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Published on September 22, 2006; 10.1104/pp.106.082891

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Received May 3, 2006
Accepted September 18, 2006

Sorghum Genes with Rhizome-Enriched Expression: Functional Classification, Genomic Organization, Putative cis-Acting Regulatory Elements, and Relationship to QTLs

Cheol Seong Jang , Terry L. Kamps , D. Neil Skinner , Stefan R. Schulze , William K. Vencill , and Andrew H. Paterson *

Plant Genome Mapping Laboratory
Plant Genome Mapping Laboratory; Department of Crop and Soil Sciences, University of Georgia, 111 Riverbend Road, Athens, GA 30602

* Corresponding author; email: paterson{at} uga.edu.

Rhizomes 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 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 were implicated in secondary and hormone metabolism, and abiotic stimuli and development. A high frequency of unknown-function genes reflect 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 homologs, sorghum 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, ESTs 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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[Abstract] [Full Text] [PDF]


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