Plant Biotechnology Reports

, Volume 7, Issue 3, pp 391–398 | Cite as

Marker development for the identification of rice seed color

  • Sun-Hyung Lim
  • Sun-Hwa HaEmail author
Original Article


Pigmented traits in rice seeds are regarded as important breeding goals for crop improvement. Marker-assisted selection is very helpful when screening for target seed color traits in the early stages of plant development. Among the genes involved in the biosynthesis of anthocyanins and proanthocyanins (PAs) that are candidates for marker development, we examined the expression of five genes encoding CHS, CHI, F3H, DFR, and ANS in the seeds of non-pigmented white and pigmented black and red rice cultivars. The transcript levels of all these genes except for CHI are higher in pigmented rice than in non-pigmented rice. Sequence variations in these biosynthetic genes revealed that the DFR gene harbors a single nucleotide substitution that generates a premature stop codon in white rice. Additional sequence variations in two regulatory genes, OSB1 and Rc, were also compared among the same cultivars. The sequence of the OSB1 gene in black rice was found to differ from that in red and white rice. The sequence of the Rc gene in red rice also differed from that in white and black rice. Based on these variations, we developed two CAPS markers for DFR and OSB1 genes and an Indel marker for the Rc gene. The combined use of these three markers could discriminate rice seeds harboring white, black and red color. We validated the usefulness of these markers in 34 rice cultivars. Hence, the combined application of our three new markers may have utility to screen the seed color prior to seed setting in rice breeding programs.


Anthocyanins CAPS marker Indel marker Proanthocyanidins Seed color 



This work was supported by a fund from the National Academy of Agricultural Science (PJ006834) and a grant from the Next-Generation BioGreen 21 Program (PJ009520), Rural Development Administration, Republic of Korea.


