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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]

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. [ABSTRACT FROM AUTHOR]

Background: Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were tested for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping-by-sequencing (GBS) and the quantitative trait loci (QTL) associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. Results: Alfalfa FT screening method optimized in this experiment comprises three major steps: clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is a useful indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL associated with four traits; nine for visual rating-based FT, five for percentage survival (PS), four for treated to control regrowth ratio (RR), and two for treated to control biomass ratio (BR). Some QTL positions overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) were from the potential genic region for a cold tolerance gene CBF. The BLAST alignment of a CBF sequence of M. truncatula, a close relative of alfalfa, against the alfalfa reference showed that the gene's ortholog resides around 75 Mb on chromosome 6. Conclusions: The indoor freezing tolerance selection method reported is useful for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources for the research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement. [ABSTRACT FROM AUTHOR]

Alfalfa leaf rust caused by the fungal pathogen Uromyces striatus compromises forage yield and quality. We investigated the genetic basis of leaf rust resistance in alfalfa using an F1 mapping population segregating for resistance to the disease in addition to segregation for fall dormancy (FD) and winter hardiness (WH). The objective of this work was to map quantitative trait loci (QTL) associated with alfalfa leaf rust resistance using genotyping-by-sequencing (GBS) SNP markers in the biparental F1 mapping population. The female parent 3010 displayed susceptibility to rust while the male parent CW 1010 was moderately resistant. The mapping population consisted of 184 F1 progenies that were planted with the parents in a randomized complete block (RCBD) design with three replications at Watkinsville and Blairsville, GA. Four clones generated from stem cuttings of each genotype were planted in each replication. Phenotyping rust severity (RS) was based on the NAAIC visual rating scores of 1–5. RS and FD exhibited a negative phenotypic correlation (r = −0.26). RS and WH also exhibited a negative correlation (r = −0.27) suggesting that the dormant and winter hardy genotypes were more susceptible to leaf rust than the non-dormant and cold sensitive. Four QTL for alfalfa leaf rust resistance and one QTL for rust susceptibility were identified in the CW 1010 genetic map while three QTL for rust susceptibility were identified in the 3010 parent. The most important QTL Us-RustR1 explained 13% (R2 = 0.13) of the phenotypic variance. This study suggests that leaf rust resistance in alfalfa is most likely incomplete and has polygenic inheritance. Comparative genome analysis of QTL regions using sequences of significant SNPs revealed homology to M. truncatula sequences that were previously reported for their role in plant defense mechanisms. Validation of the QTLs in different genetic backgrounds as well as fine mapping of the QTL regions would be the next step of this research. The markers presented in this study would be valuable resources for alfalfa genetic improvement via marker-assisted selection (MAS). • Eight QTLs associated with alfalfa rust resistance were detected using GBS of a pseudo-testcross mapping population. • In this population, the inheritance of rust resistance caused by Uromyces striatus was polygenic and incomplete. • The sequences of QTL SNPs exhibited homology with genes associated with fungal diseases defense in M. truncatula. • Alfalfa rust severity correlated with FD and WH, but the relationship might be specific to the population. [ABSTRACT FROM AUTHOR]

Molybdenum (Mo) is a critical micronutrient for nitrogen (N) fixation in legumes. Low pH limits the availability of Mo, thereby reducing nodulation and N fixation. This study investigates the effect of Mo supplementation on alfalfa nodulation and its correlation with root and shoot biomass in low-pH soil. Three experiments were conducted in the greenhouse, involving 14 genotypes of alfalfa subjected to four different treatments, unlimed low-pH soil (5.2) with Mo applied (lithium (Li)−Mo+), low-pH soil (5.2) without Mo (Li−Mo−), limed soil (pH 7.3) with Mo applied (Li+Mo+), and limed soil (pH 7.3) without Mo (Li+Mo−). Foliar application of Mo resulted in a significant increase in nodule counts in the 14 alfalfa cultivars grown in low-pH soil (5.2) even though to a lesser extent than in limed soil with neutral pH (7.3). The increase in number of nodules correlated positively with plant root weight and upper plant biomass. [ABSTRACT FROM PUBLISHER]

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]

In the article [1], in 'Methods' section and 'G x E and heritability' subsection, there is an error in the formula of heritability (H2). [ABSTRACT FROM AUTHOR]

