Transcriptomic analysis and identification of candidate genes involved in rhizome development in Agropyron michnoi Roshev.

Agropyron michnoi Roshev. is a perennial grass with rhizomes in the genus Agropyron. Agropyron michnoi has strong tolerance to drought and low temperature. It is an establishing species in sandy flat and hilly slope lands, where it constitutes sandy grassland. Therefore, Agropyron michnoi is an important forage species in dry grassland and desert steppe. Rhizomes not only enables asexual reproducibility but also confers strong resilience to stresses in Agropyron michnoi. However, in production practice, the rhizome trait is not stable, with some Agropyron michnoi plants having no rhizomes. In addition, the genomic resources for this species are scarce, which limits the studies on rhizome development. Therefore, the anatomical structure of rhizomes, roots and stems was analyzed by paraffin sectioning technique. The results showed that rhizomes were both similar to roots and stems, and had partial functions of roots and stems. Than Agropyron michnoi plants were divided into two groups: Group Y (with rhizomes) and Group W (without rhizomes). From each plant group, root (YG and WG), stem (YJ and WJ) and rhizome (YGJ) samples were harvested and subjected for RNA sequencing. De novo transcriptomic analysis was performed to identify candidate genes involved in rhizome development. From the RNA sequencing, a total of 103.73 Gb clean bases were obtained, from which 215,282 unigenes with an average length of 905.67 bp were assembled. Among these unigenes, 161,175 (74.87%) were functionally annotated based on seven common public databases. From pairwise comparisons of differentially expressed genes between the five samples, 129 candidate genes that are potentially specifically expressed in rhizomes were selected. Pathway enrichment analysis revealed that the rhizome-expressed genes are highly enriched in pathways of phenylpropanoid biosynthesis and starch and sucrose metabolism. The rhizome-specific expression pattern of ten of the 129 candidate genes were further validated using qRT-PCR. Results from this study enriched the genomic resources and the morphology information in Agropyron michnoi. The selected candidate genes involved in rhizome development provide preliminary mechanistic interpretation of rhizome development and will be informative for in-depth investigation of the molecular mechanism of rhizome development in Agropyron michnoi.