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Collisionless magnetohydrodynamic shocks are ubiquitous in solar wind and in other space plasmas. They serve as natural sites where charged particles can be accelerated to supra-thermal energies via various Fermi acceleration mechanisms. Upstream and downstream fluctuations play a key role in these processes because they can act as scatter centers. Furthermore, the downstream turbulent plasma of strong shocks driven by coronal mass ejections can enhance the coupling of this plasma with the Earth’s magnetosphere. Understanding of how the fluctuations are transmitted across the shocks can provide an invaluable insight into many shock related studies.In this paper, we investigate the interaction of fast forward (FF) shocks with magnetic island/flux rope mode fluctuations. We employ a recently developed framework of the Zank et al. (2021) transmission model. We analyze 378 FF shocks observed by the Wind spacecraft with varying upstream conditions and Mach numbers. We estimate upstream and downstream power spectra within one-hour intervals adjacent to the shock front and we calculate theoretically predicted downstream power spectrum. We analyze closely the difference between the observed and theoretically predicted spectra. On average, the model predicts the spectra with very good accuracy. We argue that large statistical spread of this difference is given mainly by the statistical uncertainties in the shock compression ratio, upstream power spectrum and by the turbulent evolution of fluctuations in the downstream region. Finally, our findings also suggest that Zank et al. (2021) model may estimate the downstream levels of fluctuations accurately even for a wider range of shocks than it was originally meant for.

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., 82 pages, 31 figures. Paper accepted by Space Science Reviews (collection: The Heliosphere in the Local Interstellar Medium: Into the Unknown), and presented at the ISSI Workshop on November 8-12, 2021

Parker Solar Probe provides a unique opportunity to study anisotropic turbulence in the inner heliosphere. We summarize our recent investigations of solar wind turbulence observed by Parker Solar Probe during its first seven orbits ranging from 0.1 to 0.6 AU. First, we analyzed turbulence anisotropy based on the 2D + slab model and determined the power ratio between the 2D and slab components. We find that the fraction of the 2D component increases with radial distance. Second, we developed a method to identify small-scale magnetic flux ropes and Alfvenic structures based on the reduced magnetic helicity. Alfvenic structures are prevalent in both slow and fast solar wind in PSP's measurements, while the small flux ropes are quasi-2D structures and are relatively abundant near the heliospheric current sheet and slow solar wind. Finally, we analyzed intervals with solar wind velocity strictly parallel to the mean magnetic field. We find a Kolmogorov-like power spectrum with a power-law index of -5/3. Wave activities in both MHD and kinetic scales are also analyzed in these field-aligned intervals. Fast magnetosonic waves and ion-scale waves are identified.

Switchgrass (Panicum virgatum L.) has gained wider attention due to its recognition and use as a model herbaceous crop species for bioenergy production. Genetic diversity information in lowland switchgrass cultivars can help to specify cultivars to be used in the breeding programs aiming for hybrid vigor. The objective of this research was to analyze genetic variation within and among five lowland switchgrass cultivars using amplified fragment length polymorphism (AFLP) markers. AFLP polymorphisms indicated the presence of high genetic variation within lowland switchgrass cultivars with ‘Alamo’ exhibiting the highest genetic variation and ‘Performer’ the lowest. The Nei’s genetic diversity parameters revealed the lowest genetic distance between cultivars ‘Alamo’ and ‘Cimarron’ and the highest value between cultivars ‘Alamo’ and ‘Kanlow’. ‘Alamo’ and ‘Cimarron’ were clustered together while ‘BoMaster’, ‘Kanlow’, and ‘Performer’ were grouped into the other cluster. In addition, there were clusters with mixed genotypes. The findings of this study can be used to select diverse lines as parents for heterosis and inbreeding studies.

The solar wind measured in situ by Parker Solar Probe in the very inner heliosphere is studied in combination with the remote-sensing observation of the coronal source region provided by the METIS coronagraph aboard Solar Orbiter. The coronal outflows observed near the ecliptic by Metis on 2021 January 17 at 16:30 UT, between 3.5 and 6.3 R ⊙ above the eastern solar limb, can be associated with the streams sampled by PSP at 0.11 and 0.26 au from the Sun, in two time intervals almost 5 days apart. The two plasma flows come from two distinct source regions, characterized by different magnetic field polarity and intensity at the coronal base. It follows that both the global and local properties of the two streams are different. Specifically, the solar wind emanating from the stronger magnetic field region has a lower bulk flux density, as expected, and is in a state of well-developed Alfvénic turbulence, with low intermittency. This is interpreted in terms of slab turbulence in the context of nearly incompressible magnetohydrodynamics. Conversely, the highly intermittent and poorly developed turbulent behavior of the solar wind from the weaker magnetic field region is presumably due to large magnetic deflections most likely attributed to the presence of switchbacks of interchange reconnection origin.