Background: The genetic and genomic basis of flowering time and biomass yield in alfalfa (Medicago sativa L.) remains poorly understood mainly due to the autopolyploid nature of the species and the lack of adequate genomic resources. We constructed linkage maps using genotyping-by-sequencing (GBS) based single dose allele (SDA) SNP and mapped alfalfa timing of flowering (TOF), spring yield (SY), and cumulative summer biomass (CSB) in a pseudo-testcross F1 population derived from a fall dormant (3010) and a non-dormant (CW 1010) cultivars. We analyzed the quantitative trait loci (QTL) to identify conserved genomic regions and detected molecular markers and potential candidate genes associated with the traits to improve alfalfa and provide genomic resources for the future studies. Results: This study showed that both fall dormant and non-dormant alfalfa cultivars harbored QTL for early and late flowering, suggesting that flowering time in alfalfa is not an indicator of its fall dormancy (FD) levels. A weak phenotypic correlation between the flowering time and fall dormancy (FD) in F1 and checks also corroborated that alfalfa FD and TOF are not the predictors of one another. The relationship between flowering time and alfalfa biomass yield was not strong, but the non-dormant had relatively more SY than dormant. Therefore, selecting superior alfalfa cultivars that are non-dormant, winter-hardy, and early flowering would allow for an early spring harvest with enhanced biomass. In this study, we found 25 QTL for TOF, 17 for SY and six QTL for CSB. Three TOF related QTL were stable and four TOF QTL were detected in the corresponding genomic locations of the flowering QTL of M. truncatula, an indication of possible evolutionarily conserved regions. The potential candidate genes for the SNP sequences of QTL regions were identified for all three traits and these genes would be potential targets for further molecular studies. Conclusions: This research showed that variation in alfalfa flowering time after spring green up has no association with dormancy levels. Here we reported QTL, markers, and potential candidate genes associated with spring flowering time and biomass yield of alfalfa, which constitute valuable genomic resources for improving these traits via marker-assisted selection (MAS). [ABSTRACT FROM AUTHOR]

The energy dissipation in collisionless plasmas as the solar wind is not yet fully understood. The intermittent nature of magnetic structures appears to be a fundamental part of the energy cascade. Understanding energy transfer and dissipation in the solar wind requires an accurate description of its intermittency. Upcoming multi-spacecraft missions will provide new insight on this matter. However, the use of multi-point data requires developing new data analysis techniques as wellas cross-validating these techniques. In this study, we address the latter and explore the intermittency in a 3D simulation of anisotropic plasma turbulence using two approaches. We implement the standard single-spacecraft partial variance increments technique as well as a multi-point partial variance increments technique. We contrast these two techniques and explore their dependence on the angle between the spacecraft-configuration travel direction and the background magnetic field. [ABSTRACT FROM AUTHOR]

The distribution of turbulence in the heliosphere remains a mystery, due to the complexity in not only modeling the turbulence transport equations but also identifying the drivers of turbulence that vary with time and spatial location. Beyond the ionization cavity (a few astronomical units (AU) from the Sun), the turbulence is driven predominantly by freshly created pickup ions (PUIs), in contrast to the driving by stream shear and compression. Understanding the source characteristics is necessary to refine turbulence transport models and interpret measurements of turbulence and solar wind temperature in the outer heliosphere. Using a recent latitude-dependent solar wind speed model and the ionization rate of neutral interstellar hydrogen (H), we investigate the temporal and spatial variation in the strength of low-frequency turbulence driven by PUIs from 1998 to 2020. We find that the driving rate is stronger during periods of high solar activity and at lower latitudes in the outer heliosphere. The driving rates for parallel and anti-parallel propagating (relative to the background magnetic field) slab turbulence have different spatial and latitude dependences. The calculated generation rate of turbulence by PUIs is an essential ingredient to investigate the latitude dependence of turbulence in the outer heliosphere, which is important to understand the heating of the distant solar wind and the modulation of cosmic rays. [ABSTRACT FROM AUTHOR]

This paper addresses the first direct investigation of the energy budget in the solar corona. Exploiting joint observations of the same coronal plasma by Parker Solar Probe and the Metis coronagraph aboard Solar Orbiter and the conserved equations for mass, magnetic flux, and wave action, we estimate the values of all terms comprising the total energy flux of the proton component of the slow solar wind from 6.3 to 13.3 R ⊙. For distances from the Sun to less than 7 R ⊙, we find that the primary source of solar wind energy is magnetic fluctuations including Alfvén waves. As the plasma flows away from the low corona, magnetic energy is gradually converted into kinetic energy, which dominates the total energy flux at heights above 7 R ⊙. It is found too that the electric potential energy flux plays an important role in accelerating the solar wind only at altitudes below 6 R ⊙, while enthalpy and heat fluxes only become important at even lower heights. The results finally show that energy equipartition does not exist in the solar corona. [ABSTRACT FROM AUTHOR]