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Genetics and molecular biology of stress tolerance and flavonoid biosynthesis in soybean.
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1. Yan F, Di S, Rojas Rodas F, Rodriguez TO, Murai Y, Iwashina T, Anai T, Takahashi R (2014) Allelic variation of soybean flower color gene W4 encoding dihydroflavonol 4-reductase 2. BMC Plant Biology 14: 58

2. Rojas Rodas F, Rodriguez TO, Murai Y, Iwashina T, Sugawara S, Suzuki M, Nakabayashi R, Yonekura-Sakakibara K, Saito K, Kitajima J, Toda K, Takahashi R (2014) Linkage mapping, molecular cloning and functional analysis of soybean gene Fg2 encoding flavonol 3-O-glucoside (1š6) rhamnosyltransferase. Plant Molecular Biology 84: 287-300.

3.
Rodriguez TO, Rojas Rodas F, Oyoo ME, Senda M, Takahashi R (2013) Inverted repeat of chalcone synthase 3 pseudogene is associated with seed coat discoloration in soybean. Crop Science 53:518–523.

4. Takahashi R, Yamagishi N, Yoshikawa N (2013) A MYB transcription factor controls flower color in soybean. Journal of Heredity 104:149–153.

5. Murai Y, Takahashi R, Rojas Rodas F, Kitajima J, Iwashina T (2013) New flavonol triglycosides from the leaves of soybean cultivars. Natural Product Communications 8:543-456.

6. Tsubokura Y, Matsumura H, Xu M, Liu B, Nakashima H, Anai T, Kong F, Yuan X, Kanamori H, Katayose Y, Takahashi R, Harada K, Abe J (2013) Genetic variation in soybean at the maturity locus E4 is involved in adaptation to long days at high latitudes. Agronomy 3: 113-137.

7. Takahashi R, Morita Y, Nakayama M, Kanazawa A, Abe J (2012) An active CACTA-family transposable element is responsible for flower variegation in wild soybean Glycine soja. Plant Genome 5:62-70.

8. Benitez ER, Hajika M, Takahashi R (2012) Single-base substitution in P1B-ATPase gene is associated with a major QTL for seed cadmium concentration in soybean. Journal of Heredity 103:278-286.

9. Toda K, Kuroiwa H, Senthil K, Shimada N, Aoki T, Ayabe S, Shimada S, Sakuta M, Miyazaki Y, Takahashi R (2012) The soybean F3fH protein is localized to the tonoplast in the seed coat hilum. Planta 236:79-89.

10. Takahashi R, Benitez ER, Oyoo ME, Khan NA, Komatsu S (2011) Nonsense mutation of an MYB transcription factor is associated with purple-blue flower color in soybean. Journal of Heredity 102:458-463.

11. Toda K, Takahashi R, Iwashina T, Hajika M (2011) Difference in chilling-induced flavonoid profiles, antioxidant activity and chilling tolerance between soybean near-isogenic lines for the pubescence color gene. Journal of Plant Research 124:173-182.

12. Oyoo ME, Benitez ER, Kurosaki H, Ohnishi S, Miyoshi T, Kiribuchi-Otobe C, Horigane A, Takahashi R (2011) QTL analysis of soybean seed coat discoloration associated with II TT genotype. Crop Science 51:464-469.

13. Watanabe S, Xia Z, Hideshima R, Tsubokura Y, Sato S, Yamanaka N, Takahashi R, Anai T, Tabata S, Kitamuta K, Harada K (2011) A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics 188:395-407.

14. Hamwich A, Tuyen DD, Cong H, Benitez ER, Takahashi R, Xu DH (2011) Identification and validation of a major QTL for salt tolerance in soybean. Euphytica 179:451-459.

15. Takahashi R, Dubouzet JG, Matsumura H, Yasuda K, Iwashina T (2010) A new allele of flower color gene W1 encoding flavonoid 3f5f-hydroxylase is responsible for light purple flowers in wild soybean Glycine soja. BMC Plant Biology 10:155.

16. Oyoo ME, Benitez ER, Matsumura H, Takahashi R (2010) QTL analysis of seed coat cracking in soybean. Crop Science 50:1230-1235.

17. Benitez ER, Khan NA, Matsumura H, Abe J, Takahashi R (2010) Varietal differences and morphology of cleistogamy in soybean. Crop Science 50:185-190.

18. Oyoo ME, Githiri SM, Benitez ER, Takahashi R (2010) QTL analysis of net-like cracking in soybean seed coats. Breeding Science 60:28-33.

19. Khan NA, Takahashi R, Abe J, Komatsu S (2010) Identification of cleistogamy-associated proteins in flower buds of near-isogenic lines of soybean by differential proteomic analysis. Peptides 30:2095-2102.

20. Matsumura H, Kitajima H, Akada S, Abe J, Minaka N, Takahashi R (2009) Molecular cloning and linkage mapping of cryptochrome multigene family in soybean. Plant Genome 2:271-281.

21. Watanabe S, Hideshima R, Xia Z, Tsubokura Y, Sato S, Nakamoto Y, Yamanaka N, Takahashi R, Ishimoto M, Anai T, Tabata S, Harada K (2009) Map-based cloning of the gene associated with soybean maturity locus E3. Genetics 182:1251-1262.

22. Takahashi R, Matsumura H, Oyoo ME, Khan NA (2008) Genetic and linkage analysis of purple-blue flower in soybean. Journal of Heredity 99:593-597.

