Functional Classification, Genomic Organization, Putatively cis-Acting Regulatory Elements, and Relationship to Quantitative Trait Loci, of Sorghum Genes with Rhizome-Enriched Expression

Abstract

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 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.

Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

“…Isolation of candidate BACs with rhizome-enriched genes Previously, genes with rhizome-enriched expression were identified from both genotypes, S. propinquum and S. halepense, which produce abundant rhizomes (Jang et al, 2006). The 30 genes from S. propinquum and S. halepense, respectively, that showed the greatest enrichment of expression in the RT relative to mature rhizome internodes (RMIs) and pooled aboveground (AG) tissues were selected.…”

“…Individual membranes containing 9216 clones with two replicates (that is, clones from six different BAC clones) were prepared as described by Jang et al (2006). Probe labeling, hybridization and detection were conducted as described above.…”

“…Twenty or fewer subclones per BAC clone were rearrayed into 96-well microtiter plates. Plasmid preparation and sequencing were performed by Jang et al (2006). Trace files were processed using phred (score420), followed by phrap assembly into contigs by clustering a minimum continuous 100 bp .…”

“…Previously, we reported the functional classification, genomic organization, putative cis-acting regulatory elements, relationship to quantitative trait locus (QTL), of Sorghum genes with rhizome-enriched expression (Jang et al, 2006). However, the evolutionary fate in nonrhizomatous S. bicolor of genes with rhizome-enriched expression in its sister S. propinquum and possibly ancestral Saccharinae remains unknown.…”

“…The Sorghum genus has become a model for dissecting the molecular control of rhizomatousness (Paterson et al, 1995;Hu et al, 2003;Jang et al, 2006). S. halepense L. Pers.…”