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Background The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. Results Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. Conclusions The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors.

A single dominant powdery mildew resistance gene MlNFS10 was identified in wild emmer wheat and mapped within a 0.3cM genetic interval spanning a 2.1Mb physical interval on chromosome arm 4AL. Wheat powdery mildew caused by Blumeria graminis forma specialis tritici (Bgt) is a globally devastating disease. The use of powdery mildew resistance genes from wild relatives of wheat is an effective method of disease management. Our previous research has shown that disruptive ecological selection has driven the discrete adaptations of the wild emmer wheat population on the south facing slope (SFS) and north facing slope (NFS) at the microsite of “Evolution Canyon” at Mount Carmel, Israel and demonstrated that 16 accessions in the NFS population display high resistance to 11 powdery mildew isolates (collected from different wheat fields in China). Here, we constructed bi-parental population by crossing the accession NFS-10 (resistant to 22 Bgt races collected from China in seedling resistance screen) and the susceptible line SFS2-12. Genetic analysis indicated that NFS-10 carries a single dominant gene, temporarily designated MlNFS10. Ultimately, 13 markers were successfully located within the long arm of chromosome 4A, thereby delineating MlNFS10 to a 0.3 cM interval covering 2.1 Mb (729275816-731365462) in the Chinese Spring reference sequence. We identified disease resistance-associated genes based on the RNA-seq analysis of both parents. The tightly linked InDel marker XWsdau73447 and SSR marker XWsdau72928 were developed and used for marker-assisted selection when MlNFS10 was introgressed into a hexaploid wheat background. Therefore, MlNFS10 can be used for improvement of germplasm in breeding programs for powdery mildew resistant cultivars.

Fungal disease meets its matchFusariumhead blight (FHB), caused by a fungus, reduces wheat crop yield and introduces toxins into the harvest. From the assembly of the genome ofThinopyrum elongatum, a wild relative of wheat used in breeding programs to improve cultivated wheat, Wanget al.cloned a gene that can address both problems (see the Perspective by Wulff and Jones). The encoded glutathioneS-transferase detoxifies the trichothecene toxin and, when expressed in wheat, confers resistance to FHB.Science, this issue p.eaba5435; see also p.822

Low-molecular-weight glutenin subunits (LMW-GSs) are one of the important factors for the dough processing quality. In this study, a novel LMW-GS, designated LMW-N13, from the wheat relative species Aegilops uniaristata PI 554421 was cloned and characterized. Unlike previously published LMW-GSs, LMW-N13 has a large molecular weight and is the largest LMW-GS published thus far. Sequence alignments demonstrated that LMW-N13 is a LMW-i-type subunit but contains nine cysteine residues which is one more than typical LMW-i-type subunits. In addition, four insertions are present in the repetitive domain that resulted in the large molecular weight. In vitro analysis showed that LMW-N13 could improve the dough quality of different base flours.

High molecular weight glutenin subunits (HMW-GSs) play an important role in affecting dough viscoelasticity and extensibility. In this work, the novel HMW-GS gene 1Dy12** in Yunnan hulled wheat was cloned and characterized, and the molecular marker for identifying this gene was developed. SDS-PAGE analysis indicated that the mobility of 1Dy12** was the same as that of 1Dy12. The coding sequence of 1Dy12** was 1953 bp, which was 33 bp less than that of 1Dy12. 1Dy12** possessed 649 amino acid residues and showed a similar molecular structure to the published y-type subunit. It possessed four domains: a signal peptide, a conservative N-terminal domain, a large repetitive domain, and a conservative C-terminal domain. Eight cysteine residues were present in 1Dy12**, which was one more than the conserved number of cysteine residues in the y-type subunit. In vitro SDS-sedimentation tests demonstrated that 1Dy12** could bring higher SDS-sedimentation volumes than those of 1Dy10 or 1Dy12. A set of functional markers for the 1Dy12** gene was developed and validated on 36 bread wheat varieties with different Glu-1 alleles and 48 recombinant inbred lines derived by Yunnan hulled wheat and Yanzhan 1. The markers could effectively distinguish 1Dy12** from other HMW-GS genes and, thus, provide a useful tool for marker-assisted selection in wheat quality improvement programs.

Low-molecular-weight glutenin subunits (LMW-GSs) are one of the important factors for the dough processing quality. In this study, a novel LMW-GS, designated LMW-N13, from the wheat relative species

High-molecular-weight glutenin subunits (HMW-GS) in wheat grain are the major determinants of dough elasticity and viscosity and thus of bread-making quality. PCR-based molecular markers designed based on DNA polymorphisms were used to analyze HMW-GS genes in wheat. The loop-mediated isothermal amplification (LAMP) assay is a simple and rapid method for specific detection of genomic DNA target sequences. In the present study, we designed a set of LAMP markers by targeting the unique sequences of 1Dx2 and 1Dx5 genes. The primers could effectively distinguish the 1Dx2 and 1Dx5 genes from other genes at the Glu-1 locus. The results were confirmed by agarose gel electrophoresis. For visualization, ethidium bromide was used, and fluorescence only appeared in the positive samples. Under optimal conditions, the detection could be finished in 1 h. Thirty-eight wheat cultivars with known HMW-GS were used to validate LAMP markers for 1Dx2 and 1Dx5 genes. Only DNA samples with target genes could be amplified, and the results could be read easily using this method. The tests using LAMP were easy to perform, rapid, and sensitive. Thus, the current study results have the potential to be a powerful tool for the detection of HMW-GS genes in wheat.

High-molecular-weight glutenin subunits (HMW-GS) in bread wheat are major determinants of dough viscoelastic properties and the end-use quality of wheat flour. Cysteine residues, which form intermolecular disulphide bonds in HMW-GS, could improve the strength of gluten. To our knowledge, the number and position of cysteine residues in HMW-GS are conserved between wheat (Triticum aestivum) and Aegilops markgrafii. In the present study, we modified a gene (1Cx1.1) from Ae. markgrafii for an HMW-GS that possessed the typical structure and conserved number of cysteines. Site-directed mutagenesis was carried out in 1Cx1.1 to investigate how the position of cysteine residues in HMW-GS affects the mixing properties of dough. Six HMW-GS containing an extra cysteine residue were expressed in Escherichia coli, and the proteins were purified at sufficient scale for incorporation into flour to test dough quality. There were large differences in dough property among samples containing different modified subunits. Cysteine substituting in the N-terminal or repetitive-domain of HMW-GS could significantly improve dough quality. The results showed that the strategy was useful for providing genetic resources for gene engineering, and hence could be valuable for improving the processing quality of wheat.