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

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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.

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Acknowledgments

This work was financially supported by the Department of Biotechnology, Government of India, the University Grants Commission and the Council of Scientific and Industrial Research, New Delhi (research fellowship to N. C. and A. N.). The TIGR, KOME, TAIR, NCBI and Populus database resources are gratefully acknowledged for the detailed sequence information.

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  1. Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India

    Neetu Chaudhary, Aashima Nijhawan, Jitendra P. Khurana & Paramjit Khurana

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  1. Neetu Chaudhary
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  2. Aashima Nijhawan
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Chaudhary, N., Nijhawan, A., Khurana, J.P. et al. Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis. Mol Genet Genomics 283, 13–33 (2010). https://doi.org/10.1007/s00438-009-0495-x

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