Molecules and Cells

, Volume 31, Issue 5, pp 437–445 | Cite as

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

  • Soon-Wook Kwon
  • Young-Chan ChoEmail author
  • Jeong-Heui Lee
  • Jung-Pil Suh
  • Jeong-Ju Kim
  • Myeong-Ki Kim
  • Im-Soo Choi
  • Hung-Goo Hwang
  • Hee-Jong KohEmail author
  • Yeon-Gyu Kim


Improved eating quality is a major breeding target in japonica rice due to market demand. In this study, we performed genetic analysis to identify quantitative trait loci (QTLs) that control rice eating quality traits using 192 recombinant inbred lines (RILs) derived from a cross between two japonica cultivars, ‘Suweon365’ and ‘Chucheongbyeo’. We evaluated the stickiness (ST) and overall evaluation (OE) of cooked rice using a sensory test, the glossiness of cooked rice (GCR) using a Toyo-taste meter, and measured the amylose content (AC), protein content (PC), alkali digestion value (ADV), and days to heading (DH) of the RILs in the years 2006 and 2007. Our analysis revealed 21 QTLs on chromosomes 1, 4, 6, 7, 8, and 11. QTLs on chromosomes 6, 7, and 8 were detected for three traits related to eating quality in both years. QTLs for ST and OE were identified by a sensory test in the same region of the QTLs for AC, PC, ADV, GCR and DH on chromosome 8. QTL effects on the GCR were verified using QTL-NILs (near-isogenic lines) of BC3F4–6 in the Suweon365 background, a low eating quality variety, and some BC1F3 lines. Chucheongbyeo alleles at QTLs on chromosomes 7 and 8 increased the GCR in the NILs and backcrossed lines. The QTLs identified by our analysis will be applicable to future marker-assisted selection (MAS) strategies for improving the eating quality of japonica rice.


