Utilizing a pan-transcriptome reveals genotype-specific responses to iron deficiency in Sorghum bicolor

Introduction Sweet sorghum genotypes are distinguished from non-sweet types by their ability to accumulate high concentrations of sugar in their stems, which makes them valuable for both bioenergy production and as an alternative source of sugar. Previous work has reported numerous gene copy number differences in metal metabolism and iron transport genes between the sweet and non-sweet genotypes. The objective of this study was to investigate which genes are differentially expressed by the sweet and non-sweet genotypes under varying iron conditions. Methods Three sweet and three non-sweet sorghum genotypes were grown hydroponically under two conditions (control and low iron), and root tissue from the plants was harvested for RNA extraction and sequencing after 9 days. To obtain a more complete picture of diverse iron-response mechanisms in sorghum, we constructed a pan-transcriptome from 10 founder parents of the Carbon-Partitioning Nested Association Mapping population. Results Differential expression analysis using the pan-transcriptome revealed 209 genes that responded differently to iron stress in the sweet and non-sweet types, which was more than twice as many genes found using only a single reference genome. Enrichment analysis based on age of duplication event showed that duplicate gene copies that are differentially expressed due to genotype effect appear to be specific to sorghum while most duplicate gene copies that are differentially expressed due to iron treatment appear to be more evolutionary conserved across plants. Discussion This study highlights the importance of the non-core genome and the utility of the pan-transcriptome in sorghum. It also revealed that different sorghum genotypes respond to iron stress differently.