Genetic analysis and molecular mapping of Rp, a mutant gene encoding red pericarp in rice (Oryza sativa L.)

Tong J., Han Z., Han A. (2021): Genetic analysis and molecular mapping of Rp, a mutant gene encoding red pericarp in rice (Oryza sativa L.). Czech J. Genet. Plant Breed., 57: 51−57.

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Coloured rice has pigments deposited in the grain pericarp; red rice is the most common type of coloured rice. Red rice is rich in essential nutrients and has been grown and consumed in China for a long time. In this study, we report the genetic characterisation and preliminary molecular mapping of a mutant gene encoding red pericarp in rice (Oryza sativa L.). To analyse the genetic basis of the red pericarp mutant, a reciprocal cross between GER-3 (red pericarp, indica cv.) and 898 (white pericarp, indica cv.) was made. The genetic analysis results confirmed that there was only one dominant gene, temporarily designated Rp (Red pericarp) controlling the segregation of the red pericarp in the F2 population. For the molecular mapping of Rp, an F2 population derived from an inter-subspecific cross between Gene Engineering Rice-3 (GER-3) and C418 (japonica cv., white pericarp) was constructed. The genotype of the pericarp colour of the F2 individuals in the mapping population was validated by progeny testing of the F2:3 families. Simple sequence repeat (SSR) markers and the bulked segregation analysis (BSA) method were used; Rp was mapped to the short arm of chromosome 7 between the SSR markers RM21182 and RM21268, with a genetic distance of 3.5 and 12.0 cM, respectively. In this paper, the potential origin of the red pericarp mutant gene Rp was also discussed.