eating quality japonica MAS QTL rice 


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  1. Asaoka, M., Okuno, T., and Fuwa, H. (1985). Effect of environmental temperature at the milky stage on amylose content and fine structure of amylopectine of waxy and non waxy endorsperm starches of rice (Oryza sativa L.). Agric. Biol. Chem. 49, 373–379.Google Scholar
  2. Ashikari, M., Sakakibara, H., Lin, S.Y., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E.R., Qian, Q., Kitano, H., and Matsuoka, M. (2005). Cytokinin oxidase regulates rice grain production. Science 29, 741–745.CrossRefGoogle Scholar
  3. Baba, T., Nishihara, M., Mizuno, K., Kawasaki, T., Shimada, H., Kobayashi, E., Ohnishi, S., Tanaka, K., and Arai, Y. (1993). Identification, cDNA cloning, and gene expression of soluble starch synthase in rice (Oryza sativa L.) immature seeds. Plant Physiol. 103, 565–573.PubMedCrossRefGoogle Scholar
  4. Bao, J.S., Zheng, X.W., Xia, Y.W., He, P., Shu, Q.Y., Lu, X., Chen, Y., and Zhu, L.H. (2000). QTL mapping for the paste viscosity characteristics in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 280–284.CrossRefGoogle Scholar
  5. Basten, C.J., Weir, B.S., and Zeng, Z.B. (1997). QTL cartographer: a reference manual and tutorial for QTL mapping. Department of statistics, North Carolina State University, Raleigh, NC, USA.Google Scholar
  6. Choi, H.C. (2006). A guide to rice breeding. Rural Development Administration (in Korean). pp. 273–299.Google Scholar
  7. Ebitani, T., Takeuchi, Y., Nonoue, N., Yamamoto, T., Takeuchi, K., and Yano, M. (2005). Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar ‘Kasalath’ in a genetic background of japonica elite cultivar ‘Koshihikari’. Breed. Sci. 55, 65–73.CrossRefGoogle Scholar
  8. Fan, C.C., Yu, X.Q., Xing, Y.Z., Xu, C.G., Luo, L.J., and Zhang, Q. (2005). The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor. Appl. Genet. 110, 1445–1452.PubMedCrossRefGoogle Scholar
  9. Harushima, Y., Yano, M., Ashomura, A., Sato, M., Shimano, T., Kuboki, Y., Yamamoto, T., Lin, S.Y., Antonio, B.A., Parco, A., et al. (1998). A high-density genetic linkage map with 2275 markers using a single F2 population. Genetics 148, 279–494.Google Scholar
  10. Hayashi, K., Hashimoto, N., Daigen, M., and Ashikawa, I. (2004). Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor. Appl. Genet. 108, 1212–1220.PubMedCrossRefGoogle Scholar
  11. Ishima, T., Taira, H., and Mikoshiba, K. (1974). Effect of nitrogenous fertilizer application and protein content in milled rice on organotropic quality of cooked rice. Rep. Natl. Food Res. Inst. 29, 9–15.Google Scholar
  12. Juliano, B.O. (1971). A simplified assay for milled rice amylose. Cereal Sci. Today 16, 334–336.Google Scholar
  13. Juliano, B.O. (1985). Criteria and test for rice grain quality. In Rice Chemistry and Technology, B.O. Juliano, ed. (American Association of Cereal Chemists, Saint Paul), pp.443–513.Google Scholar
  14. Juliano, B.O., Onate, L.U., and Mundo, A.M. (1965). Relation of starch composition, protein content, and gelatinization temperature to cooking and eating qualities of milled rice. Food Technol. 19, 1006–1011.Google Scholar
  15. Kim, B.R., Roh, J.H., Choi, S.H., Ahn, S.W., and Han, S.S. (2004). Durability of rice cultivars to blast in Korea by sequential planting method. Korean J. Breed. 36, 350–356.Google Scholar
  16. Kobayashi, A., and Tomita, K. (2008). QTL detection for stickiness of cooked rice using recombinant inbred lines derived from crosses between japonica rice cultivars. Breed. Sci. 58, 419–426.CrossRefGoogle Scholar
  17. Kwon, S.W. (2008) Analysis of quantitative trait loci associated with eating quality using a RIL population in japonica rice. In Ph. D. Thesis, Seoul Natl’ Univ., Korea, p.111.Google Scholar
