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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 ago1,2. 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. aestivum x Hordeum 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 FROM AUTHOR]

The solar wind (SW) and local interstellar medium (LISM) are turbulent media. Their interaction is governed by complex physical processes and creates heliospheric regions with significantly different properties in terms of particle populations, bulk flow and turbulence. Our knowledge of the solar wind turbulence nature and dynamics mostly relies on near-Earth and near-Sun observations, and has been increasingly improving in recent years due to the availability of a wealth of space missions, including multi-spacecraft missions. In contrast, the properties of turbulence in the outer heliosphere are still not completely understood. In situ observations by Voyager and New Horizons, and remote neutral atom measurements by IBEX strongly suggest that turbulence is one of the critical processes acting at the heliospheric interface. It is intimately connected to charge exchange processes responsible for the production of suprathermal ions and energetic neutral atoms. This paper reviews the observational evidence of turbulence in the distant SW and in the LISM, advances in modeling efforts, and open challenges. [ABSTRACT FROM AUTHOR]

As a result, in the Materials and methods, under the subheading "Plant material and germplasm - Library construction", "Next, a tagmentation reaction consisting of 1 l normalized to 0.75 ng/µl of the genomic DNA, 0.9966 l TDE1 Tagment DNA Enzyme, 0.504 l Tagment DNA Buffer, and 3.3964 l water was incubated at 55 °C for 15 min, and then cooled to room temperature." now reads: "Next, a tagmentation reaction consisting of 1 l normalized to 0.75 ng/µl of the genomic DNA, 0.09966 l TDE1 Tagment DNA Enzyme, 0.504 l Tagment DNA Buffer, and 3.3964 l water was incubated at 55 °C for 15 min, and then cooled to room temperature." Correction to: I Scientific Reports i https://doi.org/10.1038/s41598-022-19858-2, published online 20 October 2022 The original version of this Article contained an error, where the quantity of TDE1 Tagment DNA Enzyme was incorrectly given as 0.9966 l instead of 0.09966 l in the Materials and Methods section under the subheading "Plant material and germplasm - Library construction". [Extracted from the article]

Switchgrass ( Panicum virgatum L.) is a naturally allogamous species. Recent studies indicated conditional self-compatibility exists in the species and can be used to produce inbreds for the exploitation of heterosis in biomass production. However, efficient and reliable bagging methods are unavailable for development of inbreeding. This study was designed to determine the efficacy of a polyester bagging method in blocking extraneous pollen such that switchgrass may self more efficiently. In this experiment four northern lowland (NL) inbreds, four NL non-inbreds, two southern lowland (SL) non-inbreds and 16 upland-lowland (interecotypic) F1 hybrids were self-pollinated by enclosing their inflorescences in polyester bags in the field; bags were also placed on 14 F1 interecotypic hybrid plants potted in a greenhouse. The reliability of the bags was determined using eight to ten simple sequence repeat (SSR) markers that distinguished the genetic parentage of the pollen. Contaminants were identified in two groups: outcrossing contaminants (OCs) and physical contaminants (PCs) based on the amplified alleles of their progeny and their seed parents. Of 39 polyester bags field tested in 2012, 35 bags showed 100 % selfed progeny, four showed PCs; no OCs were identified. Similarly, of 61 bags tested in 2013 in two field plots, 50 bags produced 100 % selfed progeny, while four bags produced OCs, five produced PCs and the other two produced both OCs and PCs. No contaminants were identified from the progeny of 18 bags used in the greenhouse, suggesting that high wind speed, physical damage or handling errors may have resulted in the contaminations of bagged progeny in the field. The result of this experiment establishes the increased reliability of the polyester bagging method over previously tested methods for selfing switchgrass under field and greenhouse conditions. Additionally, the S1, S2 and S3 inbreds produced in this study will contribute to developing completely or near completely homozygous inbred lines in the future. [ABSTRACT FROM AUTHOR]