Goatgrasses with U- and M-genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F2 individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromosomes. Chromosome 1Mb could not be constructed due to a lack of recombination caused by rearrangements in the MvGB382 accession. The genetic map spans 2518 cM with an average marker density of 2.79 cM. The skeleton map contains 920 segregating markers, divided between the Mb sub-genome (425 markers) and the Ub sub-genome (495 markers). Chromosomes of the Mb sub-genome, originating from Aegilops comosa Sm. in Sibth. et Sm., show well-preserved collinearity with Triticum aestivum L. chromosomes. In contrast, chromosomes of the Ub sub-genome, originating from Aegilops umbellulata Zhuk., exhibit a varying degree of collinearity, with 1Ub, 3Ub, and 5Ub retaining a substantial level of collinearity with Triticum aestivum, while 2Ub, 4Ub, 6Ub, and 7Ub show significant rearrangements. A quantitative trait locus affecting fertility was identified near the centromere on the long arm of chromosome 3Mb, explaining 23.5% of the variance. The genome structure of Aegilops biuncialis, highlighted by the genetic map, provides insights into the speciation within the species and will support alien gene transfer into wheat.

• MeSH
• Aegilops * genetics   MeSH
• Chromosomes, Plant * MeSH
• Genetic Linkage MeSH
• Genetic Markers MeSH
• Genome, Plant * MeSH
• Gene Rearrangement MeSH
• Chromosome Mapping * MeSH
• Triticum * genetics   MeSH
• Publication type
• Journal Article MeSH
• Comparative Study MeSH
• Names of Substances
• Genetic Markers MeSH

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.

• MeSH
• Aegilops genetics   microbiology   MeSH
• Alleles MeSH
• Basidiomycota * pathogenicity   physiology   MeSH
• Phylogeny * MeSH
• Plants, Genetically Modified genetics   MeSH
• Plant Leaves * microbiology   genetics   MeSH
• Plant Diseases * microbiology   genetics   immunology   MeSH
• NLR Proteins * genetics   MeSH
• Disease Resistance * genetics   MeSH
• Triticum * genetics   microbiology   immunology   MeSH
• Puccinia * pathogenicity   MeSH
• Genes, Plant MeSH
• Plant Proteins * genetics   metabolism   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• NLR Proteins * MeSH
• Plant Proteins * MeSH

The genomes of many plants, animals, and fungi frequently comprise dispensable B chromosomes that rely upon various chromosomal drive mechanisms to counteract the tendency of non-essential genetic elements to be purged over time. The B chromosome of rye - a model system for nearly a century - undergoes targeted nondisjunction during first pollen mitosis, favouring segregation into the generative nucleus, thus increasing their numbers over generations. However, the genetic mechanisms underlying this process are poorly understood. Here, using a newly-assembled, ~430 Mb-long rye B chromosome pseudomolecule, we identify five candidate genes whose role as trans-acting moderators of the chromosomal drive is supported by karyotyping, chromosome drive analysis and comparative RNA-seq. Among them, we identify DCR28, coding a microtubule-associated protein related to cell division, and detect this gene also in the B chromosome of Aegilops speltoides. The DCR28 gene family is neo-functionalised and serially-duplicated with 15 B chromosome-located copies that are uniquely highly expressed in the first pollen mitosis of rye.

• MeSH
• Aegilops genetics   metabolism   MeSH
• Chromosomes, Plant * genetics   MeSH
• Karyotyping MeSH
• Mitosis * genetics   MeSH
• Nondisjunction, Genetic MeSH
• Pollen genetics   MeSH
• Gene Expression Regulation, Plant MeSH
• Genes, Plant MeSH
• Plant Proteins genetics   metabolism   MeSH
• Secale * genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Plant Proteins MeSH

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.

