De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat

•The transcriptome of A. cristatum was determined using RNA sequencing.•An abundance of stress resistance gene resources was identified in A. cristatum.•A total of 3349 EST-SSRs were predicted in A. cristatum.•6172 unigenes were identified to be specific to A. cristatum in tribe Triticeae.•The transcriptome of A. cristatum enriches genetic information on Triticeae grasses.

Agropyron cristatum is a wild grass of the tribe Triticeae that is widely grown in harsh environments. As a wild relative of wheat, A. cristatum carries many resistance genes that could be used to broaden the genetic diversity of wheat. Here, we report the transcriptome sequencing of the flag leaf and young spike tissues of a representative tetraploid A. cristatum. More than 90 million reads from the two tissues were assembled into 73,664 unigenes. All unigenes were functionally annotated against the KEGG, COG, and Gene Ontology databases and predicted long non-coding RNAs. Pfam prediction demonstrates that A. cristatum carries an abundance of stress resistance genes. The extent of specific genes and rare alleles make A. cristatum a vital genetic reservoir for the improvement of wheat. Altogether, the available gene resources in A. cristatum facilitate efforts to harness the genetic diversity of wild relatives to enhance wheat.