Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Abstract

BackgroundSorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar.ResultsHere, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome.ConclusionsSequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time.

Discovery of MicroRNA169 Gene Copies in Genomes of Flowering Plants through Positional Information

“…S1 and S6 A , Supplementary Material online). Despite the lack of Expressed Sequence Tag (EST) evidence for sbi- MIR169 r and sbi- MIR169 s annotation, our previously generated small RNA library from sorghum stem tissue (Calvino et al 2011) supported the transcription from both strands based on small RNA reads mapped to both sbi- MIR169 r and sbi- MIR169 s, respectively (supplementary fig. S6 A , Supplementary Material online).…”

“…To experimentally validate the new MIR169 gene copies found in sorghum through our syntenic analysis among grasses, we mapped previously sequenced small RNAs from sorghum stems (Calvino et al 2011) to the newly predicted MIR169 t/u/v/r/s hairpins. Similarly, to validate the newly described zma- MIR169 s gene copy in maize, we constructed small RNA libraries from endosperm tissue belonging to cultivars B73, Mo17, and their reciprocal crosses (supplementary table S1, Supplementary Material online).…”

“…We took advantage of our previously sequenced small RNA libraries from sorghum stems (Calvino et al 2011) and mapped small RNAs to the newly predicted MIR169 r/s/t/u/v hairpin sequences. To validate the newly predicted MIR169 s in maize, we used the SOLiD platform to sequence small RNAs derived from endosperm tissue from B73 and Mo17 inbred lines as well as endosperm tissue derived from their reciprocal crosses.…”

“…We have chosen miR169 as an example because of its possible role in stem-sugar accumulation in sorghum besides its previously described role in drought stress response in several plant species. We discovered allelic variation in miR169 expression between grain and sweet sorghum, suggesting that miR169 could also play a role in the sugar content of sorghum stems (Calvino et al 2011). Although high sugar content in stems is a trait shared by sorghum and sugarcane (Calvino et al 2008, 2009), this trait seems to be silent in other grasses (Calvino and Messing 2011).…”

Expression Profiling of Sucrose Metabolizing Genes in Saccharum, Sorghum and Their Hybrids

“…In sugarcane, several protein kinases and transcription factors have been identified that play a role in sucrose accumulation [9]. An involvement of miRNAs (miRNA 169) in regulating stem sugar content in sweet sorghum has also been reported [27].…”