Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

Breeding Science

Volumn 62, Issue 3, 2012, Pages 223-234

  Hori, Kiyosumi ^a   Kataoka, Tomomori ^b   Miura, Kiyoyuki ^c   Yamaguchi, Masayuki ^d   Saka, Norikuni ^e   Nakahara, Takahiro ^f   Sunohara, Yoshihiro ^g   Ebana, Kaworu ^a   Yano, Masahiro ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b NATIONAL AGRICULTURAL RESEARCH CENTER FOR KYUSHU OKINAWA REGION   (Japan)

^c FOOD RESEARCH INSTITUTE   (Japan)

^d NATIONAL AGRICULTURAL RESEARCH CENTER FOR TOHOKU REGION   (Japan)

^e Aichi Ken Agricultural Research Center   (Japan)

^f Miyazaki Agricultural Research Institute   (Japan)

^g NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

Author keywords

Agronomic traits; Japonica rice cultivars; Oryza sativa L.; Quantitative trait loci (QTLs)

Indexed keywords

JAPONICA; ORYZA SATIVA;

EID: 84869036418     PISSN: 13447610     EISSN: 13473735     Source Type: Journal    
DOI: 10.1270/jsbbs.62.223     Document Type: Article

References (38)

1. Arai-Kichise, Y., Y. Shiwa, H. Nagasaki, K. Ebana, H. Yoshikawa, M. Yano and K. Wakasa (2011) Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by wholegenome sequencing. Plant Cell Physiol. 52: 274-282.
2. Benjamini, Y. and Y. Hochberg (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57: 289-300.
3. Basten, C.J., B.S. Weir and Z.B. Zeng (2005) QTL Cartographer, version 1.17. Department of Statistics, North Carolina State University, Raleigh, p. 189.
4. Ebana, K., J. Yonemaru, S. Fukuoka, H. Iwata, H. Kanamori, N. Namiki, H. Nagasaki and M. Yano (2010) Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.). Breed. Sci. 60: 390-397.
5. Fujino, K., H. Sekiguchi, T. Sato, H. Kiuchi, Y. Nonoue, Y. Takeuchi, T. Ando, S.Y. Lin and M. Yano (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor. Appl. Genet. 108: 794-749.
6. Fujino, K. and H. Sekiguchi (2005) Mapping of QTLs conferring extremely early heading in rice (Oryza sativa L.). Theor. Appl. Genet. 111: 393-398.
7. Fujino, K. and H. Sekiguchi (2008a) Mapping of quantitative trait loci controlling heading date among rice cultivars in the northernmost region of Japan. Breed. Sci. 58: 367-373.
8. Fujino, K., H. Sekiguchi, Y. Matsuda, K. Sugimoto, K. Ono and M. Yano (2008b) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proc. Natl. Acad. Sci. USA 105: 12623-12628.
9. Fujino, K. and N. Iwata (2011) Identification of QTLs controlling heading date on the short arm of chromosome 3 in rice (Oryza sativa L.). Breed. Sci. 62: 294-300.
10. Guo, Y. and D. Hong (2010) Novel pleiotropic loci controlling panicle architecture across environments in japonica rice (Oryza sativa L.). J. Genet. Genomics 37: 533-544.
11. Hallauer, A.R. and J.B. Miranda (1988) Quantitative genetics in maize breeding, 2nd edn. Iowa State University Press, Ames, p. 205.
12. Hori, K., T. Yamamoto, K. Ebana, Y. Takeuchi and M. Yano (2009) A novel quantitative trait locus, qCL1, involved in semi-dwarfism derived from Japanese rice cultivar Nipponbare. Breed. Sci. 59: 285-295.
13. Hori, K., K. Sugimoto, Y. Nonoue, N. Ono, K. Matsubara, U. Yamanouchi, A. Abe, Y. Takeuchi and M. Yano (2010) Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theor. Appl. Genet. 120: 1547-1557.
14. International Rice Genome Sequencing Project (IRGSP) (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
15. Kobayashi, A., B. Genliang, Y. Shenghai and K. Tomita (2007) Detection of quantitative trait loci for white-back and basal-white kernels under high temperature stress in japonica rice varieties. Breed. Sci. 57: 107-116.
16. Kobayashi, A., K. Tomita, F. Yu, Y. Takeuchi and M. Yano (2008) Verification of quantitative trait locus for stickiness of cooked rice and amylose content by developing near-isogenic lines. Breed. Sci. 58: 235-242.
17. Kobayashi, A. and K. Tomita (2008) QTL detection for stickiness of cooked rice using recombinant inbred lines derived from crosses between japonica rice cultivars. Breed. Sci. 58: 419-426.