• Keywords
• Aegilops biuncialis, Chromosome addition lines, DArTseq analysis, Thousand-grain weight, Wheat-Aegilops introgressions,
• MeSH
• Aegilops * genetics   MeSH
• Chromatin * genetics   metabolism   MeSH
• Chromosomes, Plant * genetics   MeSH
• Genetic Markers MeSH
• Genome, Plant * MeSH
• Genotype MeSH
• Genotyping Techniques MeSH
• Genetic Introgression MeSH
• Chromosome Mapping MeSH
• Triticum * genetics   MeSH
• Plant Breeding methods   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Chromatin * MeSH
• Genetic Markers MeSH

Cultivated and wild species of the genus rye (Secale) are important but underexploited gene sources for increasing the genetic diversity of bread wheat. Gene transfer is possible via bridge genetic materials derived from intergeneric hybrids. During this process, it is essential to precisely identify the rye chromatin in the wheat genetic background. In the present study, backcross generation BC2F8 from a cross between Triticum aestivum (Mv9kr1) and S. cereanum ('Kriszta,' a cultivar from the artificial hybrid of S. cereale and S. strictum) was screened using in-situ hybridization (GISH and FISH) and analyzed by DArTseq genotyping in order to select potentially agronomically useful genotypes for prebreeding purposes. Of the 329,267 high-quality short sequence reads generated, 27,822 SilicoDArT and 8,842 SNP markers specific to S. cereanum 1R-7R chromosomes were identified. Heatmaps of the marker densities along the 'Lo7' rye reference pseudomolecules revealed subtle differences between the FISH- and DArTseq-based results. This study demonstrates that the "exotic" rye chromatin of S. cereanum introgressed into wheat can be reliably identified by high-throughput DArTseq genotyping. The Mv9kr1-'Kriszta' addition and translocation lines presented here may serve as valuable prebreeding genetic materials for the development of stress-tolerant or disease-resistant wheat varieties.

• Keywords
• DArTseq markers, Secale cereanum, Triticum aestivum, chromosome rearrangements, genotyping, heatmap, introgression lines,
• Publication type
• Journal Article MeSH

Characterisation and genetic mapping of a key gene defining root morphology in bread wheat. Root morphology is central to plants for the efficient uptake up of soil water and mineral nutrients. Here we describe a conditional mutant of hexaploid wheat (Triticum aestivum L.) that when grown in soil with high Ca2+ develops a larger rhizosheath accompanied with shorter roots than the wild type. In wheat, rhizosheath size is a reliable surrogate for root hair length and this was verified in the mutant which possessed longer root hairs than the wild type when grown in high Ca2+ soil. We named the mutant Stumpy and showed it to be due to a single semi-dominant mutation. The short root phenotype at high Ca2+ was due to reduced cellular elongation which might also explain the long root hair phenotype. Analysis of root cell walls showed that the polysaccharide composition of Stumpy roots is remodelled when grown at non-permissive (high) Ca2+ concentrations. The mutation mapped to chromosome 7B and sequencing of the 7B chromosomes in both wild type and Stumpy identified a candidate gene underlying the Stumpy mutation. As part of the process to determine whether the candidate gene was causative, we identified wheat lines in a Cadenza TILLING population with large rhizosheaths but accompanied with normal root length. This finding illustrates the potential of manipulating the gene to disconnect root length from root hair length as a means of developing wheat lines with improved efficiency of nutrient and water uptake. The Stumpy mutant will be valuable for understanding the mechanisms that regulate root morphology in wheat.

• MeSH
• Plant Roots genetics   MeSH
• Chromosome Mapping MeSH
• Mutation MeSH
• Triticum * metabolism   MeSH
• Soil * MeSH
• Water metabolism   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Soil * MeSH
• Water MeSH

UNLABELLED: Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum, was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm's high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and 'Mv Karizma.' Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA)7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-024-01439-y.

• Keywords
• Agropyron glael, FISH, Flow cytometric sorting, GISH, Tillering, Yield potential,
• Publication type
• Journal Article MeSH

Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

• MeSH
• Cloning, Molecular MeSH
• Chromosome Mapping MeSH
• Multigene Family MeSH
• Triticum * genetics   MeSH
• Genes, Plant * genetics   MeSH
• Publication type
• Journal Article MeSH

The annual goatgrass, Aegilops biuncialis is a rich source of genes with considerable agronomic value. This genetic potential can be exploited for wheat improvement through interspecific hybridization to increase stress resistance, grain quality and adaptability. However, the low throughput of cytogenetic selection hampers the development of alien introgressions. Using the sequence of flow-sorted chromosomes of diploid progenitors, the present study enabled the development of chromosome-specific markers. In total, 482 PCR markers were validated on wheat (Mv9kr1) and Ae. biuncialis (MvGB642) crossing partners, and 126 on wheat-Aegilops additions. Thirty-two markers specific for U- or M-chromosomes were used in combination with GISH and FISH for the screening of 44 Mv9kr1 × Ae. biuncialis BC3F3 genotypes. The predominance of chromosomes 4M and 5M, as well as the presence of chromosomal aberrations, may indicate that these chromosomes have a gametocidal effect. A new wheat-Ae. biuncialis disomic 4U addition, 4M(4D) and 5M(5D) substitutions, as well as several introgression lines were selected. Spike morphology and fertility indicated that the Aegilops 4M or 5M compensated well for the loss of 4D and 5D, respectively. The new cytogenetic stocks represent valuable genetic resources for the introgression of key genes alleles into wheat.

• MeSH
• Aegilops * genetics   MeSH
• Chromosomes, Plant genetics   MeSH
• Genetic Markers MeSH
• Genomics MeSH
• In Situ Hybridization, Fluorescence MeSH
• Triticum * genetics   MeSH
• Translocation, Genetic MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Genetic Markers MeSH

INTRODUCTION: Meiotic recombination is one of the most important processes of evolution and adaptation to environmental conditions. Even though there is substantial knowledge about proteins involved in the process, targeting specific DNA loci by the recombination machinery is not well understood. OBJECTIVES: This study aims to investigate a wheat recombination hotspot (H1) in comparison with a "regular" recombination site (Rec7) on the sequence and epigenetic level in conditions with functional and non-functional Ph1 locus. METHODS: The DNA sequence, methylation pattern, and recombination frequency were analyzed for the H1 and Rec7 in three mapping populations derived by crossing introgressive wheat line 8.1 with cv. Chinese Spring (with Ph1 and ph1 alleles) and cv. Tähti. RESULTS: The H1 and Rec7 loci are 1.586 kb and 2.538 kb long, respectively. High-density mapping allowed to delimit the Rec7 and H1 to 19 and 574 bp and 593 and 571 bp CO sites, respectively. A new method (ddPing) allowed screening recombination frequency in almost 66 thousand gametes. The screening revealed a 5.94-fold higher recombination frequency at the H1 compared to the Rec7. The H1 was also found out of the Ph1 control, similarly as gamete distortion. The recombination was strongly affected by larger genomic rearrangements but not by the SNP proximity. Moreover, chromatin markers for open chromatin and DNA hypomethylation were found associated with crossover occurrence except for the CHH methylation. CONCLUSION: Our results, for the first time, allowed study of wheat recombination directly on sequence, shed new light on chromatin landmarks associated with particular recombination sites, and deepened knowledge about role of the Ph1 locus in control of wheat recombination processes. The results are suggesting more than one recombination control pathway. Understanding this phenomenon may become a base for more efficient wheat genome manipulation, gene pool enrichment, breeding, and study processes of recombination itself.

• Keywords
• Crossovers, DNA methylation, Hotspot, Ph1 locus, Recombination, Wheat,
• MeSH
• Chromatin * genetics   MeSH
• Chromosomes MeSH
• DNA MeSH
• Triticum * genetics   MeSH
• Plant Breeding MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Chromatin * MeSH
• DNA MeSH