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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. 

Abstract The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T.aestivumxHordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs. 

Abstract Hessian fly (HF;Mayetiola destructorSay) causes severe damage to wheat (Triticum aestivumL.) worldwide. Several resistance genes have been identified in wheat and wild relatives; however, HF populations are under strong selection pressure and evolve rapidly to overcome resistance. To ensure the availability of resistance sources, HF‐resistant germplasm KS18WGRC65 (TA5110, Reg. no. GP‐1042, PI 688251) was developed by Wheat Genetics Resource Center at Kansas State University as a breeding stock that carries resistance geneH26fromAegilops tauschiiCoss. KS18WGRC65 is a cytogenetically stable, homozygous, BC₃F_3:6line derived from the cross betweenAe. tauschiiaccession KU2147 and hard red winter wheat recurrent parent ‘Overley’. KS18WGRC65 exhibited no penalty for yield or other agronomic characters, making it a suitable source of HF resistance for wheat breeding. 

Abstract Genebanks are valuable resources for crop improvement through the acquisition,ex-situconservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections ofAegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources. 

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.