Transcriptomics analyses of genes regulating anthocyanin production in black rice

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• 作者：Jae-Hee Lee (1)
  Young-Joo Seol (1)
  Jang-Ho Hahn (1)
  So-Youn Won (1)
  Yong-Jae Won (2)
  Yong-Kab Kim (3)
  Yong-Hwan Kim (4)
  Byung-Ki Kim (5)
  Chang-Kug Kim (1)
  
  1. Genomics Division ; National Academy of Agricultural Science (NAAS) ; Rural Development Administration ; Jeonju ; 560-500 ; Korea
  2. Rice Research Division ; National Institute of Crop Science ; Suwon ; 441-857 ; Korea
  3. School of Electrical Information Communication Engineering ; Wonkwang University ; Iksan ; 570-749 ; Korea
  4. Chonbuk National University ; Industrial Cooperation Foundation ; R&D Center ; Jeonju ; 561-756 ; Korea
  5. Department of Computer Science ; Chonnam National University ; Gwang-Ju ; 500-757 ; Korea
  
• 关键词：Anthocyanin pathway ; Circos diagram ; Phylogenetic tree ; Rice microarray
• 刊名：BioChip Journal
• 出版年：2015
• 出版时间：March 2015
• 年：2015
• 卷：9
• 期：1
• 页码：59-66
• 全文大小：541 KB
• 参考文献：1. Zhang, M.W., Guo, B.J., Peng, Z.M. (2005) Genetic effects on grain characteristics of indica black rice and thei uses on indirect selections for some mineral elemen contents in grains. Genet. Resour. Crop. 52: pp. 1121-1128 CrossRef
  2. Kim, C.K. (2011) Identification and characterization o seed-specific transcription factors regulating antho cyanin biosynthesis in black rice. J. Appl. Genet. 52: pp. 161-169 CrossRef
  3. Kong, J.M., Chia, L.S., Goh, N.K., Chia, T.F., Brouillard, R. (2003) Analysis and biological activities of antho cyanins. Phytochemistry 64: pp. 923-933 CrossRef
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  5. Zhang, Z., Kou, X., Fugal, K., McLaughlin, J. (2004) Com parison of HPLC methods for determination of antho cyanins and anthocyanidins in bilberry extracts. J Agric. Food Chem. 52: pp. 688-691 CrossRef
  6. Lee, J.C., Kim, J.D., Hsieh, F.H., Eun, J.B. (2008) Produc tion of black rice cake using ground black rice and medium-grain brown rice. Int. J. Food Sci. Tech. 43: pp. 1078-1082 CrossRef
  7. Yao, S.L., Xu, Y., Zhang, Y.Y., Lu, Y.H. (2013) Black rice and anthocyanins induce inhibition of cholesterol ab sorption in vitro. Food Funct. 4: pp. 1602-1608 CrossRef
  8. Guo, H.H. (2007) Effect of anthocyaninrich extract from black rice (Oryza sativa L. india) on hyperlipidemia and insulin resistance in fructose-fed rats. Plant Foods Hum. Nutr. 62: pp. 1-6 CrossRef
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  10. Chen, P.N. (2006) Black rice anthocyanins inhibit can- cer cells invasion via repressions of MMPs and u-PA expression. Chemico-Biological Interactions 163: pp. 218-229 CrossRef
  11. Hou, Z.H. (2013) Identification of anthocyanins isolated from black rice (Oryza sativa L.) and their degradation kinetics. Food Res. Int. 50: pp. 691-697 CrossRef
  12. Ichikawa, H. (2001) Antioxidant activity of anthocya- nin extract from purple black rice. J. Med. Food 4: pp. 211-218 CrossRef
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  13. Reddy, A.M. (2007) Novel transgenic rice overexpres sing anthocyanidin synthase accumulates a mixture of flavonoids leading to an increased antioxidant poten tial. Metab Eng. 9: pp. 95-111 CrossRef
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  15. Krzywinski, M. (2009) Circos: an Information Aesthetic for Comparative Genomics. Genome Res. 19: pp. 1639-1645 CrossRef
  16. Kim, J.S. et al. A Pepper MSRB2 Gene Confers Drought Tolerance in Rice through the Protection of Chloroplast-Targeted Genes. / PLoS ONE 9, e90588 (2014).
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Biotechnology
  
• 出版者：The Korean BioChip Society, in co-publication with Springer Verlag GmbH
• ISSN：2092-7843

文摘

We used a 135K rice microarray to identify genes involved in anthocyanin biosynthesis and metabolism in black rice. Using our multi-interaction screening method, we then screened 427 expression genes, 754 orthologous genes, and 416 pathway-network related genes associated with anthocyanin bio-synthesis. Finally, we identified eight candidate genes by comparing pathway-expression genes, including ortholog-ontology genes. To verify the candidate genes, each was mapped to the black rice genome, and functional predictions were confirmed via phylogenetic reconstructions using the candidate genes and their homologous proteins. While the eight genes identified by our method require further characterization and validation, our study demonstrates the power of multi-interaction screening after the initial identification of genes with microarrays.