Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass

Abstract

The molecular basis behind shade tolerance in plants is not fully understood. Previously, we have shown that a connection may exist between shade tolerance and dwarfism, however, the mechanism connecting these phenotypes is not well understood. In order to clarify this connection, we analyzed the transcriptome of a previously identified shade-tolerant mutant of perennial ryegrass (<i>Lolium perenne</i> L.) called <i>shadow-1</i>. <i>shadow-1</i> mutant plants are dwarf, and are significantly tolerant to shade in a number of environments compared to wild-type controls. In this study, we treated <i>shadow-1</i> and wild-type plants with 95% shade for 2 weeks and compared the transcriptomes of these shade-treated individuals with both genotypes exposed to full light. We identified 2,200 differentially expressed genes (DEGs) (1,096 up-regulated and 1,104 down-regulated) in <i>shadow-1</i> mutants, compared to wild type, following exposure to shade stress. Of these DEGs, 329 were unique to <i>shadow-1</i> plants kept under shade and were not found in any other comparisons that we made. We found 2,245 DEGs (1,153 up-regulated and 1,092 down-regulated) in <i>shadow-1</i> plants, compared to wild-type, under light, with 485 DEGs unique to <i>shadow-1</i> plants under light. We examined the expression of gibberellin (GA) biosynthesis genes and found that they were down-regulated in <i>shadow-1</i> plants compared to wild type, notably gibberellin 20 oxidase (<i>GA20ox</i>), which was down-regulated to 3.3% (96.7% reduction) of the wild-type expression level under shade conditions. One GA response gene, lipid transfer protein 3 (<i>LTP3</i>), was also down-regulated to 41.5% in <i>shadow-1</i> plants under shade conditions when compared to the expression level in the wild type. These data provide valuable insight into a role that GA plays in dwarfism and shade tolerance, as exemplified by <i>shadow-1</i> plants, and could serve as a guide for plant breeders interested in developing new cultivars with either of these traits.