Polymorphisms of IFS1 and IFS2 gene are associated with isoflavone concentrations in soybean seeds

Plant Science

Volumn 175, Issue 4, 2008, Pages 505-512

  Cheng, Hao ^a   Yu, Oliver ^b   Yu, Deyue ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

Author keywords

Association analysis; Isoflavone; Isoflavone synthase; Linkage disequilibrium; Soybean

Indexed keywords

GLYCINE MAX; GLYCINE SOJA;

EID: 49349090255     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2008.05.020     Document Type: Article

References (59)

1. Messina M. Soy, soy phytoestrogens (isoflavones), and breast cancer. Am. J. Clin. Nutr. 70 (1999) 574-575
2. Nestel P. Isoflavones: their effects on cardiovascular risk and functions. Curr. Opin. Lipidol. 14 (2003) 3-8
3. Williamson-Hughes P.S., Flickinger B.D., Messina M.J., and Empie M.W. Isoflavone supplements containing predominantly genistein reduce hot flash symptoms: a critical review of published studies. Menopause 13 (2006) 831-839
4. Duffy C., Perez K., and Partridge A. Implications of phytoestrogen intake for breast cancer. CA Cancer J. Clin. 57 (2007) 260-277
5. Goetzl M.A., Van Veldhuizen P.J., and Thrasher J.B. Effects of soy phytoestrogens on the prostate. Prostate Cancer Prostatic Dis. 10 (2007) 216-223
6. Wuttke W., Jarry H., and Seidlova-Wuttke D. Isoflavones-safe food additives or dangerous drugs. Ageing Res. Rev. 6 (2007) 150-188
7. Turck D. Soy protein for infant feeding: what do we know. Curr. Opin. Clin. Nutr. Metab. Care 10 (2007) 360-365
8. Nielsen I.L., and Williamson G. Review of the factors affecting bioavailability of soy isoflavones in humans. Nutr Cancer 57 (2007) 1-10
9. Yu O., and McGonigle B. Metabolic engineering of isoflavone biosynthesis. Adv. Agron. 86 (2005) 147-190
10. Wang H.J., and Murphy P.A. Mass balance study of isoflavones during soybean processing. J. Agric. Food Chem. 44 (1996) 2377-2383
11. Griffith A.P., and Collison M.W. Improved methods for the extraction and analysis of isoflavones from soy-containing foods and nutritional supplements by reversed-phase high-performance liquid chromatography and liquid chromatography-mass spectrometry. J. Chromatogr. A 913 (2001) 397-413
12. Eldridge A., and Kwolek W. Soybean isoflavones: effect of environment and variety on composition. J. Agric. Food Chem. 31 (1983) 394-396
13. Wang H.J., and Murphy P.A. Isoflavone composition of American and Japanese soybeans in Iowa: effects of variety, crop, year, and location. J. Agric. Food Chem. 42 (1994) 1674-1677
14. Hoeck J.A., Fehr W.R., Murphy P.A., and Welke G.A. Influence of genotype and environment on isoflavone contents of soybean. Crop Sci. 40 (2000) 48-51
15. Choi J.S., Kwon T.W., and Kim J.S. Isoflavone contents in some varieties of soybean. Foods Biotechnol. 5 (1996) 167-169
16. Kassem M.A., Meksem K., Iqbal M.J., Njiti V.N., Banz W.J., Winters T.A., Wood A., and Lightfoot D.A. Definition of soybean genomic regions that control seed phytoestrogen amounts. J. Biomed. Biotechnol. 2004 (2004) 52-60
17. Primomo V.S., Poysa V., Ablett G.R., Jackson C.J., Gijzen M., and Rajcan I. Mapping QTL for individual and total isoflavone content in soybean seeds. Crop Sci. 45 (2005) 2454-2464
18. Lopez C., Piégu B., Cooke R., Delseny M., Tohme J., and Verdier V. Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz). Theor. Appl. Genet. 110 (2005) 425-431
19. Akashi T., Aoki T., and Ayabe S. Cloning and functional expression of a cytochrome P450 cDNA encoding 2-hydroxyisoflavanone synthase involved in biosynthesis of the isoflavonoid skeleton in licorice. Plant Physiol. 121 (1999) 821-828
20. Steele C.L., Gijzen M., Qutob D., and Dixon R.A. Molecular characterization of the enzyme catalyzing the aryl migration reaction of isoflavonoid biosynthesis in soybean. Arch. Biochem. Biophys. 367 (1999) 146-150
21. Jung W., Yu O., Lau S.M., O'Keefe D.P., Odell J., Fader G., and McGonigle B. Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes. Nat. Biotechnol. 18 (2000) 208-212
22. Subramanian S., Stacey G., and Yu O. Endogenous isoflavones are essential for the establishment of symbiosis between soybean and Bradyrhizobium japonicum. Plant J. 48 (2006) 261-273
23. Edwards D., Forster J., Chagné D., and Batley J. What are SNPs. In: Oraguzie N., Rikkerink E., Gardiner S., and Silva H.D. (Eds). Association Mapping in Plants (2007), Springer 41-52
24. Flint-Garcia S.A., Thornsberry J.M., and Edwards B. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54 (2003) 357-374
25. Kerem B., Rommens J.M., Buchanan J.A., Markiewicz D., Cox T.K., Chakravarti A., Buchwald M., and Tsui L.C. Identification of the cystic fibrosis gene: genetic analysis. Science 245 (1989) 1073-1080
