Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of Cd in edible tissues, which poses a major hazard to human health. It has been reported that heat shock transcription factor A 4a (HsfA4a) of wheat and rice conferred Cd tolerance by upregulating metallothionein gene expression. However, genome-wide identification, classification, and comparative analysis of the Hsf family in wheat is lacking. Further, because of the promising role of Hsf genes in Cd tolerance, there is need for an understanding of the expression of this family and their functions on wheat under Cd stress. Therefore, here we identify the wheat TaHsf family and to begin to understand the molecular mechanisms mediated by the Hsf family under Cd stress. We first identified 78 putative Hsf homologs using the latest available wheat genome information, of which 38 belonged to class A, 16 to class B and 24 to class C subfamily. Then, we determined chromosome localizations, gene structures, conserved protein motifs, and phylogenetic relationships of these TaHsfs. Using RNA sequencing data over the course of development, we surveyed expression profiles of these TaHsfs during development and under different abiotic stresses to characterise the regulatory network of this family. Finally, we selected 13 TaHsf genes for expression level verification under Cd stress using qRT-PCR. To our knowledge, this is the first report of the genome organization, evolutionary features and expression profiles of the wheat Hsf gene family. This work therefore lays the foundation for targeted functional analysis of wheat Hsf genes, and contributes to a better understanding of the roles and regulatory mechanism of wheat Hsfs under Cd stress.

Synthetic hexaploid wheat (SHW) is a useful genetic resource that can be used to improve the performance of common wheat by transferring favorable genes from a wide range of tetraploid or diploid donors. From the perspectives of physiology, cultivation, and molecular genetics, the use of SHW has the potential to increase wheat yield. Moreover, genomic variation and recombination were enhanced in newly formed SHW, which could generate more genovariation or new gene combinations compared to ancestral genomes. Accordingly, we presented a breeding strategy for the application of SHW—the ‘large population with limited backcrossing method’—and we pyramided stripe rust resistance and big-spike-related QTLs/genes from SHW into new high-yield cultivars, which represents an important genetic basis of big-spike wheat in southwestern China. For further breeding applications of SHW-derived cultivars, we used the ‘recombinant inbred line-based breeding method’ that combines both phenotypic and genotypic evaluations to pyramid multi-spike and pre-harvest sprouting resistance QTLs/genes from other germplasms to SHW-derived cultivars; consequently, we created record-breaking high-yield wheat in southwestern China. To meet upcoming environmental challenges and continuous global demand for wheat production, SHW with broad genetic resources from wild donor species will play a major role in wheat breeding.

Leaf pubescence is an important trait closely associated with plant adaptability to specialized habitats. Baimaomai (BMM) is a wheat (Triticum aestivum L.) landrace originating from the high-altitude, drought-prone environment of Sichuan Province, China with long, dense leaf pubescence. A population of 234 recombinant inbred lines (F₁₀) developed from the cross between Chuanmai104 (CM104), which lacks leaf pubescence, and BMM with pubescent leaves, was used to conduct a phenotypic evaluation of leaf pubescence. Three quantitative trait loci (QTLs) were detected on chromosome arms 7BS, 3DL and 3AL using a high-density wheat 50K single-nucleotide polymorphism array in four environments. The QTLs were designated QLp.saas-7BS, QLp.saas-3DL and QLp.saas-3AL. QLp.saas-3AL, derived from BMM, and QLp.saas-3DL, derived from CM104, were new minor-effect loci. QLp.saas-7BS, derived from BMM, was a novel major-effect locus detected in all environments and was localized in a 0.48 Mb interval on chromosome arm 7BS based on the wheat ‘Chinese Spring’ reference genome. QLp.saas-7BS explained up to 40.77% of the total phenotypic variance. KASP markers tightly linked to QLp.saas-7BS were developed and verified. The present results provide valuable information for further fine mapping, cloning, and marker-assisted selection with QLp.saas-7BS in wheat.

