Abstract
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.
Similar content being viewed by others
References
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 25:133–137
Dixon RA, Xie DY, Sharma SB (2005) Proanthocyanidins—A final frontier in flavonoid research? New Phytol 165:9–28
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 4:90–102
Grotewold E (2006) The genetics and biochemistry of floral pigments. Annu Rev Plant Biol 57:761–780
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 8:928–938
Harborne JB, Williams CA (2000) Advances in flavonoid research since 1992. Phytochemistry 55:481–504
Hu J, Anderson B, Wessler SR (1996) Isolation and characterization of rice R genes: evidence for distinct evolutionary paths in rice and maize. Genetics 142:1021–1031
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 58:12804–12809
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 25:31–38
Koes R, Verweij W, Quattrocchio F (2005) Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci 10:236–242
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 57:405–430
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 104:1253–1262
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 6:203–211
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 15:221–225
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 52:3679–3687
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 168:997–1007
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 42:982–991
Schijlen EGWM, Ric de Vos CH, Van Tunen AJ, Bovy AG (2004) Modification of flavonoid biosynthesis in crop plants. Phytochemistry 65:2631–2648
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 54:693–699
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 49:106–111
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 228:1043–1054
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 18:283–294
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:e133
Winkel BSJ (2004) Metabolic channeling in plants. Annu Rev Plant Biol 55:85–107
Acknowledgments
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.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Lim, SH., Ha, SH. Marker development for the identification of rice seed color. Plant Biotechnol Rep 7, 391–398 (2013). https://doi.org/10.1007/s11816-013-0276-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11816-013-0276-1