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TitleFunctional Classification, Genomic Organization, Putatively cis-Acting Regulatory Elements, and Relationship to Quantitative Trait Loci, of Sorghum Genes with Rhizome-Enriched Expression
AuthorsCheol Seong Jang, Terry L. Kamps, D. Neil Skinner, Stefan R. Schulze, William K. Vencill, and Andrew H. Paterson
Year2006
Taxonsorghum
PDFJang_et_al_2006.pdf
PublicationPlant Physiology 142:1148-1159
Journal_linkhttp://www.plantphysiol.org/
Publisher_note
Supplemental
AbstractRhizomes are organs of fundamental importance to plant competitiveness and invasiveness. We have identified genes
expressed at substantially higher levels in rhizomes than other plant parts, and explored their functional categorization,
genomic organization, regulatory motifs, and association with quantitative trait loci (QTLs) conferring rhizomatousness. The
finding that genes with rhizome-enriched expression are distributed across a wide range of functional categories suggests
some degree of specialization of individual members of many gene families in rhizomatous plants. A disproportionate share of
genes with rhizome-enriched expression was implicated in secondary and hormone metabolism, and abiotic stimuli and
development. A high frequency of unknown-function genes reflects our still limited knowledge of this plant organ. A putative
oligosaccharyl transferase showed the highest degree of rhizome-specific expression, with several transcriptional or regulatory
protein complex factors also showing high (but lesser) degrees of specificity. Inferred by the upstream sequences of their
putative rice (Oryza sativa) homologs, sorghum (Sorghum bicolor) genes that were relatively highly expressed in rhizome tip
tissues were enriched for cis-element motifs, including the pyrimidine box, TATCCA box, and CAREs box, implicating the
gibberellins in regulation of many rhizome-specific genes. From cDNA clones showing rhizome-enriched expression,
expressed sequence tags forming 455 contigs were plotted on the rice genome and aligned to QTL likelihood intervals for
ratooning and rhizomatous traits in rice and sorghum. Highly expressed rhizome genes were somewhat enriched in QTL
likelihood intervals for rhizomatousness or ratooning, with specific candidates including some of the most rhizome-specific
genes. Some rhizomatousness and ratooning QTLs were shown to be potentially related to one another as a result of ancient
duplication, suggesting long-term functional conservation of the underlying genes. Insight into genes and pathways that
influence rhizome growth set the stage for genetic and/or exogenous manipulation of rhizomatousness, and for further
dissection of the molecular evolution of rhizomatousness.

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