Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

Shenghui Zhou,Lihui Li,Weihua Liu,Xiuquan Li,Yuqing Lu,Haiming Han,Jinpeng Zhang,Zhi Zhang,Xinming Yang,Jing Zhang,Huihui Ma

doi:10.1186/s12864-019-6416-4

Abstract

BackgroundAgropyron 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.ResultsSingle-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 3398 novel and 1352 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.ConclusionsFull-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.

Highlights

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
We present the first report on the singlemolecule FL sequencing, annotation and expression of the A. cristatum Z559 transcriptome and the application of this transcriptome in the identification of candidate alien genes associated with thousand-grain weight in the wheat-A. cristatum translocation Pubing 3035 (Fig. 1)
Notes: CCS represents circular consensus sequence; FLNC represents full-length, non-concatemer longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies [20, 21] (Fig. 2; Table 2)

Summary

Introduction

Fukuhokumugi (Fukuho) and A. cristatum accession Z559 and embryo rescue [11] Several of these lines, including additional lines, disomic substitution lines, translocation lines and introgression lines, exhibit potentially valuable traits for wheat improvement, such as disease resistance, abiotic and biotic stress tolerance and high yield, and these lines have been used in wheat-breeding programmes [12,13,14,15]. Among these lines, Pubing 3035, a Ti1AS-6PL1AS·1AL intercalary translocation, was derived from the offspring of a wheat-A. cristatum 6P chromosome addition line; notably, the 6P chromosomal segment played an important role in regulating the thousand-grain weight and spike length [15]. The growth characteristics and utilization of wheat-A. cristatum derivative lines in wheatbreeding programmes have been extensively investigated, little is known regarding the nature of the gene and the mechanism by which it confers superior traits

Methods

Results

Discussion

Conclusion