  18. Kwon, S.J., Cho, Y.C., Kwon, S.W., Oh, C.S., Suh, J.P., Shin, Y.S., Kim, Y.G., Holligan, D., Wessler, S.R., Hwang, H.G., et al. (2008a). 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.CrossRefGoogle Scholar
  19. Kwon, S.W., Cho, Y.C., Kim, Y.G., Suh, J.P., Jeung, J.U., Roh, J.H., Lee, S.K., Jeon, J.S., Yang, S.J., and Lee, Y.T. (2008b). Development of near-isogenic japonica rice lines with enhanced resistance to Magnaporthe grisea. Mol. Cells 25, 407–416.PubMedGoogle Scholar
  20. Lee, J.K., Nam, J.K., Lee, K.S., Shin, M.S., Ko, J.K., Lee, S.Y., Noh, T.H., Choung, J.I., Kim, K.Y., et al. (2007). A new middle-late maturity rice cultivar with excellent grain quality “Hopyeongbyeo”. Korean J. Breed. 39, 246–247.Google Scholar
  21. Lestari, P., Ham, T.H., Lee, H.H., Woo, M.O., Jiang, W., Chu, S.H., Kwon, S.W., Ma, K.H., Lee, J.H., Cho, Y.C., et al. (2009). PCR marker-based evaluation of the eating quality of japonica rice (Oryza sativa L.). J. Agric. Food Chem. 57, 2754–2762.PubMedCrossRefGoogle Scholar
  22. Li, Z., Wan, J., Xia, J., and Yano, Y. (2003). Mapping of quantitative trait loci controlling physico-chemical properties of rice grains (Oryza sativa L.). Breed. Sci. 53, 209–215.CrossRefGoogle Scholar
  23. Little, R., Hilder, G., and Dawson, E. (1958). Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem. 35, 111–126.Google Scholar
  24. Neeraja, C.N., Maghirang-Rodriguez, R., Pamplona, A., Heuer, S., Collard, B.C., Septiningsih, E.M., Vergara, G., Sanchez, D., Xu, K., Ismail, A.M., et al. (2007). A marker-assisted backcross approach for developing submergene-tolerant rice cultivars. Theor. Appl. Genet. 115, 767–776.PubMedCrossRefGoogle Scholar
  25. Nelson, J.C. (1997). Qgene: software for marker-based genomic analysis and breeding. Mol. Breed. 3, 239–245.CrossRefGoogle Scholar
  26. Nishimura, M., Yamauchi, F., Ohuchi, K., and Hamamura, K. (1985). Evaluation of the eating quality of recent rice varieties and lines in Hokkaido — The relation between organoleptic and physicochemical qualities of milled rice harvested in an extremely cool year and a very hot year during the summer. Res. Bull. Hokkaido Natl. Agric. Exp. Stn. 144, 77–89.Google Scholar
  27. Ogata, T., Yoshimura, A., Matsue, Y., Tsunematsu, H., and Iwata, N. (1996). QTL analysis for palatability and physicochemical properties of milled rice. Breed. Sci. 46(Suppl. 2), 201.Google Scholar
  28. Otsuki, H., Shimizu, H., Uehara, Y., Yagi, T., Ogawa, N., Ashikawa, I., Shimizu, H., Tamura, K., Ohta, H., Kuroda, K., et al. (1997). QTL analysis of taste in rice. Breed. Sci. 47(Suppl. 2), 147.Google Scholar
  29. Rural Development Administration (RDA). (1975). A handbook on cultivars of major crop (in Korean). p. 469.Google Scholar
  30. Sano, Y. (1984). Differential regulation of waxy gene expression in rice endosperm. Theor. Appl. Genet. 68, 467–473.CrossRefGoogle Scholar
  31. Singh, S., Sidhu, J.S., Huang, N., Vikal, Y., Li, Z., Brar, D.S., Dhaliwal, H.S., and Khush, G.S. (2001). Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106. Theor. Appl. Genet. 102, 1011–1015.CrossRefGoogle Scholar
  32. Sugiura, N., Tsuji, T., Fujii, K., Kato, T., Saka, N., Touyama, T., Hayano-Saito, Y., and Izawa, T. (2004). Molecular marker-assisted selection in a recurrent backcross breeding for the incorporation of resistance to rice stripe virus and panicle blast in rice (Oryza sativa L.). Breed. Res. 6, 143–148.CrossRefGoogle Scholar
  33. Suh, J.P., Choi, Y.H., Kim, K.J., Cho, Y.C., Kwon, S.J., Jeong, J.P., Jeung, J.U., Choi, I.S., Kim, Y.G., Choi, H.C., et al. (2004). Genetic diversity and QTLs for grain quality in japonica rice. Korean J. Breed. 36, 31–37.Google Scholar
  34. Suh, J.P., Cho, Y.C., Kwon, S.J., Choi, I.S., Hong, H.C., Kim, Y.G., Ahn, S.N., and Hwang, H.G. (2006). Identification of QTLs for grain quality on RIL population derived from a cross between japonica rices. Korean J. Breed. 38, 105–112.Google Scholar