  1. Akihisa T, Tokuda H, Ukiya M, Iizuka M, Schneider S, Ogasawara K, Mukainaka T, Iwatsuki K, Suzuki T, Nishino H (2003) Chalcones, coumarins, and flavanones from the exudate of Angelica keiskei and their chemopreventive effects. Cancer Lett 25:133–137CrossRefGoogle Scholar
  2. Dixon RA, Xie DY, Sharma SB (2005) Proanthocyanidins—A final frontier in flavonoid research? New Phytol 165:9–28PubMedCrossRefGoogle Scholar
  3. Furukawa T, Maekawa M, Oki T, Suda I, Iida S, Shimada H, Takamure I, Kadowaki K (2007) The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant J 4:90–102Google Scholar
  4. Grotewold E (2006) The genetics and biochemistry of floral pigments. Annu Rev Plant Biol 57:761–780PubMedCrossRefGoogle Scholar
  5. Ha SH, Liang YS, Jung H, Ahn MJ, Suh SC, Kweon SJ, Kim DH, Kim YM, Kim JK (2010) Application of two bicistronic systems involving 2A and IRES sequences to the biosynthesis of carotenoids in rice endosperm. Plant Biotechnol J 8:928–938PubMedCrossRefGoogle Scholar
  6. Harborne JB, Williams CA (2000) Advances in flavonoid research since 1992. Phytochemistry 55:481–504PubMedCrossRefGoogle Scholar
  7. Hu J, Anderson B, Wessler SR (1996) Isolation and characterization of rice R genes: evidence for distinct evolutionary paths in rice and maize. Genetics 142:1021–1031PubMedGoogle Scholar
  8. Kim JK, Lee SY, Chu SM, Lim SH, Suh SC, Lee YT, Cho HS, Ha SH (2010) Variation and correlation analysis of flavonoids and carotenoids in Korean pigmented rice (Oryza sativa L.) cultivars. J Agric Food Chem 58:12804–12809PubMedCrossRefGoogle Scholar
  9. Kim JK, Ha SH, Park SY, Lee SM, Kim HJ, Lim SH, Suh SC, Kim DH, Cho HS (2012) Determination of lipophilic compounds in genetically modified rice using gas chromatography-time-of-flight mass spectrometry. J Food Compos Anal 25:31–38CrossRefGoogle Scholar
  10. Koes R, Verweij W, Quattrocchio F (2005) Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci 10:236–242PubMedCrossRefGoogle Scholar
  11. Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, Nesi N, Caboche M (2006) Genetics and biochemistry of seed flavonoids. Annu Rev Plant Biol 57:405–430PubMedCrossRefGoogle Scholar
  12. Lim SH, Cho HJ, Lee SJ, Cho YH, Kim BD (2002) Identification and classification of S haplotypes in Raphanus sativus by PCR-RFLP of the S locus glycoprotein (SLG) gene and the S locus receptor kinase (SRK) gene. Theor Appl Genet 104:1253–1262PubMedCrossRefGoogle Scholar
  13. Lim SH, Sohn SH, Kim DH, Kim JK, Lee JY, Kim YM, Ha SH (2012) Use of an anthocyanin production phenotype as a visible selection marker system in transgenic tobacco plant. Plant Biotechnol Rep 6:203–211CrossRefGoogle Scholar
  14. Nakai K, Inagaki Y, Nagata H, Miyazaki C, Iida S (1998) Molecular characterization of the gene for dihydroflavonol 4-reductase of Japonica rice varieties. Plant Biotech 15:221–225CrossRefGoogle Scholar
  15. Parejo I, Jauregui O, Sanchez-Rabaneda F, Viladomat F, Bastida J, Codina C (2004) Separation and characterization of phenolic compounds in fennel (Foeniculum vulgare) using liquid chromatography–negative electrospray ionization tandem spectrometry. J Agric Food Chem 52:3679–3687PubMedCrossRefGoogle Scholar
  16. Saitoh K, Onishi K, Mikami I, Thidar K, Sano Y (2004) Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associated with phenotypes. Genetics 168:997–1007PubMedCrossRefGoogle Scholar
  17. Sakamoto W, Ohmori T, Kageyama K, Miyzaki C, Saito A, Murata M, Noda K, Maekawa M (2001) The purple leaf (pl) locus of rice: The Plw allele has a complex organization and includes two genes encoding basic helix-loop-helix proteins involved in anthocyanin biosynthesis. Plant Cell Physiol 42:982–991PubMedCrossRefGoogle Scholar
  18. Schijlen EGWM, Ric de Vos CH, Van Tunen AJ, Bovy AG (2004) Modification of flavonoid biosynthesis in crop plants. Phytochemistry 65:2631–2648PubMedCrossRefGoogle Scholar
  19. Seo WD, Kim JY, Han SI, Ra JE, Lee JH, Song YC, Park MJ, Kang HW, Oh SK, Jang KC (2011) Relationship of radical scavenging activities and anthocyanin contents in the 12 colored rice varieties in Korea. J Korean Soc Appl Biol Chem 54:693–699CrossRefGoogle Scholar
  20. Shen Y, Jin L, Xiao P, Lu Y, Bao JS (2009) Total phenolics, flavonoids, antioxidant capacity in rice grain and their relations to grain color, size and weight. J Cereal Sci 49:106–111CrossRefGoogle Scholar
  21. Shih CH, Chu H, Tang LK, Sakamoto W, Maekawa M, Chu IK, Wang M, Lo C (2008) Functional characterization of key structural genes in rice flavonoid biosynthesis. Planta 228:1043–1054PubMedCrossRefGoogle Scholar
  22. Sweeney MT, Thomson MJ, Pfeil BE, McCouch S (2006) Caught red-handed: Rc encodes a basic Helix-Loop-Helix protein conditioning red pericarp in rice. Plant Cell 18:283–294PubMedCrossRefGoogle Scholar
  23. Sweeney MT, Thomson MJ, Cho Y, Park Y, Williamson S, Bustamante C, McCouch S (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet 3:e133PubMedCrossRefGoogle Scholar
  24. Winkel BSJ (2004) Metabolic channeling in plants. Annu Rev Plant Biol 55:85–107PubMedCrossRefGoogle Scholar

Copyright information

© Korean Society for Plant Biotechnology and Springer Japan 2013

Authors and Affiliations

  1. 1.National Academy of Agricultural ScienceRural Development AdministrationSuwonRepublic of Korea
  2. 2.Department of Genetic Engineering and Crop Biotech InstituteKyung Hee UniversityYonginKorea

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