, 213:115 | Cite as

Genetic mapping of the qGCR6 locus affecting glossiness of cooked rice

  • Sheng-Shan Wang
  • Kai-Yi Chen
  • Yann-Rong Lin
  • Rong-Kuen ChenEmail author


A japonica variety, Koshihikari, is known to have favorable eating quality. Two rice backcross inbred lines (BILs) developed from Koshihikari exhibited significantly different glossiness of cooked rice (GCR), an eating quality trait measured using the Toyo-taste meter. Genetic analysis indicated that the genetic composition of these two BILs differed only on the short arm of chromosome 6, which led to the identification of the qGCR6 locus. Through high-resolution genetic mapping, the qGCR6 locus was further delimited to a 43.9 kb chromosomal region containing ten putative genes. The DNA marker SNP2175, which tightly links to qGCR6, was developed and can be used in marker-assisted breeding programs.


Eating quality Genetic mapping DNA marker Rice 



This study was supported by grants from the Tainan District Agricultural Research and Extension Station, Council of Agriculture, Executive Yuan, Taiwan.

Supplementary material

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Supplementary material 1 (TIFF 341 kb)
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Supplementary material 2 (TIFF 347 kb)
10681_2017_1904_MOESM3_ESM.pdf (98 kb)
Supplementary material 3 (PDF 98 kb)


  1. Bett-Garber KL, Champagne ET, McClung AM et al (2001) Categorizing rice cultivars based on cluster analysis of amylose content, protein content and sensory attributes. Cereal Chem 78:551–558CrossRefGoogle Scholar
  2. Bi YM, Kant S, Clark J et al (2009) Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. Plant Cell Environ 32:1749–1760CrossRefPubMedGoogle Scholar
  3. Chen RK, Chen CL (2015) Effects of nitrogen fertilization rates on the culm development of rice. Res Bull Tainan Dist Agric Improv Stn 66:24–38Google Scholar
  4. Chen CS, Chen RK, Chin HH et al (2010) Introgression of three heading date genes, hd1, Hd6, and ehd1, to Oryza sativa L. japonica cv. Koshihikari by marker-assisted selection. Crop Environ Bioinform 7:1–20Google Scholar
  5. Cho YC, Suh JP, Yoon MR et al (2013) QTL mapping for paste viscosity characteristics related to eating quality and QTL-NIL development in japonica rice (Oryza sativa L.). Plant Breed Biotechnol 1:333–346CrossRefGoogle Scholar
  6. Cho YC, Baek MK, Suh JP et al (2014) QTL detection associated with eating quality based on palatability test in japonica rice (Oryza sativa L.). Plant Breed Biotechnol 2:342–353CrossRefGoogle Scholar
  7. Jan YS, Lin SF (2010) Studies on DNA sequence variation in Waxy gene of rice. Bull DARES 19:19–26Google Scholar
  8. Juliano BO, Onate LU, Mundo AM (1965) Relation of starch composition, protein content, and gelatinization temperature to cooking and eating qualities of milled rice. Food Technol 19:1006–1011Google Scholar
  9. Kawahara Y, de la Bastide M, Hamilton JP et al (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4CrossRefPubMedPubMedCentralGoogle Scholar
  10. Kipreos ET, Pagano M (2000) The F-box protein family. Genome Biol 1(5):Reviews 3002Google Scholar
  11. Kwon SW, Cho YC, Lee JH et al (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 31:437–445CrossRefPubMedPubMedCentralGoogle Scholar
  12. Lechner E, Achard P, Vansiri A et al (2006) F-box proteins everywhere. Curr Opin Plant Biol 9:631–638CrossRefPubMedGoogle Scholar
  13. Leng Y, Xue D, Yang Y et al (2014) Mapping of QTLs for eating and cooking quality-related traits in rice (Oryza sativa L.). Euphytica 197:99–108CrossRefGoogle Scholar
  14. Lestari P, Ham TH, Lee HH et al (2009) PCR marker-based evaluation of the eating quality of Japonica rice (Oryza sativa L.). J Agric Food Chem 57:2754–2762CrossRefPubMedPubMedCentralGoogle Scholar
  15. Murrary MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325CrossRefGoogle Scholar
  16. Oldroyd GED, Downie JA (2008) Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol 59:519–546CrossRefPubMedGoogle Scholar
  17. R Core Team (2013) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria.
  18. Sabouri A, Rabiei B, Toorchi M et al (2012) Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.). Aust J Crop Sci 6:808–814Google Scholar
  19. Sano Y, Katsumata M, Okuno K (1986) Genetic studies of speciation in cultivated rice. 5. Inter and intraspecific differentiation in the waxy gene expression of rice. Euphytica 35:1–9CrossRefGoogle Scholar
  20. Takeuchi Y, Nonoue Y, Ebitani T et al (2007) QTL detection for eating quality including glossiness, stickiness, taste and hardness of cooked rice. Breed Sci 57:231–242CrossRefGoogle Scholar
  21. Takeuchi Y, Hori K, Suzuki K et al (2008) Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3. Breed Sci 58:437–445CrossRefGoogle Scholar
  22. Tanaka I, Kobayashi A, Tomita K et al (2006) Detection of quantitative trait loci for stickiness and appearance based on eating quality test in japonica rice cultivar. Breed Res 8:39–47CrossRefGoogle Scholar
  23. Tian Z, Qian Q, Liu Q et al (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765CrossRefPubMedPubMedCentralGoogle Scholar
  24. Untergrasser A, Cutcutache I, Koressaar T et al (2012) Primer3-new capabilities and interfaces. Nucleic Acids Res 40:e115CrossRefGoogle Scholar
  25. Wada T, Ogata T, Tsubone M et al (2008) Mapping of QTLs for eating quality and physicochemical properties of the japonica rice ‘Koshihikari’. Breed Sci 58:427–435CrossRefGoogle Scholar
  26. Wan XY, Wan JM, Su CC et al (2004) QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theor Appl Genet 110:71–79CrossRefPubMedGoogle Scholar
  27. Wang ZY, Zhen FQ, Shen GZ et al (1995) The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 7:613–622CrossRefPubMedGoogle Scholar
  28. Yamamoto Y, Ogawa T (1992) Eating quality in Japanese rice cultivars. Jpn J Breed 42:177–183CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Sheng-Shan Wang
    • 1
  • Kai-Yi Chen
    • 2
  • Yann-Rong Lin
    • 2
  • Rong-Kuen Chen
    • 1
    Email author
  1. 1.Tainan District Agricultural Research and Extension StationTainanTaiwan
  2. 2.Department of AgronomyNational Taiwan UniversityTaipeiTaiwan

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