Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis

  • Neetu Chaudhary
  • Aashima Nijhawan
  • Jitendra P. Khurana
  • Paramjit Khurana
Original Paper

DOI: 10.1007/s00438-009-0495-x

Cite this article as:
Chaudhary, N., Nijhawan, A., Khurana, J.P. et al. Mol Genet Genomics (2010) 283: 13. doi:10.1007/s00438-009-0495-x
  • 532 Downloads

Abstract

Carotenoids, important lipid-soluble antioxidants in photosynthetic tissues, are known to be completely absent in rice endosperm. Many studies, involving transgenic manipulations of carotenoid biosynthesis genes, have been performed to get carotenoid-enriched rice grain. Study of genes involved in their biosynthesis can provide further information regarding the abundance/absence of carotenoids in different tissues. We have identified 16 and 34 carotenoid biosynthesis genes in rice and Populus genomes, respectively. A detailed analysis of the domain structure of carotenoid biosynthesis enzymes in rice, Populus and Arabidopsis has shown that highly conserved catalytic domains, along with other domains, are present in these proteins. Phylogenetic analysis of rice genes with Arabidopsis and other characterized carotenoid biosynthesis genes has revealed that homologous genes exist in these plants, and the duplicated gene copies probably adopt new functions. Expression of rice and Populus genes has been analyzed by full-length cDNA- and EST-based expression profiling. In rice, this analysis was complemented by real-time PCR, microarray and signature-based expression profiling, which reveal that carotenoid biosynthesis genes are highly expressed in light-grown tissues, have differential expression pattern during vegetative/reproductive development and are responsive to stress.

Keywords

CarotenoidsMicroarrayMPSSPopulusPhylogenetic analysisRice

Supplementary material

438_2009_495_MOESM1_ESM.ppt (102 kb)
Supplementary Fig. S1 (PPT 102 kb)
438_2009_495_MOESM2_ESM.ppt (94 kb)
Supplementary Fig. S2 (PPT 93 kb)
438_2009_495_MOESM3_ESM.doc (39 kb)
Supplementary Table S1 (DOC 39 kb)
438_2009_495_MOESM4_ESM.doc (126 kb)
Supplementary Table S2 (DOC 126 kb)
438_2009_495_MOESM5_ESM.doc (28 kb)
Supplementary Table S3 (DOC 28 kb)
438_2009_495_MOESM6_ESM.xls (30 kb)
Supplementary Table S4 (XLS 30 kb)
438_2009_495_MOESM7_ESM.doc (320 kb)
Supplementary Table S5 (DOC 320 kb)
438_2009_495_MOESM8_ESM.doc (124 kb)
Supplementary Table S6 (DOC 124 kb)
438_2009_495_MOESM9_ESM.doc (37 kb)
Supplementary Table S7 (DOC 37 kb)

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Neetu Chaudhary
    • 1
  • Aashima Nijhawan
    • 1
  • Jitendra P. Khurana
    • 1
  • Paramjit Khurana
    • 1
  1. 1.Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia