Explore the vast range of titles available.

Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel. The treasure trove of disease resistance genes present in wild relatives of domesticated crops is rapidly discovered using association genetics and enrichment sequencing.

The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat ( Triticum aestivum ) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease 1 . We identified the race-specific disease resistance gene Yr27 , which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13 ; the Yr27 and Lr13 proteins show 97% sequence identity 2 , 3 . Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future. Chromosome-scale genome assembly of the South African bread wheat ( Triticum aestivum ) cultivar Kariega facilitates the cloning of the stripe rust resistance gene Yr27 .

Einkorn ( Triticum monococcum ) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago 1 , 2 . Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat ( Triticum aestivum ) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat. Around 1% of the A subgenome of modern bread wheat ( Triticum aestivum ) originates from einkorn ( Triticum monococcum ), the first domesticated wheat species.

Key messageMulti-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci.Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker–trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.

The cloning of disease resistance genes in wheat has been disproportionately slow, tedious and costly because of the large and complex genome. Wheat gene cloning projects in the late 1990s and early 2000s were multi-year endeavors, often spanning a decade or longer. The development of genomics-assisted gene cloning tools and speed breeding have significantly accelerated gene cloning in wheat over the past years. Here, we present an optimized high-throughput disease resistance gene cloning workflow that allows to identify causal genes in less than six months. As a proof-of-principle, we clone the stem rust resistance gene Sr6 , which has been a historically relevant source of resistance to confine a major stem rust outbreak in North America in the mid-20 th century. Sr6 encodes a CC-BED-domain-containing nucleotide-binding and leucine-rich repeat (NLR) immune receptor. The workflow provides a basis to tackle the systematic cloning of all the genetically described disease resistance genes by the wheat community, which will facilitate knowledge-guided deployment of resistance genes in wheat breeding. Gene cloning in wheat has long been hampered by its exceptionally large and complex genome, and long life cycle. Here, the authors report an optimized, high-throughput disease resistance gene cloning workflow and demonstrate its application in cloning stem rust resistance gene Sr6 .

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.Krattinger, Abrouk et al. use genome wide association study and haplotype analyses to investigate the genetics of glume colour in ten reference grade wheat genomes. Haplotype comparison identifies a MYB transcription factor as a candidate gene for red glume colour.

Einkorn wheat ( Triticum monococcum ) is an ancient grain crop and a close relative of the diploid progenitor ( T. urartu ) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars. Integration of skim sequencing data for a recombinant inbred line population derived from a cross between wild and domesticated einkorn wheat accessions with a reference genome assembly enables high-resolution mapping of agronomic traits.

The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes 1 . Here we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9 , which was introduced into bread wheat from the wild grass species Aegilops umbellulata 2 . We established that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58 , which was reportedly introgressed from Aegilops triuncialis 3 , but has an identical coding sequence compared to Lr9 . Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding. The resistance gene Lr9 , which was introduced into bread wheat from the wild grass species Aegilops umbellulata , encodes an unusual tandem kinase fusion protein that confers wheat leaf rust resistance.

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.

Key messageStripe rust resistance gene YrAet672 from Aegilopstauschii accession CPI110672 encodes a nucleotide-binding and leucine-rich repeat domain containing protein similar to YrAS2388 and both these members were haplotypes of Yr28.New sources of host resistance are required to counter the continued emergence of new pathotypes of the wheat stripe rust pathogen Pucciniastriiformis Westend. f. sp. tritici Erikss. (Pst). Here, we show that CPI110672, an Aegilopstauschii accession from Turkmenistan, carries a single Pst resistance gene, YrAet672, that is effective against multiple Pst pathotypes, including the four predominant Pst lineages present in Australia. The YRAet672 locus was fine mapped to the short arm of chromosome 4D, and a nucleotide-binding and leucine-rich repeat gene was identified at the locus. A transgene encoding the YrAet672 genomic sequence, but lacking a copy of a duplicated sequence present in the 3′ UTR, was transformed into wheat cultivar Fielder and Avocet S. This transgene conferred a weak resistance response, suggesting that the duplicated 3′ UTR region was essential for function. Subsequent analyses demonstrated that YrAet672 is the same as two other Pst resistance genes described in Ae.tauschii, namely YrAS2388 and Yr28. They were identified as haplotypes encoding identical protein sequences but are polymorphic in non-translated regions of the gene. Suppression of resistance conferred by YrAet672 and Yr28 in synthetic hexaploid wheat lines (AABBDD) involving Langdon (AABB) as the tetraploid parent was associated with a reduction in transcript accumulation.