  35. Suh, J.P., Yang, S.J., Jeung, J.U., Pamplona, A., Kim, J.J., Lee, J.H., Hong, H.C., Yang, C.I., Kim, Y.G., and Jena, K.K. (2011). Development of elite lines conferring Bph18 gene-dereived resistance to brown planthopper (BPH) by marker-assisted selection and genome-wide background analysis in japonica rice (Oryza sativa L.). Field Crops Res. 120, 215–222.CrossRefGoogle Scholar
  36. Takeuchi, Y., Nonoue, Y., Ebitani, T., Suzuki, K., Aoki, N., Sato, H., Ideta, O., Hirabayashi, H., Hirayama, M., Ohta, H., et al. (2007). QTL detection for eating quality including glossiness, stickiness, taste and hardness of cooked rice. Breed. Sci. 57, 231–242.CrossRefGoogle Scholar
  37. Takeuchi, Y., Hori, K., Suzuki, K., Nonoue, Y., Takemoto-Kuno, Y., Maeda, H., Sato, H., Hirabayashi, H., Ohta, H., Ishii, T., 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.CrossRefGoogle Scholar
  38. Tan, Y.F., Li, J., Yu, S., Xing, Y., and Xu, G. (1999). The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor. Appl. Genet. 99, 642–648.CrossRefGoogle Scholar
  39. Tanaka, K., Ohnishi, S., Kishimoto, N., Kawasaki, T., and Baba, T. (1995). Structure, organization, and chromosomal location of the gene encoding a form of rice soluble starch synthase. Plant Physiol. 108, 677–683.PubMedCrossRefGoogle Scholar
  40. Tanaka, I., Kobayashi, A., Tomita, K., Takeuchi, Y., Yamagishi, M., Yano, M., Sasaki, T., and Horiuchi, H. (2006). Detection of quantitative trait loci for stikiness and appearance based on eating quality test in japonica rice cultiva. Breed. Res. 8, 39–47.CrossRefGoogle Scholar
  41. Umemoto, T., Yano, M., Satoh, H., Shomura, A., and Nakamura, Y. (2002). Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theor. Appl. Genet. 104, 1–8.PubMedCrossRefGoogle Scholar
  42. Wan, X.Y., Wan, J.M., Su, C.C., Wang, C.M., Shen, W.B., Li, J.M., Wang, H.L., Jiang, L., Liu, S.J., Chen, L.M., et al. (2004). QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theor. Appl. Genet. 110, 71–79.PubMedCrossRefGoogle Scholar
  43. Wada, T., Uchimura, Y., Ogata, T., Tsubone, M., and Matsue, Y. (2006). Mapping of QTLs for physicochemical properties in japonica rice. Breed. Sci. 56, 253–260.CrossRefGoogle Scholar
  44. Wada, T., Ogata, T., Tsubone, M., Uchimura, Y., and Matsue, Y. (2008). Mapping of QTLs for eating quality and physicochemical properties of the japonica rice ‘Koshihikari’. Breed. Sci. 58, 427–435.CrossRefGoogle Scholar
  45. Wang, Z.X., Sakaguchi, S., Oka, Y., Kitazawa, N., and Minobe, Y. (2005). Breeding of semi-dwarf Koshihikari by using genomic breeding method. Breed. Res. 7(Suppl. 1 and 2), 217.Google Scholar
  46. Yamamoto, Y., and Ogawa, T. (1992). Eating quality in japanese rice cultivars. Jpn. J. Breed. 42, 177–183.Google Scholar
  47. Yamamoto, T., Kuboki, Y., Lin, S.Y., Sasaki, T., and Yano, M. (1998). Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor. Appl. Genet. 97, 37–44.CrossRefGoogle Scholar
  48. Yu, T.Q., Jiang, W., Ham, T.H., Chu, S.H., Lestari, P., Lee, J.H., Kim, M.K., Xu, F.R., Han, L., Dai, L.Y., and Koh, H.J. (2008). Comparison of grain quality traits between Japonica rice cultivars from Korea and Yunnan Province of China. J. Crop Sci. Biotech. 11, 135–140.Google Scholar

Copyright information

© The Korean Society for Molecular and Cellular Biology and Springer Netherlands 2011

Authors and Affiliations

  • Soon-Wook Kwon
    • 1
  • Young-Chan Cho
    • 1
    Email author
  • Jeong-Heui Lee
    • 1
  • Jung-Pil Suh
    • 1
  • Jeong-Ju Kim
    • 1
  • Myeong-Ki Kim
    • 1
  • Im-Soo Choi
    • 1
  • Hung-Goo Hwang
    • 1
  • Hee-Jong Koh
    • 2
    Email author
  • Yeon-Gyu Kim
    • 1
  1. 1.Rural Development Administration (RDA)National Institute of Crop ScienceSuwonKorea
  2. 2.Department of Plant ScienceSeoul National UniversitySeoulKorea

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