26. Corder E.H., Saunders A.M., Risch N.J., Strittmatter W.J., Schmechel D.E., Gaskell P.C., Rimmler J.B., Locke P.A., Conneally P.M., and Schmader K.E. Protective effect of apolipoprotein E type 2 allele for late onset Alzheimer disease. Nat. Genet. 7 (1994) 180-184
27. Chanock S.J., Manolio T., Boehnke M., Boerwinkle E., Hunter D.J., Thomas G., Hirschhorn J.N., Abecasis G., Altshuler D., and Bailey-Wilson J.E. Replicating genotype-phenotype associations. Nature 447 (2007) 655-660
28. Buckler E.S., and Thornsberry J.M. Plant molecular diversity and applications to genomics. Curr. Opin. Plant Biol. 5 (2002) 107-111
29. 3;5,13,14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. Am. J. Hum. Genet. 43 (1988) 520-526
30. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
31. Thornsberry J.M., Goodman M.M., Doebley J., Kresovich S., Nielsen D., and Buckler Iv E.S. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28 (2001) 286-289
32. 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. U.S.A. 99 (2002) 12959-12962
33. 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
34. Andersen J.R., Zein I., Wenzel G., Krützfeldt B., Eder J., Ouzunova M., and Lübberstedt T. High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds. Theor. Appl. Genet. 114 (2007) 307-319
35. Aranzana M.J., Kim S., Zhao K., Bakker E., Horton M., Jakob K., Lister C., Molitor J., Shindo C., Tang C., et al. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet. 1 (2005) e60
36. Zhao K., Aranzana M.J., Kim S., Lister C., Shindo C., Tang C., Toomajian C., Zheng H., Dean C., Marjoram P., et al. An Arabidopsis example of association mapping in structured samples. PLoS Genet. 3 (2007) e4
37. Ravel C., Praud S., Canaguier A., Dufour P., Giancola S., Balfourier F., Chalhoub B., Brunel D., Linossier L., and Dardevet M. DNA sequence polymorphisms and their application to bread wheat quality. Euphytica 158 (2007) 331-336
38. Wang Y., and Gai J. Study on the ecological regions of soybean in China II. Ecological environment and representative varieties. Ying Yong Sheng Tai Xue Bao 13 (2002) 71-75
39. Bennett J., Yu O., Heatherly L., and Krishnan H. Accumulation of genistein and daidzein, soybean isoflavones implicated in promoting human health, is significantly elevated by irrigation. J. Agric. Food Chem. 52 (2004) 7574-7579
40. Keim P., Olson T.C., and Shoemaker R.C. A rapid protocol for isolating soybean DNA. Soybean Genet. Newsl. 15 (1988) 150-152
41. Subramanian S., Hu X., Lu G., Odelland J.T., and Yu O. The promoters of two isoflavone synthase genes respond differentially to nodulation and defense signals in transgenic soybean roots. Plant Mol. Biol. 54 (2004) 623-639
42. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
43. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., Rozas R., and Dna S.P. DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
44. Nei M. Molecular Evolutionary Genetics (1987), Columbia University Press, New York
45. Watterson G. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7 (1975) 256-276
46. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
47. Fu Y., and Li W. Statistical tests of neutrality of mutations. Genetics 133 (1993) 693-709
48. Bradbury P.J., Zhang Z., Kroon D.E., Casstevens T.M., Ramdoss Y., and Buckler E.S. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23 (2007) 2633-2635
49. Weir B. Genetic Data Analysis. Chinese ed. (1996), Publishing House of Agricultural Science, Beijing
50. Falush D., Stephens M., and Pritchard J.K. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes 7 (2007) 574-578
51. Wang H.J., and Murphy P.A. Isoflavone content in commercial soybean foods. J. Agric. Food Chem. 42 (1994) 1666-1673
52. Zhu Y., Song Q., Hyten D., Tassell C.V., Matukumalli L., Grimm D., Hyatt S., Fickus E., Young N., and Cregan P. Single-nucleotide polymorphisms in soybean. Genetics 163 (2003) 1123-1134
53. Hyten D., Choi I., Song Q., Shoemaker R., Nelson R., Costa J., Specht J., and Cregan P. Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175 (2007) 1937-1944
54. Cronk Q. Plant eco-devo: the potential of poplar as a model organism. New Phytol. 166 (2005) 39-48
55. 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. U.S.A. 98 (2001) 9161-9166
56. Long A., Lyman R., Langley C., and Mackay T. Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. Genetics 149 (1998) 999-1017
57. Yu J., and Buckler E. Genetic association mapping and genome organization of maize. Curr. Opin. Biotechnol. 17 (2006) 155-160
58. Sharbel T., Haubold B., and Mitchell-Olds T. Genetic isolation by distance in Arabidopsis thaliana: bio-geography and postglacial colonization of Europe. Mol. Ecol. 9 (2000) 2109-2118
59. Andersen J., and Lübberstedt T. Functional markers in plants. Trends Plant Sci. 8 (2003) 554-560