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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.

 

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 A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.), and Triticum urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC) using genotyping by sequencing and identified 13,860 curated single-nucleotide polymorphisms. Genomic analysis detected misclassified and genetically identical (>99%) accessions, with most of the identical accessions originating from the same or nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were genetically identical, supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that T. urartu is the closest A-genome diploid to the A-subgenome in common wheat (Triticum aestivum L.) through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring a domestication selection signature at the Non-brittle rachis 1 (Btr1) locus on the short arm of chromosome 3Am at ∼70 Mb. We established an A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 79% of allelic variants in the A-genome collection and constituted a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs. 

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.