Search for: All records

Abstract BackgroundPrioritizing wild relative diversity for improving crop adaptation to emerging drought-prone environments is challenging. Here, we combine the genome-wide environmental scans (GWES) in wheat diploid ancestorAegilops tauschii(Ae. tauschii) with allele testing in the genetic backgrounds of adapted cultivars to identify diversity for improving wheat adaptation to water-limiting conditions. ResultsWe evaluate the adaptive allele effects inAe. tauschii-wheat introgression lines phenotyped for multiple traits under irrigated and water-limiting conditions using both unmanned aerial system-based imaging and conventional approaches. The GWES show that climatic gradients alone explain more than half of genomic variation inAe. tauschii, with many alleles associated with climatic factors inAe. tauschiibeing linked with improved performance of introgression lines under water-limiting conditions. We find that the most significant GWES signals associated with temperature annual range in the wild relative are linked with reduced canopy temperature in introgression lines and increased yield. ConclusionsOur results suggest that introgression of climate-adaptive alleles fromAe. tauschiihas the potential to improve wheat performance under water-limiting conditions, and that variants controlling physiological processes responsible for maintaining leaf temperature are likely among the targets of adaptive selection in a wild relative. Adaptive variation uncovered by GWES in wild relatives has the potential to improve climate resilience of crop varieties. 

Abstract Background and ObjectivesFlour quality is a key target of hard winter wheat breeding. The Farinograph is important for assessing quality before cultivar release in the United States, but large sample size requirements and long test times render it impractical for early‐stage selection relative to the GlutoPeak. To improve GlutoPeak utility for breeding, we calculated new parameters from device raw output and used random forest regression to predict key Farinograph parameters in a winter wheat population containing wild relative introgressions. FindingsThe key quality parameters of absorption, bake absorption, tolerance stability, and mixing tolerance index were moderately well predicted (R²ranging from 0.488 to 0.745). Classification of samples as acceptable or unacceptable for mixing tolerance index and tolerance stability was more accurate than prediction of numeric values. ConclusionsNew features calculated from the GlutoPeak raw data were useful predictors of quality. Prediction accuracies are sufficient to improve breeding populations. Significance and NoveltyThis study is the first to use wheat wild relative introgressions in GlutoPeak Farinograph prediction, the first to generate features from raw data, and is one of the few random forest models for quality prediction. The tools that we provide will improve ability to cull poor‐quality lines early in the breeding pipeline can support efficient wheat cultivar development. 

Abstract BACKGROUNDThe wheat stem sawfly (WSS,Cephus cinctus) is a major pest of wheat (Triticum aestivum) and can cause significant yield losses. WSS damage results from stem boring and/or cutting, leading to the lodging of wheat plants. Although solid‐stem wheat genotypes can effectively reduce larval survival, they may have lower yields than hollow‐stem genotypes and show inconsistent solidness expression. Because of limited resistance sources to WSS, evaluating diverse wheat germplasm for novel resistance genes is crucial. We evaluated 91 accessions across five wild wheat species (Triticum monococcum,T. urartu,T. turgidum,T. timopheevii, andAegilops tauschii) and common wheat cultivars (T. aestivum) for antixenosis (host selection) and antibiosis (host suitability) to WSS. Host selection was measured as the number of eggs after adult oviposition, and host suitability was determined by examining the presence or absence of larval infestation within the stem. The plants were grown in the greenhouse and brought to the field for WSS infestation. In addition, a phylogenetic analysis was performed to determine the relationship between the WSS traits and phylogenetic clustering. RESULTSOverall,Ae. tauschii,T. turgidumandT. urartuhad lower egg counts and larval infestation thanT. monococcum, andT. timopheevii.T. monococcum,T. timopheevii,T. turgidum, andT. urartuhad lower larval weights compared withT. aestivum. CONCLUSIONThis study shows that wild relatives of wheat could be a valuable source of alleles for enhancing resistance to WSS and identifies specific germplasm resources that may be useful for breeding. © 2024 The Authors.Pest Management Sciencepublished by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. 

Abstract 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. 

Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041Aegilopsaccessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC)Aegilopsgermplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for allAegilopsspecies together, giving one of the most comprehensive views ofAegilops. TheSitopsissection and the U genomeAegilopsclade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair ofAegilopsspecies provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two speciesAe.neglectaandAe.columnarisbased on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed amongAegilopsspecies indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize theseAegilopsspecies, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploidAegilops. 

Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041Aegilopsaccessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC)Aegilopsgermplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for allAegilopsspecies together, giving one of the most comprehensive views ofAegilops. TheSitopsissection and the U genomeAegilopsclade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair ofAegilopsspecies provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two speciesAe.neglectaandAe.columnarisbased on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed amongAegilopsspecies indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize theseAegilopsspecies, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploidAegilops. 

Abstract 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. 

Abstract Extrachromosomal circular DNAs (eccDNAs) are found in many eukaryotic organisms. EccDNA-powered copy number variation plays diverse roles, from oncogenesis in humans to herbicide resistance in crop weeds. Here, we report interspecific eccDNA flow and its dynamic behavior in soma cells of natural populations and F1 hybrids of Amaranthus sp. The glyphosate-resistance (GR) trait is controlled by eccDNA-based amplification harboring the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene (eccDNA replicon), the molecular target of glyphosate. We documented pollen-mediated transfer of eccDNA in experimental hybrids between glyphosate-susceptible Amaranthus tuberculatus and GR Amaranthus palmeri. Experimental hybridization and fluorescence in situ hybridization (FISH) analysis revealed that the eccDNA replicon in Amaranthus spinosus derived from GR A. palmeri by natural hybridization. FISH analysis also revealed random chromosome anchoring and massive eccDNA replicon copy number variation in soma cells of weedy hybrids. The results suggest that eccDNAs are inheritable across compatible species, contributing to genome plasticity and rapid adaptive evolution.