Premium wheat with a high end-use quality is generally lacking in China, especially high-quality hard and soft wheat. Pina-D1 and Pinb-D1 (puroindoline genes) influence wheat grain hardness (i.e., important wheat quality-related parameter) and are among the main targets in wheat breeding programs. However, the mechanism by which puroindoline genes control grain hardness remains unclear. In this study, three hard wheat puroindoline variants (MY26, GX3, and ZM1) were compared with a soft wheat variety (CM605) containing the wild-type puroindoline genotype. Specifically, proteomic methods were used to screen for differentially abundant proteins (DAPs). In total, 6253 proteins were identified and quantified via a high-throughput tandem mass tag quantitative proteomic analysis. Of the 208 DAPs, 115, 116, and 99 proteins were differentially expressed between MY26, GX3, and ZM1 (hard wheat varieties) and CM605, respectively. The cluster analysis of protein relative abundances divided the proteins into six clusters. Of these proteins, 67 and 41 proteins were, respectively, more and less abundant in CM605 than in MY26, GX3, and ZM1. Enrichment analyses detected six GO terms, five KEGG pathways, and five IPR terms that were shared by all three comparisons. Furthermore, 12 proteins associated with these terms or pathways were found to be differentially expressed in each comparison. These proteins, which included cysteine proteinase inhibitors, invertases, low-molecular-weight glutenin subunits, and alpha amylase inhibitors, may be involved in the regulation of grain hardness. The candidate genes identified in this study may be relevant for future analyses of the regulatory mechanism underlying grain hardness.

Formerly considered nonfunctional “junk DNA,” pseudogenes have been re-evaluated in light of technological advances in bioinformatics and high-throughput sequencing. The limited research to date on pseudogenes in hexaploid common wheat (Triticum aestivum L.) is largely confined to individual gene families, thus hindering our understanding of the long-term evolutionary dynamics among the A, B, and D subgenomes. Using the IWGSC RefSeq v2.1 genome assembly, we performed genome-wide identification, classification, and analysis of pseudogenes in wheat, including their distribution, evolutionary history, and parental gene functions. Marked asymmetries in pseudogene abundance, distribution, evolutionary dynamics, and constraints were detected among the subgenomes. The B subgenome harbored significantly more pseudogenes and showed distinct evolutionary patterns compared with the A and D subgenomes. Pseudogenes were strongly associated with transposable elements and peaks in their formation were incongruent with ancient genomic upheavals of wheat ancestral lineages. The parent genes were predominantly enriched in non-core functions and showed tissue-specific expression. The findings provide direct evidence for long-term asymmetric, post-polyploidization evolution in wheat, enhance our understanding of polyploid genome evolution, and offer a methodological framework for research on other genetically complex polyploid crops.

Allopolyploidy increases its evolutionary potential by fixing heterosis and the advantage of gene redundancy. Allelic combinations generated from genetic recombination potentially provide many variations to the selection pools for evolution. May there be any relationship between allopolyploidization and genetic recombination? To study the impact of polyploidy on genetic recombination, we selected wheat as a model and simulated its evolution pathway of allopolyploidy by developing synthetic hexaploid wheat. The change of homologous chromosome recombination were investigated on their diploid DD and tetraploid AABB genomes after their allohexaploidization, respectively. The genetic recombination of the ancestral diploid genome of Aegilops tauschii was enhanced significantly more than 2 folds after their hexaploidization. Hexaploidization enhancing genetic recombination of the ancestral diploid D genome was firstly reported to be a new way to increase evolutionary potential of wheat, which is beneficial for wheat to conquer their narrow origination of D genome, quickly spread and make it a major crop of the world. Finally, re-synthetizing hexaploid wheat using diverse Ae. tauschii species with tetraploid wheat can be considered as a pleiotropic strategy to speed adaptive evolution of bread wheat in breeding processes by increasing both gene allele types and genetic recombination variations.