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Key messageAlthoughAe. tauschiihas been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. In this review, we discuss approaches that can be used to exploit the D genomes of the differentAegilopsspecies for the improvement of bread wheat.The D genome of allohexaploid bread wheat (Triticum aestivum, 2n = AABBDD) is the least diverse of the three wheat genomes and is unarguably less diverse than that of diploid progenitor Aegilops tauschii (2n = DD). Useful genetic variation and phenotypic traits also exist within each of the wheat group species containing a copy of the D genome: allopolyploid Aegilops species Ae. cylindrica (2n = DcDcCcCc), Ae. crassa 4x (2n = D1D1XcrXcr), Ae. crassa 6x (2n = D1D1XcrXcrDcrDcr), Ae. ventricosa (2n = DvDvNvNv), Ae. vavilovii (2n = D1D1XcrXcrSvSv) and Ae. juvenalis (2n = D1D1XcrXcrUjUj). Although Ae. tauschii has been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. Some of these D genomes appear to be modified relative to the bread wheat and Ae. tauschii D genomes, and others present in the allopolyploids may also contain useful variation as a result of adaptation to an allopolyploid, multi-genome environment. We summarise the genetic relationships, karyotypic variation and phenotypic traits known to be present in each of the D genome species that could be of relevance for bread wheat improvement and discuss approaches that can be used to exploit the D genomes of the different Aegilops species for the improvement of bread wheat. Better understanding of factors controlling chromosome inheritance and recombination in wheat group interspecific hybrids, as well as effective utilisation of new and developing genetics and genomics technologies, have great potential to improve the agronomic potential of the bread wheat D genome.

We applied fluorescent in situ hybridization (FISH) using (GAA)₁₀ microsatellite repeat alone or in combination with oligo pSc119.2-1, pTa535-1, pAs1-1, 5S and 45S rDNA probes to identify individual chromosomes and produce banded karyotypes for five allopolyploid Aegilops species that were thought to possess M subgenome. Labelling patterns of GAA repeats allow identification of individual chromosomes in the studied species including diploid Ae. comosa subsp. heldreichii (2n = MhMh) and Ae. umbellulata (2n = UU); and allopolyploid Ae. biuncialis (2n = UbUbMbMb), Ae. geniculata (2n = UgUgMgMg), Ae. columnaris (2n = UcUcXcXc), Ae. neglecta (2n = UⁿUⁿXⁿXⁿ) and Ae. crassa (2n = 4x = D¹D¹XcrXcr and 2n = 6x = D¹D¹XcrX-crDcrDcr). Intraspecific polymorphisms of GAA labelling patterns were observed between different genotypes in each species. FISH results showed that the X* subgenomes of Ae. columnaris and Ae. neglecta are highly similar, implying that both species originated from a common ancestor. However, these X* subgenomes were also distinct from and more heterochromatic when compared to the M* subgenomes of Ae. biuncialis and Ae. geniculata. This suggests that the X* subgenomes may not have originated from the Ae. comosa, as previously thought. Although (GAA)n bands are relatively few and weak in Ae. tauschii (DD genome), all 4x Ae. crassa (D¹D¹XcrXcr genome) chromosomes showed distinct GAA patterns. (GAA)₁₀ probe alone was not sufficient for the discrimination of all the chromosomes of 6x Ae. crassa (D¹D¹XcrXcr DcrDcr), which needs a combination of (GAA)₁₀ with the pTa535-1 or pAs1-1 probes.

Nucleotide-binding leucine-rich repeat (NLR) disease resistance genes typically confer resistance against races of a single pathogen. Here, we report that Yr87 / Lr85 , an NLR gene from Aegilops sharonensis and Aegilops longissima , confers resistance against both P. striiformis tritici ( Pst ) and  Puccinia triticina ( Pt ) that cause stripe and leaf rust, respectively. Yr87/Lr85 confers resistance against Pst and Pt in wheat introgression as well as transgenic lines. Comparative analysis of Yr87/Lr85 and the cloned Triticeae NLR disease resistance genes shows that Yr87/Lr85 contains two distinct LRR domains and that the gene is only found in Ae. sharonensis and Ae. longissima . Allele mining and phylogenetic analysis indicate multiple events of Yr87/Lr85 gene flow between the two species and presence/absence variation explaining the majority of resistance to wheat leaf rust in both species. The confinement of Yr87/Lr85 to Ae. sharonensis and Ae. longissima and the resistance in wheat against Pst and Pt highlight the potential of these species as valuable sources of disease resistance genes for wheat improvement. Leaf rust and stripe rust of wheat are two important fungal diseases of cultivated wheat and they are caused by infection of different pathogens. Here, the authors report the nucleotide-binding leucine-rich repeat (NLR) protein encoding gene Yr87/Lr85 confers resistance to both diseases.

