Diploid Thinopyrum elongatum ( EE , 2 n = 2 x = 14) and related polyploid species constitute an important gene pool for improving Triticeae grain and forage crops. However, the genomic and molecular marker resources are generally poor for these species. To aid the genetic, molecular, breeding and ecological studies involving Thinopyrum species, we developed a strategy for mining and validating E‐genome‐specific SNP s using Th. elongatum and common wheat ( Triticum aestivum , AABBDD , 2 n = 6 x = 42) as experimental materials. By comparing the transcriptomes between Chinese Spring ( CS , a common wheat variety) and the CS ‐ Th. elongatum octoploid, 35,193 candidate SNP s between E genome genes and their common wheat orthologs were computed. Through comparative genomic analysis, these SNP s were putatively assigned to the seven individual E genome chromosomes. Among 420 randomly selected SNP s, 373 could be validated. Thus, approximately 89% of the mined SNP s may be authentic with respect to their polymorphism and chromosomal location. Using 14 such SNP s as molecular markers, complex E genome introgressions were reliably identified in 78 common wheat‐ Th. elongatum hybrids, and the structural feature of a novel recombinant chromosome formed by 6E and 7E was revealed. Finally, based on testing 33 SNP s assigned to chromosome 3E in multiple genotypes of Th. elongatum , Pseudoroegneria stipifolia (carrying the St genome related to E) and common wheat, we suggest that some of the SNP markers may also be applicable for genetic studies within and among the Thinopyrum species (populations) carrying E and/or St genomes in the future.

Gliadins, specified by six compound chromosomal loci ( Gli-A1/B1/D1 and Gli-A2/B2/D2 ) in hexaploid bread wheat, are the dominant carriers of celiac disease (CD) epitopes. Because of their complexity, genome-wide characterization of gliadins is a strong challenge. Here, we approached this challenge by combining transcriptomic, proteomic and bioinformatic investigations. Through third-generation RNA sequencing, full-length transcripts were identified for 52 gliadin genes in the bread wheat cultivar Xiaoyan 81. Of them, 42 were active and predicted to encode 25 α-, 11 γ-, one δ- and five ω-gliadins. Comparative proteomic analysis between Xiaoyan 81 and six newly-developed mutants each lacking one Gli locus indicated the accumulation of 38 gliadins in the mature grains. A novel group of α-gliadins (the CSTT group) was recognized to contain very few or no CD epitopes. The δ-gliadins identified here or previously did not carry CD epitopes. Finally, the mutant lacking Gli-D2 showed significant reductions in the most celiac-toxic α-gliadins and derivative CD epitopes. The insights and resources generated here should aid further studies on gliadin functions in CD and the breeding of healthier wheat.