This paper reports the first possible evidence for the development of the Kelvin–Helmholtz (KH) instability at the border of coronal holes separating the associated fast wind from the slower wind originating from adjacent streamer regions. Based on a statistical data set of spectroscopic measurements of the UV corona acquired with the UltraViolet Coronagraph Spectrometer on board the SOlar and Heliospheric Observatory during the minimum activity of solar cycle 22, high temperature–velocity correlations are found along the fast/slow solar wind interface region and interpreted as manifestations of KH vortices formed by the roll-up of the shear flow, whose dissipation could lead to higher heating and, because of that, higher velocities. These observational results are supported by solving coupled solar wind and turbulence transport equations including a KH-driven source of turbulence along the tangential velocity discontinuity between faster and slower coronal flows: numerical analysis indicates that the correlation between the solar wind speed and temperature is large in the presence of the shear source of turbulence. These findings suggest that the KH instability may play an important role both in the plasma dynamics and in the energy deposition at the boundaries of coronal holes and equatorial streamers.

The A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and 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 T. urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC), using genotyping-by-sequencing (GBS) and identified 13,089 curated SNPs. Genomic analysis detected misclassified and duplicated accessions with most duplicates originated from the same or a nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were duplicates 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 the T. urartu as the closest A-genome diploid to wheat 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 domestication selection signature (Btr1) on the short arm of chromosome 3Am at ~ 70 Mb. We established A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 80% of allelic variants in the A-genome collection and constitute a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.One-sentence summaryGenotyping of gene bank collections of diploid A-genome relatives of wheat uncovered relatively higher genetic diversity and unique evolutionary relationships which gives insight to the effective use of these germplasm for wheat improvement.

Aims. An interplanetary coronal mass ejection (ICME) event was observed by the Solar Orbiter at 0.8 AU on 2020 April 19 and by Wind at 1 AU on 2020 April 20. Futhermore, an interplanetary shock wave was driven in front of the ICME. Here, we focus on the transmission of the magnetic fluctuations across the shock and we analyze the characteristic wave modes of solar wind turbulence in the vicinity of the shock observed by both spacecraft. Methods. The observed ICME event is characterized by a magnetic helicity-based technique. The ICME-driven shock normal was determined by magnetic coplanarity method for the Solar Orbiter and using a mixed plasma and field approach for Wind. The power spectra of magnetic field fluctuations were generated by applying both a fast Fourier transform and Morlet wavelet analysis. To understand the nature of waves observed near the shock, we used the normalized magnetic helicity as a diagnostic parameter. The wavelet-reconstructed magnetic field fluctuation hodograms were used to further study the polarization properties of waves. Results. We find that the ICME-driven shock observed by Solar Orbiter and Wind is a fast, forward oblique shock with a more perpendicular shock angle at the Wind position. After the shock crossing, the magnetic field fluctuation power increases. Most of the magnetic field fluctuation power resides in the transverse fluctuations. In the vicinity of the shock, both spacecraft observe right-hand polarized waves in the spacecraft frame. The upstream wave signatures fall within a relatively broad and low frequency band, which might be attributed to low frequency MHD waves excited by the streaming particles. For the downstream magnetic wave activity, we find oblique kinetic Alfvén waves with frequencies near the proton cyclotron frequency in the spacecraft frame. The frequency of the downstream waves increases by a factor of ∼7–10 due to the shock compression and the Doppler effect.

The development of next generation sequencing (NGS) enabled a shift from array-based genotyping to high-throughput genotyping by directly sequencing genomic libraries. Even though whole genome sequencing was initially too costly for routine analysis in large populations, such as those utilized for breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to utilize whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage, a limitation comes in the time and high 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 amount of data required and extended to 3,072 samples or more. Panels of double 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 1x down to 0.01x per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the low coverage 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.

A detailed study of solar wind turbulence throughout the heliosphere in both the upwind and downwind directions is presented. We use an incompressible magnetohydrodynamic (MHD) turbulence model that includes the effects of electrons, the separation of turbulence energy into proton and electron heating, the electron heat flux, and Coulomb collisions between protons and electrons. We derive expressions for the turbulence cascade rate corresponding to the energy in forward and backward propagating modes, the fluctuating kinetic and magnetic energy, the normalized cross-helicity, and the normalized residual energy, and calculate the turbulence cascade rate from 0.17 to 75 au in the upwind and downwind directions. Finally, we use the turbulence transport models to derive cosmic ray (CR) parallel and perpendicular mean free paths (mfps) in the upwind and downwind heliocentric directions. We find that turbulence in the upwind and downwind directions is different, in part because of the asymmetric distribution of new born pickup ions in the two directions, which results in the CR mfps being different in the two directions. This is important for models that describe the modulation of cosmic rays by the solar wind.

