J Appl Genetics (2011) 52:161–169 DOI 10.1007/s13353-011-0027-3 PLANT GENETICS ORIGINAL PAPER Identification and characterization of seed-specific transcription factors regulating anthocyanin biosynthesis in black rice C.-K Kim & M.-A. Cho & Y.-H. Choi & J.-A. Kim & Y.-H. Kim & Y.-K. Kim & S.-H. Park Received: 18 May 2010 / Revised: 16 November 2010 / Accepted: 8 December 2010 / Published online: 1 February 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Black rice is rich in anthocyanin and is expected to have more healthful dietary potential than white rice. We assessed expression of anthocyanin in black rice cultivars using a newly designed 135 K Oryza sativa microarray. A total of 12,673 genes exhibited greater than 2.0-fold up- or down-regulation in comparisons between three rice cultivars and three seed developmental stages. The 137 transcription factor genes found to be associated with production of anthocyanin pigment were classified into 10 groups. In C.-K. Kim : S.-H. Park (*) Genomics Division, National Academy of Agricultural Science (NAAS), Suwon 441-707, Korea e-mail: shp1790@rda.go.kr M.-A. Cho Fruit Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Suwon 440-706, Korea Y.-H. Choi Bioenergy Crop Research Center, National Institute of Crop Science (NICS), Suwon 441-706, Korea J.-A. Kim Bio-crop Development Division, National Academy of Agricultural Science (NAAS), Suwon 441-707, Korea Y.-H. Kim Policy Development Office, Korea Institute of Planning & Evaluation for Technology in Food, Agriculture, Forestry & Fisheries, Anyang 431-060, Korea Y.-K. Kim School of Electrical Information Communication Engineering, Wonkwang University, Iksan, Korea addition, 17 unknown and hypothetical genes were identified from comparisons between the rice cultivars. Finally, 15 out of the 17 candidate genes were verified by RT-PCR analysis. Among the genes, nine were up-regulated and six exhibited down-regulation. These genes likely play either a regulatory role in anthocyanin biosynthesis or are related to anthocy- anin metabolism during flavonoid biosynthesis. While these genes require further validation, the results here underline the potential use of the new microarray and provide valuable insight into anthocyanin pigment production in rice. Keywords Anthocyanin . Black rice . Pigmentation . Rice microarray . Transcription factor Introduction Rice, one of the most economically important cereal crops in the world, is a significant staple for feeding much of the world's population. Although white rice is most commonly consumed, several rice cultivars contain color pigments, such as black and red rice. Black rice has a high anthocyanin content located in the pericarp layers, which gives it a dark purple color (Ryu et al. 1998; Takashi et al. 2001). Anthocyanins, a group of reddish-purple water-soluble flavonoids, are the primary pigments in the red and black grains, and are responsible for the attractive red, purple, and blue colors of many flowers, fruits, and vegetables. Based on several reviews, it is estimated that more than 400 naturally occurring anthocyanins have been found (Kong et al. 2003). The pigment composes a group of natural colorants belonging to the flavonoid family and is produced by tissues in response to developmental and environmental signals (Quattrocchio et al. 1993). The regulatory elements that confer tissue-specific accumulation of anthocyanin have