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

Abstract Carotenoids, important lipid-soluble antioxi-dants in photosynthetic tissues, are known to be completely absent in rice endosperm. Many studies, involving trans-genic 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 carote-noids in diVerent tissues. We have identiWed 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 Arabid-opsis and other characterized carotenoid biosynthesis genes has revealed that homologous genes exist in these plants, and the duplicated gene copies probably adopt new func-tions. Expression of rice and Populus genes has been ana-lyzed by full-length cDNA- and EST-based expression proWling. In rice, this analysis was complemented by real-time PCR, microarray and signature-based expression pro-Wling, which reveal that carotenoid biosynthesis genes are highly expressed in light-grown tissues, have diVerential expression pattern during vegetative/reproductive develop-ment and are responsive to stress