A Sorghum bicolorexpression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

Abstract

BackgroundEffective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement.ResultsThis study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes.ConclusionsHere we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.

Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.)

“…This observation provides confidence that the number of sampled tissue types was sufficient to support a high confidence reference transcript assembly. The preferential expression of transcripts in specific tissues identified the largest number (1.8%) in leaf, also observed in sorghum [52]. Identities of some of the tissue-specific transcripts were clearly related to a particular organ function.…”

Accumulation of stem sugar and its remobilisation in response to drought stress in a sweet sorghum genotype and its near‐isogenic lines carrying different stay‐green loci

“…Higher SUS and INV activity has been reported to play a role in creating a strong sink for sucrose unloading in sugarcane internodes (Sch€ afer et al 2004;Grof et al 2006). Higher expression of INV3, SUS3, SPS2 and SPS5 was observed in the internode tissue of a sweet sorghum genotype as compared to expression in a grain sorghum genotype, although activities of the sugar metabolising enzymes were not studied (Shakoor et al 2014). Expression of genes involved in sugar transport also differed in the two NILs as compared to that in the parent line S35.…”

Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis

“…Fortunately, sorghum possesses significant genetic diversity for N use efficiency (Gelli et al., , ), yield potential and drought tolerance (Mace et al., ). Furthermore, the availability of a reference genome (Paterson et al., ), an expression atlas (Shakoor et al., ), and over 400,000 markers (Morris et al., ) identified for marker‐assisted breeding makes sorghum well‐suited for significant crop improvement.…”