Bao T.P., Zhong X.X., Zheng W. (1994): Brief introduction to Genetic Engineering Rice-3. Journal of Hubei Agricultural Science, 6: 15.
Bate-Smith E.C. (1973): Tannins of herbaceous Leguminosae. Phytochemistry, 12: 1809–1812.
Brooks S.A., Yan W., Jackson A.K., Deren C.W. (2008): A natural mutation in rc reverts white-rice-pericarp to red and results in a new, dominant, wild-type allele Rc-g. Theoretical and Applied Genetics, 117: 575–580.
Dong Y.J., Xu J.L., Xiao K.A., Zhang Y.J., Zhang J.Z., Luo L.J., Matsuo M. (2008): Genomic regions associated with the degree of red coloration in pericarp of rice (Oryza sativa L.). Journal of Cereal Science, 48: 556–560.
Doyle J.T., Doyle J.L. (1987): A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Photochemical Bulletin, 19: 11–15.
Finocchiaro F., Ferrari B., Gianinetti A., Dall’asta C., Galaverna G., Scazzina F., Pellegrini N. (2007): Characterization of antioxidant compounds of red and white rice and changes in total antioxidant capacity during processing. Molecular Nutrition & Food Research, 51: 1006–1019.
Furukawa T., Maekawa M., Oki T., Suda I., Iida S., Shimada H., Takamure I., Kadowaki K-I. (2007): The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant Journal, 49: 91–102.
Gai J.Y. (ed.) (2000): Test Statistical Method. Beijing, China Agricultural Publishing House: 134–138.
Gunaratne A., Wu K., Li D., Bentota A., Corke H., Cai Y.Z. (2013): Antioxidant activity and nutritional quality of traditional red-grained rice varieties containing proanthocyanidins. Food Chemistry, 138: 1153–1161.
International Rice Genome Sequencing Project (2005): The map-based sequence of the rice genome. Nature, 436: 793–799.
Kato S., Ishikawa J. (1921): On the inheritance of the pigment of red rice. Japan Journal of Genetics, 1: 1–7.
Lee D., Lupotto E., Powell W. (2009): G-string slippage turns white rice red. Genome, 52: 490–493.
Lincoln S., Daly M., Lander E. (1992): Constructing genetic maps with MAPMAKER/EXP 3.0. In: Martin D.N., Proebsting W.M. (eds.): Whitehead Institute Technical Report. 2nd Ed. Cambridge, Whitehead Institute: 7–10.
Ling W.H., Cheng Q.X., Ma J., Wang T. (2001): Red and black rice decrease atherosclerotic plaque formation and increase antioxidant status in rabbits. Journal of Nutrition, 131: 1421–1426.
Mbanjo E.G.N., Kretzschmar T., Jones H., Ereful N., Blanchard Ch., Boyd L.A., Sreenivasulu N. (2020): The genetic basis and nutritional benefits of pigmented rice grain. Frontiers in Genetics, 11: 229.
Michelmore R.W., Paran I., Kesseli R.V. (1991): Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Sciences of the USA, 88: 9828–9832.
Nagao S., Takahashi M. (1947): Ein Beitrag zu einer genotypischen Analyse der Farbeigenschaften der Spelze und der anderen Pflanzenteile bei der Reispflanze. Japanese Journal of Genetics, Suppl. 1: 1–27.
Nagao S., Takahashi M., Miyamoto T. (1957): Genetic studies on rice plant, XXI. Biochemical studies on red rice pigmentation. Japanese Journal of Genetics, 32: 124–128.
Oki T., Masuda M., Kobayashi M., Nishiba M., Furuta Y., Suda I.S., Sato T. (2002): Polymeric procyanidins as radical-scavenging components in red-hulled rice. Journal of Agricultural Food Chemistry, 50: 7524–7529.
Qiu Y., Liu Q., Beta T. (2010): Antioxidant properties of commercial wild rice and analysis of soluble and insoluble phenolic acids. Food Chemistry, 121: 140–147.
Ragers O.S., Bendich A.J. (1998): Extraction of total DNA from plant tissue. Plant Molecular Biology Manual, A6: 1010.
Rahman M.M., Lee K.E., Lee E.S., Matin M.N., Lee D.S., Yun J.S., Kim B.J., Kang S.G. (2013): The genetic constitutions of complementary genes Pp and Pb determine the purple color variation in pericarps with cyanidin-3-O-glucoside depositions in black rice. Journal of Plant Biology, 56: 24–31.
Scalbert A. (1991): Antimicrobial properties of tannins. Phytochemistry, 30: 3875–3883.
Sharma N., Kaur R., Mangat G.S., Singh K. (2014): Red pericarp introgression lines derived from interspecific crosses of rice: physicochemical characteristics, antioxidative properties and phenolic content. Journal of Science of Food and Agriculture, 94: 2912–2920.
Swain T. (1978): Plant-animal coevolution: A synoptic view of the paleozoic and mesozoic. In: Harborne J.B. (ed.): Biochemical Aspects of Plant and Animal Coevolution. London, Academic Press: 3–19.
Sweeney M.T., Thomson M.J., Pfeil B.E., McCouch S. (2006): Caught red-handed Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. The Plant Cell, 18: 283–294.
Tsutsui T., Yamaji N., Huang C.F., Motoyama R., Nagamura Y., Ma J.F. (2012): Comparative genome-wide transcriptional analysis of Al-responsive genes reveals novel Al tolerance mechanisms in rice. PLoS One, 7: e48197.
Winkel-Shirley B. (2001): Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiology, 126: 485–493.
Yang W.Y., Tu N.M. (2003): Crop Cultivation Science. China Agricultural Press, Beijing: 5–60.
Zhang H., Shao Y., Bao J., Beta T. (2015): Phenolic compounds and antioxidant properties of breeding lines between the white and black rice. Food Chemistry, 172: 630–639.
Zhang Z.X., Yang Z.Y. (2006): Viewing the situation of boat goes up as river rises in Northern Japonic hybrid rice from the development of C418. Breeding practice. In: Deng H.Y. (ed.): Theory and Practice of Hybrid Japonica Rice. Beijing, China Agricultural Publishing House: 181–184.
Zhu Y., Lin Y., Chen S., Liu H., Chen Z., Fan M., Hu T., Mei F., Chen J., Chen L., Wang F. (2019): CRISPR/Cas9-mediated functional recovery of the recessive rc allele to develop red rice. Plant Biotechnology Journal, 17: 2096–2105.
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