18. Kato, T., S. Segami, M. Toriyama, I. Kono, T. Ando, M. Yano, H. Kitano, K. Miura and Y. Iwasaki (2011) Detection of QTLs for grain length from large grain rice (Oryza sativa L.). Breed. Sci. 61: 269-274.
19. Kwon, S.J., Y.C. Cho, S.W. Kwon, C.S. Oh, J.P. Suh, Y.S. Shin, Y.G. Kim, D. Holligan, S.R. Wessler, H.G. Hwang et al. (2008) QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.). Breed. Sci. 58: 271-279.
20. Kwon, S.W., Y.C. Cho, J.H. Lee, J.P. Suh, J.J. Kim, M.K. Kim, I.S. Choi, H.G. Hwang, H.J. Koh and Y.G. Kim (2011) Identification of quantitative trait loci associated with rice eating quality traits using a population of recombinant inbred lines derived from a cross between two temperate japonica cultivars. Mol. Cells 31: 437-445.
21. Lander, E.S., P. Green, J. Abrahamson, A. Barlow, M.J. Daly, S.E. Lincoln and L. Newburg (1987) Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
22. Mackill, D.J. (1995) Classifying japonica rice cultivars with RAPD markers. Crop Sci. 35: 889-894.
23. Mao, B., W.J. Cai, Z.H. Zhang, Z.L. Hu, P. Li, L.H. Zhu and Y.G. Zhu (2003) Characterization of QTLs for harvest index and source-sink characters in a DH population of rice (Oryza sativa L.). Yi Chuan Xue Bao 30: 1118-1126.
24. Matsubara, K., I. Kono, K. Hori, Y. Nonoue, N. Ono, A. Shomura, T. Mizubayashi, S. Yamamoto, U. Yamanouchi, K. Shirasawa et al. (2008) Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from crosses between Japonica rice cultivars. Theor. Appl. Genet. 117: 935-945.
25. McCouch, S.R., L. Teytelman, Y. Xu, K.B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Z. Li, Y. Xing et al. (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9: 257-279.
26. Mei, H.W., L.J. Luo, C.S. Ying, Y.P. Wang, X.Q. Yu, L.B. Guo, A.H. Paterson and Z.K. Li. (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor. Appl. Genet. 107: 89-101.
27. Monden, Y., K. Naito, Y. Okumoto, H. Saito, N. Oki, T. Tsukiyama, O. Ideta, T. Nakazaki, S.R. Wessler and T. Tanisaka (2009) High potential of a transposon mPing as a marker system in japonica × japonica cross in rice. DNA Res. 16: 131-140.
28. Murray, M.G. and W.F. Thompson (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8: 4321-4325.
29. Nagasaki, H., K. Ebana, T. Shibaya, J. Yonemaru and M. Yano (2010) Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population. Breed. Sci. 60: 648-655.
30. Sasahara, H., Y. Fukuta and T. Fukuyama (1999) Mapping of QTLs for vascular bundle system and spike morphology in rice, Oryza sativa L. Breed. Sci. 49: 75-81.
31. Shibaya, T., Y. Nonoue, N. Ono, U. Yamanouchi, K. Hori and M. Yano (2011) Genetic interaction is involved in inhibition of heading by Heading date 2 in rice under long day conditions. Theor. Appl. Genet. 123: 1133-1143.
32. Tabata, M., H. Hirabayashi, Y. Takeuchi, I. Ando, Y. Iida and R. Ohsawa (2007) Mapping of quantitative trait loci for the occurrence of white-back kernels associated with high temperatures during the ripening period of rice (Oryza sativa L.). Breed. Sci. 57: 47-52.
33. Takeuchi, Y., K. Hori, K. Suzuki, Y. Nonoue, Y. Takemoto-Kuno, H. Maeda, H. Sato, H. Hirabayashi, H. Ohta, T. Ishii et al. (2008) Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3. Breed. Sci. 58: 437-445.
34. Wada, T., T. Ogata, M. Tsubone, Y. Uchimura and Y. Matsue (2008) Mapping of QTLs for eating quality and physicochemical properties of the japonica rice 'Koshihikari'. Breed. Sci. 58: 427-435.
35. Yamamoto, R., N. Horisue and R. Ikeda (1996) Rice Breeding Manual. Yokendo, Tokyo, Japan.
36. Yamamoto, T., H. Nagasaki, J. Yonemaru, K. Ebana, M. Nakajima, T. Shibaya and M. Yano (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics 11: 267-280.
37. Yokoo, M., M. Hirao and T. Imai (2005) Annual change in leading rice varieties between 1956 and 2000 in Japan. Bull. Natl. Inst. Crop Sci. 7: 19-125.
38. Yonemaru, J., T. Yamamoto, S. Fukuoka, Y. Uga, K. Hori and M. Yano (2010) Q-TARO: QTL Annotation Rice Online Database. Rice 3: 194-203.