This letter exploits the radial alignment between the Parker Solar Probe and BepiColombo in late 2022 February, when both spacecraft were within Mercury’s orbit. This allows the study of the turbulent evolution, namely, the change in spectral and intermittency properties, of the same plasma parcel during its expansion from 0.11 to 0.33 au, a still unexplored region. The observational analysis of the solar wind turbulent features at the two different evolution stages is complemented by a theoretical description based on the turbulence transport model equations for nearly incompressible magnetohydrodynamics. The results provide strong evidence that the solar wind turbulence already undergoes significant evolution at distances less than 0.3 au from the Sun, which can be satisfactorily explained as due to evolving slab fluctuations. This work represents a step forward in understanding the processes that control the transition from weak to strong turbulence in the solar wind and in properly modeling the heliosphere.

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).

The first radial alignment between Parker Solar Probe and Solar Orbiter spacecraft is used to investigate the evolution of solar wind turbulence in the inner heliosphere. Assuming ballistic propagation, two 1.5 hr intervals are tentatively identified as providing measurements of the same plasma parcels traveling from 0.1 to 1 au. Using magnetic field measurements from both spacecraft, the properties of turbulence in the two intervals are assessed. Magnetic spectral density, flatness, and high-order moment scaling laws are calculated. The Hilbert–Huang transform is additionally used to mitigate short sample and poor stationarity effects. Results show that the plasma evolves from a highly Alfvénic, less-developed turbulence state near the Sun, to fully developed and intermittent turbulence at 1 au. These observations provide strong evidence for the radial evolution of solar wind turbulence.

Recent studies of unusual or atypical energetic particle flux events (AEPEs) observed at 1 au show that another mechanism, different from diffusive shock acceleration, can energize particles locally in the solar wind. The mechanism proposed by Zank et al. is based on the stochastic energization of charged particles in regions filled with numerous small-scale magnetic islands (SMIs) dynamically contracting or merging and experiencing multiple magnetic reconnection in the super-Alfvénic solar wind flow. A first- and second-order Fermi mechanism results from compression-induced changes in the shape of SMIs and their developing dynamics. Charged particles can also be accelerated by the formation of antireconnection electric fields. Observations show that both processes often coexist in the solar wind. The occurrence of SMIs depends on the presence of strong current sheets like the heliospheric current sheet (HCS), and related AEPEs are found to occur within magnetic cavities formed by stream–stream, stream–HCS, or HCS–shock interactions that are filled with SMIs. Previous case studies comparing observations with theoretical predictions were qualitative. Here we present quantitative theoretical predictions of AEPEs based on several events, including a detailed analysis of the corresponding observations. The study illustrates the necessity of accounting for local processes of particle acceleration in the solar wind.

Aims. Solar Orbiter (SolO) was launched on February 9, 2020, allowing us to study the nature of turbulence in the inner heliopshere. We investigate the evolution of anisotropic turbulence in the fast and slow solar wind in the inner heliosphere using the nearly incompressible magnetohydrodynamic (NI MHD) turbulence model and SolO measurements. Methods. We calculated the two dimensional (2D) and the slab variances of the energy in forward and backward propagating modes, the fluctuating magnetic energy, the fluctuating kinetic energy, the normalized residual energy, and the normalized cross-helicity as a function of the angle between the mean solar wind speed and the mean magnetic field (θUB), and as a function of the heliocentric distance using SolO measurements. We compared the observed results and the theoretical results of the NI MHD turbulence model as a function of the heliocentric distance. Results. The results show that the ratio of 2D energy and slab energy of forward and backward propagating modes, magnetic field fluctuations, and kinetic energy fluctuations increases as the angle between the mean solar wind flow and the mean magnetic field increases from θUB = 0° to approximately θUB = 90° and then decreases as θUB → 180°. We find that solar wind turbulence is a superposition of the dominant 2D component and a minority slab component as a function of the heliocentric distance. We find excellent agreement between the theoretical results and observed results as a function of the heliocentric distance.

Additional file 1: Supplementary File S1. Tag sequences for flanking and peak markers identified within the QTL regions. Two variant alleles for each SNP were denoted as ‘query’ and ‘hit’.

Additional file 2: Supplementary File S2. Fasta sequence of M. truncatula cold tolerance related gene dehydration-responsive element-binding protein 1C (also known as CBF5) obtained from the National Center for Biotechnology Information (NCBI).