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Identification of novel members in sweet orange carotenoid biosynthesis gene families

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Abstract

Novel expressed and genomic members in sweet orange (Citrus sinensis [L.] Osbeck) carotenoid biosynthesis gene families have been identified through mining of an expressed sequence tags (ESTs) database and hybridization with a bacterial artificial chromosome (BAC) library. These new expressed members included one phytoene synthase (PSY), one phytoene desaturase (PDS), ten zeta-carotene desaturases (ZDS), one lycopene beta-cyclase (LCYB), one lycopene epsilon-cyclase (LCYE), four carotenoid beta-ring hydroxylases (CHYB), and one capsanthin/capsorubin synthase (CCS). Most unigenes with multiple ESTs, including the ones containing the known genes and these new members, were heterozygous, in which putative single nucleotide polymorphisms distinguished two alleles. According to digital gene expression profiling, fruit was the primary tissue where at least one member of each gene family was specifically or highly expressed. Digital expression levels varied among the members and tissues. According to Southern hybridization of the identified BAC clones, genomic members of the families were either clustered in a single BAC contig or distributed in several different contigs. PSY has four members in one contig, PDS two in one, ZDS 12 in three, LCYB 11 in three, LCYE three in two, CHYB eight in one, and CCS 14 in four, respectively. The number of the genomic members in most families tended to be more than that of the expressed members, suggesting that some genomic members may not be expressed or structurally functional. These new carotenoid gene members, along with much first-hand genomic information, can be used further for functional genomics and genetic map**.

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Acknowledgments

The authors thank Drs. R. Niedz and M. Bausher (USDA-ARS, Fort Pierce) for access to the selected clones from the BAC library, Drs. M.-C. Luo and J. Dvorak (University of California, Davis) for access to the BAC library physical map, and Mrs. M. Wendell and M. Holt for their technical assistance. This research was supported in part by grants from the State of Bahia Research Foundation (FAPESB), Salvador, Brazil (to MGCC) and from the Florida Citrus Production Research Advisory Council (FCPRAC), Peter McClure, Chairman (to FGG). We gratefully acknowledge the ‘International Cooperation’ scholarship to MGCC by FAPESB (INT007/2006).

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Authors and Affiliations

  1. Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA

    Chunxian Chen, Qibin Yu & Fred G. Gmitter Jr.

  2. Center for Biotechnology and Genetics, Biological Sciences Department, State University of Santa Cruz, Rod. Ilhéus-Itabuna km 16, Ilhéus, Bahia, 45662-000, Brazil

    Marcio G. C. Costa

  3. Horticultural Sciences Department, University of Florida, 1301 Fifield Hall, Gainesville, FL, 32611, USA

    Gloria A. Moore

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  1. Chunxian Chen
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Correspondence to Fred G. Gmitter Jr..

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Communicated by E. Dirlewanger

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Chen, C., Costa, M.G.C., Yu, Q. et al. Identification of novel members in sweet orange carotenoid biosynthesis gene families. Tree Genetics & Genomes 6, 905–914 (2010). https://doi.org/10.1007/s11295-010-0300-3

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