• DNA methylation is dynamically involved in plant immunity, but little information is known about its roles in plant interactions with biotrophic fungi, especially in temperate grasses such as wheat (Triticum aestivum). • Using wheat diploid progenitor Aegilops tauschii accession AL8/78, the genome of which has been sequenced, we assessed the extent of DNA methylation in response to infection with Blumeria graminis f. sp. tritici (Bgt), which causes powdery mildew. • Upon Bgt infection, ARGONAUTE4a (AGO4a) was significantly downregulated in A. tauschii, which was accompanied by a substantial reduction in AGO4a-sorted 24-nt siRNA levels, especially for genes near transposable elements (TAGs). Bisulfite sequencing revealed abundant differentially methylated regions (DMRs) with CHH hypomethylation. TAGs bearing CHH-hypomethylated DMRs were enriched for ‘response to stress’ functions, including receptor kinase, peroxidase, and pathogenesis-related genes. Virus-induced gene silencing (VIGS) of a DOMAINS REARRANGED METHYLASE 2 (DRM2) homolog enhanced plant resistance to Bgt. The effect of CHH hypomethylation was exemplified by the upregulation of a pathogenesis-related β-1,3-glucanse gene implicated in Bgt defense. • These findings support the idea that dynamic DNA methylation represents a regulatory layer in the complex mechanism of plant immunity, which could be exploited to improve disease resistance in common wheat.

Leaf rust, caused by Puccinia triticina Eriks., is the most common rust disease of wheat ( Triticum aestivum L.) worldwide. Owing to the rapid evolution of virulent pathotypes, new and effective leaf rust resistance sources must be found. Aegilops tauschii , an excellent source of resistance genes to a wide range of diseases and pests, may provide novel routes for resistance to this disease. In this study, we aimed to elucidate the transcriptome of leaf rust resistance in two contrasting resistant and susceptible Ae. tauschii accessions using RNA-sequencing. Gene ontology, analysis of pathway enrichment and transcription factors provided an apprehensible review of differentially expressed genes and highlighted biological mechanisms behind the Aegilops – P. triticina interaction. The results showed the resistant accession could uniquely recognize pathogen invasion and respond precisely via reducing galactosyltransferase and overexpressing chromatin remodeling, signaling pathways, cellular homeostasis regulation, alkaloid biosynthesis pathway and alpha-linolenic acid metabolism. However, the suppression of photosynthetic pathway and external stimulus responses were observed upon rust infection in the susceptible genotype. In particular, this first report of comparative transcriptome analysis offers an insight into the strength and weakness of Aegilops against leaf rust and exhibits a pipeline for future wheat breeding programs.

Key message The rust resistance genes Lr53 and Yr35 were introgressed into bread wheat from Aegilops longissima or Aegilops sharonensis or their S-genome containing species and mapped to the telomeric region of chromosome arm 6BS. Wheat leaf and stripe rusts are damaging fungal diseases of wheat worldwide. Breeding for resistance is a sustainable approach to control these two foliar diseases. In this study, we used SNP analysis, sequence comparisons, and cytogenetic assays to determine that the chromosomal segment carrying Lr53 and Yr35 was originated from Ae.longissima or Ae. sharonensis or their derived species. In seedling tests, Lr53 conferred strong resistance against all five Chinese Pt races tested, and Yr35 showed effectiveness against Pst race CYR34 but susceptibility to race CYR32. Using a large population (3892 recombinant gametes) derived from plants homozygous for the  ph1b  mutation obtained from the cross 98M71 × CS ph1b , both Lr53 and Yr35 were successfully mapped to a 6.03-Mb telomeric region of chromosome arm 6BS in the Chinese Spring reference genome v1.1. Co-segregation between Lr53 and Yr35 was observed within this large mapping population. Within the candidate region, several nucleotide-binding leucine-rich repeat genes and protein kinases were identified as candidate genes. Marker pku6B3127 was completely linked to both genes and accurately predicted the absence or presence of alien segment harboring Lr53 and Yr35 in 87 tetraploid and 149 hexaploid wheat genotypes tested. We developed a line with a smaller alien segment (< 6.03 Mb) to reduce any potential linkage drag and demonstrated that it conferred resistance levels similar to those of the original donor parent 98M71. The newly developed introgression line and closely linked PCR markers will accelerate the deployment of Lr53 and Yr35 in wheat breeding programs.

Bread wheat ( Triticum aestivum ) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks 1 , 2 . Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch’s goatgrass ( Aegilops tauschii ), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement. Analysis of 46 newly sequenced or re-sequenced Tausch’s goatgrass ( Aegilops tauschii ) accessions establishes the origin of the bread wheat ( Triticum aestivum ) D genome from genetically and geographically discrete Ae. tauschii subpopulations.

