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

2019 unpublished
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
more » ... eaves, 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 thousandgrain 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. Background As the most widely cultivated crop on Earth, wheat (Triticum aestivum L., 2n = 6x = 42, genomes AABBDD) contributes approximately a fifth of the total calories consumed by humans and provides more protein than any other food source [1]. However, due to historical artificial selection and domestication, the genetic diversity of modern wheat is relatively narrow, which is one of the bottlenecks for breakthroughs in wheat improvement [2] [3][4]. Natural variation from collections of wild wheat relatives has been and remains an important facilitator of wheat genetic advances, since these 4 relatives conserve considerable genetic variability of adaptive traits that can be transferred via artificially innovated introgression lines by direct hybridization [5-9]. The genus Agropyron Gaertn., called the crested wheatgrass complex, is an out-crossing tertiary gene pool relative of wheat and built upon one basic P genome with 3 ploidy levels [10]. The tetraploid crested wheatgrass Agropyron cristatum (L.) Gaertn. (2n = 4x = 28, genome PPPP) not only provides protein as a forage source but also possesses several desirable traits for wheat improvement. In the early 1990s, several wheat-A. cristatum derivative lines were produced via the intergeneric hybridization of wheat cv. 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 therefore been used in wheat-breeding programmes [12] [13] [14] [15] . Among these lines, Pubing 3035, a Ti1AS-6PL-1AS·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] . Although the growth characteristics and utilization of wheat-A. cristatum derivative lines in wheat-breeding programmes have been extensively investigated, little is known regarding the nature of the gene and the mechanism by which it confers superior traits. As a result of the low frequency of pairing and suppressed recombination between the genomes of wild wheat relatives and wheat, it is extremely difficult to characterize genes from wheat wild relatives through a map-based cloning strategy under a wheat genetic background. Comprehensive approaches, including cytogenetic stock development, mutagenesis, resistance gene enrichment and sequencing-Pacific Biosciences (PacBio), long-range assembly, and functional analysis, were successively used to successfully clone the Pm21 gene, which confers high resistance to Blumeria graminis f. sp. tritici (Bgt) in wheat throughout all growth stages, from the wild species Haynaldia villosa [16] . At the same time, Pm21 was also isolated and functionally validated via the discovery of Bgt-susceptible Dasypyrum villosum resources and construction of a genetic population using Methods Plant materials The A. cristatum accession Z559 (2n = 4x = 28, PPPP, from Xinjiang, China), a representative tetraploid A. cristatum, has been previously described [20] and cultivated in the experimental field of
doi:10.21203/rs.2.9773/v2 fatcat:bxtfw47o6jgljkfgdxtdmq2ms4