1101/gr.144500.
13. Koornneef, M., Alonso-Blanco, C., and Vreugdenhil, D. 2004. Naturally occurring genetic variation in Arabidopsis thaliana. Annu. Rev. Plant Biol. 55: 141-172. doi:10.1146/annurev.arplant.55.031903.141605.
14. Kraakman, A.T.W., Niks, R.E., van den Berg, P.M.M.M., Stam, P., and van Eeuwijk, F.A. 2004. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics, 168: 435-446. doi:10.1534/genetics.104.026831.
15. Kraakman, A.T.W., Martinez, F., Mussiraliev, B., van Eeuwijk, F.A., and Niks, R.E. 2006. Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol. Breed. 17: 41-58. doi:10.1007/s11032-005-1119-8.
16. Kruglyak, L. 1999. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139-144. doi:10.1038/9642.
17. Lander, E.S., and Schork, N.J. 1994. Genetic dissection of complex traits. Science (Washington, DC), 265: 2037-2048. doi:10.1126/science. 8091226.
18. Lou, P., Zhao, J., Kim, J.S., Shen, S., Pino Del Carpio, D., Song, X., et al. 2007. Quantitative trait loci for flowering time and morphological traits in multiple populations of Brassica rapa. J. Exp. Bot. In press.
19. Mackay, I., and Powell, W. 2007. Methods for linkage disequilibrium mapping in crops. Trends Plant Sci. 12: 57-63. doi:10.1016/j.tplants. 2006.12.001.
20. Malosetti, M., Linden, C.G., Vosman, B., and Eeuwijk, F.A. 2007. A mixed model approach to association mapping using pedigree information with an illustration to resistance for Phytophthora infestans in potato. Genetics, 175: 879-889. doi:10.1534/genetics. 105.054932.
21. Mollers, C., Lickfett, T., Matthaus, B., and Velasco, L. 1999. Influence of P-fertilizer on phytic acid content in seeds of Brassica napus L. and development of a NIRS calibration. In Proceedings of the 10th International Rapeseed Congress, Canberra, Australia, 26-29 September 1999. Edited by N. Wratten and P.A. Salisbury, pp. 26-29.
22. Nordborg, M., Borevitz, J.O., Bergelson, J., Berry, C.C., Chory, J., Hagenblad, J., et al. 2002. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30: 190-193. doi:10.1038/ng813.
23. Nordborg, M., Hu, T.T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., et al. 2005. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3(7): e196. doi:10.1371/journal.pbio.0030196.
24. Nsengimana, J., Baret, P., Haley, C.S., and Visscher, P.M. 2004. Linkage disequilibrium in the domesticated pig. Genetics, 166: 1395-1404. doi:10.1534/genetics.166.3.1395.
25. Palaisa, K.A., Morgante, M., Williams, M., and Rafalski, A. 2003. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell, 15: 1795-1806. doi:10.1105/tpc.012526.
26. Payne, R.W., and Arnold, G.M. 2002. Genstat Release 6.1. Reference manual. Part 3. Procedure Library PL14. VSN International, Oxford, U.K.
27. Peng, J., Slominsiki, B.A., Guenter, W., Campbell, L.D., and Xiong, Y.Z. 2001. The anti-nutritional factors in Chinese double-low rapeseed meal. J Chinese Cereals and Oil Association, 16: 6-10.
28. Pritchard, J.K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155: 945-959.
29. Raboy, V., Young, K.A., Dorsch, J.A., and Cook, A. 2001. Genetics and breeding of seed phosphorus and phytic acid. J. Plant Physiol. 158: 489-497. doi:10.1078/0176-1617-00361.
30. 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.
31. SAS Institute Inc. 1999. SAS/STAT®. Version 9.1 [computer program]. SAS Institute Inc., Cary, N.C.
32. 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.
33. Varshney, R.K., Graner, A., and Sorrells, M.E. 2005. Genomics-assisted breeding for crop improvement. Trends Plant Sci. 10: 621-630. doi:10.1016/j.tplants.2005.10.004.
34. White, P.J., and Broadley, M.R. 2005. Biofortifying crops with essential mineral elements. Trends Plant Sci. 10: 586-593. doi:10.1016/j.tplants. 2005.10.001.
35. Yu, J., Pressoir, G., Briggs, W.H., Bi, I.V., Yamasaki, M., Doebley, J.F., et al. 2006. A unified mixed-model method for association mapping accounting for multiple levels of relatedness. Nat. Genet. 38: 203-208. doi:10.1038/ng1702.
36. Zhao, J. 2007. The genetics of phytate content and morphological traits in Brassica rapa. Ph.D. thesis. Wageningen University, the Netherlands. ISBN 90-8504-588-6. pp. 61-107.
37. Zhao, J., Wang, X., Deng, B., Lou, P., Wu, J., Sun, R., et al. 2005. Genetic relationships within Brassica rapa as inferred from AFLP fingerprints. Theor. Appl. Genet. 110: 1301-1314. doi:10.1007/s00122-005- 1967-y.