Background  Aegilops ovata a wild relative of wheat. As a valuable genetic source, it can be used for wheat breeding and improvement. However, the interspecific variation, evolutionary mechanism and phylogenetic relationship of the chloroplast genome from the nucleoplasmic hybrid between Ae. ovata and wheat are still unclear. Results In this study, the CMS line (Ae.ovata)-Xinong1376 and its maintainer line Xinong1376 were used as the materials. We compared their phenotypes. The anthers of (Ae.ovata)-Xinong1376 were indehiscent and lighter in color at the late stage of microspore development, and the male gametophytes lacked starch. The abortion appeared at binucleate stage. Subsequently, we assembled and compared the chloroplast genomes of the CMS line (Ae. ovata)-Xinong1376 and its maintainer line Xinong1376 via high-throughput sequencing technology for the first time. The data revealed the cp. genome was 136,170 bp long for the CMS (Ae.ovata)-Xinong1376 and 135,885 bp for common wheat Xinong1376, with typical quadripartite structures. The unique genes consisted of 66 protein-coding genes, 4 rRNA genes, and 27 tRNA genes. There were similar gene categories and numbers between (Ae.ovata)-Xinong1376 and Xinong1376, but different codon preferences. 186 possible SSRs were found in (Ae.ovata)-Xinong1376, and 183 possible SSRs in Xinong1376. Single nucleotide repeats are more abundant in SSRs. Phylogenetic analysis revealed that (Ae.ovata)-Xinong1376 was the most closely related to Ae. ovata , and Xinong1376 was the most closely related to common wheat. We identified two highly variable regions, and 20 nonsynonymous mutations through sequence comparison of two lines. In addition, the chlorophyll level was relatively low in the male sterile line (Ae.ovata)-Xinong1376, and correspondingly, most of 12 genes selected were downregulated via qRT–PCR. Conclusions Our study provides valuable information on the chloroplast genome of the male sterile line with the cytoplasm of Ae.ovata and its maintainer line, evolutionary implications for the scientific community, and novel perspective on the exploration of wheat CMS.

Wild wheat relative Aegilops biuncialis offers valuable traits for crop improvement through interspecific hybridization. However, gene transfer from Aegilops has been hampered by difficulties in detecting introgressed Ub- and Mb-genome chromatin in the wheat background at high resolution. The present study applied DArTseq technology to genotype two backcrossed populations (BC382, BC642) derived from crosses of wheat line Mv9kr1 with Ae. biuncialis accession, MvGB382 (early flowering and drought-tolerant) and MvGB642 (leaf rust-resistant). A total of 11,952 Aegilops-specific Silico-DArT markers and 8,998 wheat-specific markers were identified. Of these, 7,686 markers were assigned to Ub-genome chromosomes and 4,266 to Mb-genome chromosomes and were ordered using chromosome scale reference assemblies of hexaploid wheat and Ae. umbellulata. Ub-genome chromatin was detected in 5.7% of BC382 and 22.7% of BC642 lines, while 88.5% of BC382 and 84% of BC642 lines contained Mb-genome chromatin, predominantly the chromosomes 4Mb and 5Mb. The presence of alien chromatin was confirmed by microscopic analysis of mitotic metaphase cells using GISH and FISH, which allowed precise determination of the size and position of the introgression events. New Mv9kr1-Ae. biuncialis MvGB382 4Mb and 5Mb disomic addition lines together with a 5DS.5DL-5MbL recombination were identified. A possible effect of the 5MbL distal region on seed length has also been observed. Moreover, previously developed Mv9kr1-MvGB642 introgression lines were more precisely characterized. The newly developed cytogenetic stocks represent valuable genetic resources for wheat improvement, highlighting the importance of utilizing diverse genetic materials to enhance wheat breeding strategies.Key messageDArTseq genotyping supported by chromosome-scale assemblies of wheat and Aegilops genomes facilitates the selection of wheat‑Aegilops biuncialis addition, substitution and translocation lines.

This study estimated the genotype × environment interactions for ten yield associated traits in advanced generation hybrids of several cultivars of common wheat (Triticum aestivum L.) with Aegilops kotschyi Boiss. and A. variabilis Eig. using the additive main effects and multiplicative interaction (AMMI) models. Tests were ran over five years at one location in replicated field trials. The AMMI model showed significant genotypic and environmental effects for all analysed traits. A majority of the hybrid lines were less stable in the analysed traits than their parental wheats. The older wheat cultivars, with lower environmental sensitivity, were the most stable. The best total genotype selection index, for all ten traits combined, was observed for the oldest cvs. Gama and Rusałka, and among the hybrid lines, for Ae. kotschyi/Rusałka//Smuga and Ae. kotschyi/Rusałka//Muza. The lines Ae. kotschyi/Rusałka//Smuga, Ae. kotschyi/Rusałka//Muza, Ae. kotschyi/Rusałka//Korweta, Ae. kotschyi/Rusałka//Begra///Smuga, and Ae. kotschyi/Rusałka//Begra///Turnia are recommended for inclusion in breeding programmes due to their greater stability and the good average values for the observed traits.