23. Iwashina T, Oyoo ME, Khan NA, Matsumura H, Takahashi R (2008) Analysis of flavonoids in flower petals of soybean flower color variants. Crop Science 48:1918-1924.

24. Khan NA, Githiri SM, Benitez ER, Abe J, Kawasaki S, Hayashi T, Takahashi R (2008) QTL analysis of cleistogamy in soybean. Theoretical and Applied Genetics 117:479-487.

25. Matsumura H, Liu B, Abe J, Takahashi R (2008) AFLP mapping of soybean maturity gene E4. Journal of Heredity 99:193-197.

26. Liu B, Kanazawa A, Matsumura H, Takahashi R, Harada K, Abe J (2008) Genetic redundancy in soybean photoresponses associated with duplication of phytochrome A gene. Genetics 180:995-1007.

27. Githiri SM, Yang D, Khan NA, Xu D, Komatsuda T, Takahashi R (2007) QTL analysis of low temperature-induced browning in soybean seed coats. Journal of Heredity 98: 360-366.

28. Takahashi R, Githiri SM, Hatayama K, Dubouzet EG, Shimada N, Aoki T, Ayabe S, Toda K, Matsumura H (2007) A single-base deletion in soybean flavonol synthase gene is associated with magenta flower color. Plant Molecular Biology 63: 125-135.

29. Iwashina T, Githiri SM, Benitez ER, Takemura T, Kitajima J, Takahashi R (2007) Analysis of flavonoids in flower petals of soybean near-isogenic lines for flower and pubescence color genes. Journal of Heredity 98: 250-257.

30. Iwashina T, Benitez ER, Takahashi R (2006) Analysis of flavonoids in pubescence of soybean near-isogenic lines for pubescence color loci. Journal of Heredity 97: 438-443.

31 Githiri SM, Watanabe S, Harada K, Takahashi R (2006) QTL analysis of flooding tolerance in soybean at an early vegetative growth stage. Plant Breeding 125: 613-618.

32. Takahashi R, Benitez ER, Funatsuki H, Ohnishi S (2005) Soybean maturity and pubescence color genes improve chilling tolerance. Crop Science 45: 1387-1393.

33. Toda K, Akasaka M, Dubouzet EG, Kawasaki S, Takahashi R (2005) Structure of flavonoid 3'-hydroxylase gene for pubescence color in soybean. Crop Science 45: 2212-2217.

34. Matsumura H, Watanabe S, Harada K, Senda M, Akada S, Kawasaki S, Dubouzet EG, Minaka N, Takahashi R (2005) Molecular linkage mapping and phylogeny of the chalcone synthase multigene family in soybean. Theoretical and Applied Genetics 110: 1203-1209.

35. Yamanaka N, Watanabe S, Toda K, Hayashi M, Fuchigami H, Takahashi R, Harada K (2005) Fine mapping of FT1 locus for soybean flowering time, using a residual heterozygous line derived from a recombinant inbred line. Theoretical and Applied Genetics 110: 634-639.

36. Benitez ER, Funatsuki H, Kaneko Y, Matsuzawa Y, Bang SW, Takahashi R (2004)Soybean maturity gene effects on seed coat pigmentation and cracking in response to low temperatures. Crop Science 44: 2038-2042.

37. Nakamura T, Yang D, Kalaiselvi S, Uematsu Y, Takahashi R (2003) Genetic analysis of net-like cracking in soybean seed coats. Euphytica 133: 179-184.

38. Toda K, Yang D, Yamanaka N, Watanabe S, Harada K, Takahashi R (2002) A single-base deletion in soybean flavonoid 3'-hydroxylase gene is associated with gray pubescence color. Plant Molecular Biology 50: 187-196.

39. Yang D, Nakamura T, Ohtsubo N, Takahashi K, Takahashi R (2001) Seed coat cracking in soybean isolines for pubescence color and maturity. Crop Science 42: 71-75.

40. Takahashi R, Kurosaki H, Yumoto S, Han OK, Abe J (2001) Genetic and linkage analysis of cleistogamy in soybean. Journal of Heredity 92: 89-92.

41. Yamanaka N, Nagamura Y, Tsubokura Y, Yamamoto K, Takahashi R, Kouchi H, Yano M, Sasaki T, Harada K (2000) Quantitative trait locus analysis of flowering time in soybean using a RFLP linkage map. Breeding Science 50: 109-115.

42. Takahashi R, Abe J (1999) Soybean maturity genes associated with seed coat pigmentation and cracking in response to low temperatures. Crop Science 39: 1657-1662.

43. Takahashi R (1997) Association of soybean genes I and T with low-temperature induced seed coat deterioration. Crop Science 37: 1755-1759.

44. Takahashi R, Asanuma S (1996) Association of T gene with chilling tolerance in soybean. Crop Science 36: 559-562.

45. Takahashi R, Abe J (1994) Genetic and linkage analysis of low-temperature induced seed coat browning in soybean seed coats. Journal of Heredity 85: 447-450.

46. Takahashi R, Shimosaka E (1994) cDNA sequence analysis and expression of two cold responsive genes in soybean. Plant Science 123: 93-104.

47. Takahashi R, Joshee N, Kitagawa Y (1994) Induction of chilling resistance by water stress, and cDNA sequence analysis and expression of water-stress-regulated genes in rice. Plant Molecular Biology 26: 339-352.

48. Takahashi R, Akiyama T (1993) Characterization of a melanin associated with low temperature- induced browning. in soybean seed coats. Phytochemistry 34: 587-588.