Background

Agropyron cristatum (L.) Gaertn. (2n=4x=28, PPPP), which is a wild relative of common wheat and has a P genome, has many excellent characteristics (for example, it is disease resistant, is stress resistant and is high yielding) and has important utilization value for the genetic improvement of wheat. In this study, the wheat– A. cristatum 3P addition line I-27 and 3P(3B) substitution line I-15 were identified for the first time via in situ hybridization (ISH) and specific molecular marker (EST-STS) from wheat– A. cristatum -derived lines, which laid an representing important material for the utilization of excellent genes from A. cristatum chromosome 3P for wheat genetic improvement. In terms of agronomic traits, that the tiller number and spike length of 3P addition line I-27 were significantly higher than those of Fukuhokomugi. The spike length and spikelet number per spike of 3P substitution line I-15 were significantly greater than those of Fukuho. Additionally, wheat– A. cristatum 3P substitution line I-15 was resistant to wheat leaf rust. The generation of the 3P addition line I-27 and 3P substitution line I-15 was essential for the transfer of the excellent genes of the A. cristatum 3P chromosome into common wheat and resulted in the wheat– A. cristatum addition line containing a complete set of genetic research materials, laying a foundation for comparative studies of the P genome and subsequent fine mapping.

Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies.Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3,398 novel and 1,352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035.Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.