Genotype frequency of black hull locus (Bh4) in weedy rice (Oryza sativa f. spontanea) populations

Main Article Content

Preecha Prathepha


Black hull 4 (Bh4), is a hull color candidate gene that causes a black pigmentation in the ripened hulls of rice. A 22-bp deletion within exon 3 of the Bh4 variant disrupted the Bh4 function, which lead to a straw-white hull in Asian cultivated rice and African cultivated rice. A survey for the Bh4 locus in a collection of weedy rice from Thailand and Laos was performed. The data showed that 37.5% of the samples were heterozygous, 15.5% with the black hull genotype (BB) and 5.5% with yellow genotype (YY). The allele frequencies were 0.71 and 0.29 for the Y and B alleles, respectively. Based on the Hardy-Weinberg principle, this Bh4 locus of weedy rice is in Hardy-Weinberg equilibrium (HWE).

Article Details



Arrieta-Espinoza, G., Sa’nchez, E., Vargas, S., Lobo, J., Quesada, T. and Espinoza, M. 2005. The weedy rice complex in Costa Rica. I. Morphological study of relationships between commercial rice varieties, wild Oryza relatives and weedy types. Genetic Resources and Crop Evolution 52, 575-587.

Basu, C., Halfhill, M. D., Mueller, T. C. and Stewart, Jr . C. N. 2004. Weed genomics: new tools to understand weed biology. Trends in Plant Sciences 9, 391-398.

Cao, Q., Lu, B. R., Xia, H., Rong, J., Sala, F., Spada, A. and Grassi, F. 2006. Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers. Annals of Botany 98, 1241-1252.

Chen, L. J., Lee, D. S., Song , Z. P., Suh, H. S. and Lu, B. R. 2004. Gene fl ow from cultivated rice (Oryza sativa) to its weedy and wild relatives. Annals of Botany 93, 67-73.

Doyle, J. J. and Doyle, J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19, 11-15.

Fukuda, A., Shimizu, H., Shiratsuchi, H., Yamaguchi, H., Ohdaira, Y. and Mochida H. 2012. Complementary genes that cause black ripen hulls in F1 plants of crosses between indicaand japonica rice cultivars. Plant Production Science 15, 270-273.

Gealy, D. R., Mitten, D. H. and Rutger, J. N. 2003. Gene fl ow between red rice (Oryza sativa) and herbicideresistant rice (O. sativa): implications for weed management. Weed Technology 17, 627-645.

Hoagland, R. E. and Paul, R.V. 1978. A comparative SEM study of red rice and several commercial rice (Oryza sativa) varieties. Weed Science 26, 619-625.

Huang, S., Pan, Y., Gan, D., Ouyang, X., Tang, S., Ekunwe, S. I. N. and Wang, H. 2011. Antioxidant activities and UV-protective properties of melanin from the berry of Cinnamomum burmannii and Osmanthus fragrans. Medicinal Chemistry Research 20, 475-481.

Isshiki, M., Morino, K., Nakajima, M., Okagaki, R. J., Wessler, S. R., Izawa, T., Kuroda, Y., Sato, Y. I., Bounphanousay, C., Kono, Y. and Tanaka, K. 2005. Gene fl ow from cultivated rice (Oryza sativa L.) to wild Oryza species (Oryzarufipogon Griff. & O. nivara Sharma and Shastry) on the Vientiane plain of Laos. Euphytica 142, 75-83.

Kuroda, Y., Sato, Y. I., Bounphanousay, C., Kono, Y. and Tanaka, K. 2007. Genetic structure of three Oryza AA genome species (O. rufi pogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos. Conservation Genetics 8, 149-158.

Londo, J. P. and Schaal, B. A. 2007. Origins and population genetics of weedy rice in the USA. Molecular Ecology 16, 4523-4536.

Oka, H. I. 1988. Origin of cultivated rice. Japanese Scientifi c Societies Press, Tokyo. Olofsdotter, M., Valverde, B. E. and Madsen, K. H. 2000. Herbicide resistant rice (Oryza sativa L.): Global implications for weedy rice and weed management. Annals of Applied Biology 137, 279-295.

Prathepha, P. 2009. Seed morphological traits and genotypic diversity of weedy rice (Oryza sativa f. spontanea) populations found in the Thai Hom Mali rice fi elds of north-eastern Thailand. Weed Biology and Management 9, 1-9.

Prathepha, P. 2011. Microsatellite analysis of weedy rice (Oryza sativa f. spontanea) from Thailand and Lao PDR. Australian Journal of Crop Science 5, 49-54.

Ramarathnam, N., Osawa, T., Kawakishi, S. and Mitsuo Namiki, M. 1987. Effect of oxidative damage induced by irradiation on germination potentials of rice seeds. Journal of Agricultural and Food Chemistry 35, 8-11.

Reagon, M., Thurber, C. S., Gross B. L., Olsen, K. M., Jia, Y. and Caicedo A. L. 2010. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evolutionary Biology 10,180 ( (Open Access)

Sweeney, M. T., Thomson, M. J., Pfeil, B. E. and 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.

Tang, L. H. and Morishima, H. 1997. Genetic characterization of weedy rices and the interference on their origins. Breeding Science 47, 153-160.

Thurber, C. S., Reagon, M., Gross, B. L., Olsen, K. M., Jia Y. and Caicedo, A. L. 2010. Molecular evolution of shattering loci in U.S. weedy rice. Molecular Evolution 19, 3271-3284.

Yu, G. Q., Bao, Y., Shi, C. H., Dong, C. Q. and Ge, S. 2005. Genetic diversity and population differentiation of Liaoning weedy rice detected by RAPD and SSR markers. Biochemical Genetics 43, 261-270.

Vigueira, C. C., Li, W. and Olsen, K. M. 2013. The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice. Journal of Evolutionary Biology 26, 1738-1749.

Xia, H. B., Wang, W, Xia, H., Zhao, W. and Lu, B. R. 2011. Conspecific crop-weed introgression infl uences evolution of weedy rice (Oryza sativa f. spontanea) across a geographical range. Online PLoSONE6:e16189.

Zhu, B. F., Si, L., Wang, Z., Zhou, Y., Zhu, J., Shangguan, Y., Lu, D., Fan, D., Li, C., Lin, H., Qian, Q., Sang, T., Zhou, B., Minobe, Y. and Han, B. 2011. Genetic control of a transition from black to straw-white seed hull in rice domestication. Plant Physiology 155, 1301-1311.

Zhu, Y., Ellstrand, N. C. and Lu, B. R. 2012. Sequence polymorphisms in wild, weedy, and cultivated rice suggest seed-shattering locus sh4 played a minor role in Asian rice domestication. Ecology and Evolution 2, 2106-2113