An online database for einkorn wheat to aid in gene discovery and functional genomics studies.

Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL  https://wheat.pw.usda.gov/GG3/pangenome.

Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata.

Wild wheat relatives have been explored in plant breeding to increase the genetic diversity of bread wheat, one of the most important food crops. Aegilops umbellulata is a diploid U genome-containing grass species that serves as a genetic reservoir for wheat improvement. In this study, we report the construction of a chromosome-scale reference assembly of Ae. umbellulata accession TA1851 based on corrected PacBio HiFi reads and chromosome conformation capture. The total assembly size was 4.25 Gb with a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We benchmarked the performance of hifiasm and LJA, two of the most widely used assemblers using standard and corrected HiFi reads, revealing a positive effect of corrected input reads. Comparative genome analysis confirmed substantial chromosome rearrangements in Ae. umbellulata compared to bread wheat. In summary, the Ae. umbellulata assembly provides a resource for comparative genomics in Triticeae and for the discovery of agriculturally important genes.

Einkorn genomics sheds light on history of the oldest domesticated wheat.

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.

Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits.

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.

An unusual tandem kinase fusion protein confers leaf rust resistance in wheat.

The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. 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 umbellulata2. 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 triuncialis3, 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.

An Atlas of Optical Coherence Tomography (OCT): Elucidating In Vivo Differences of Scar Types Using OCT in Order to Guide Laser Treatment Parameters.

Objective: When using laser therapy to effectively treat scars, the choice of treatment parameters depends on the knowledge accuracy of the underlying scar pathology, which is often difficult to judge by gross physical exam. As such, more quantitative measures are needed. In recent years, optical coherencetomography (OCT) has shown promise as a real-time imaging technolgoy of skin microstructure. A key step in developing a methodology for utilizing OCT to develop a comprehensive 'atlas' of OCT characteristics of a wide variety of scar types. This atlas may then be used as a tool for selecting the optimal treatment modality and parameters for each scar type. Methods: One hundred and fifty scars of a wide range of anatomical locations were imaged using OCT, capturing both vascular and structural data. A variety of scar etiologies (e.g. burn, surgical, traumatic) and types (e.g. hypertrophic, keloidal, atrophic) were included. Comparator scans were also taken from normal, unscarred skin. Results: OCT revealed morphological differences in the epidermis and dermis between scars and normal tissue, and between scar subtypes. Features affected by scar pathology included epidermal thickness, skin surface texture, dermal epidermal junction rugosity, blood vessel density, vessel shape and diameter, vessel direction and vascular network, dermis scattering intensity and non-uniformity. Each scar subtype showed consistent characteristics distinct from other scar subtypes. Limitations: This was a single-site study of a patient population in South Florida. Conclusion: OCT is a powerful new objective tool for the clinician to utilize in the pursuit of effective laser treatment parameters by enabling personalized treatment based on individual scar characteristics in order to maximize treatment capabilities.

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning.

The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future.

Prospective study of intense pulsed light versus pulsed dye laser with or without blue light in the activation of PDT for the treatment of actinic keratosis and photodamage.

BACKGROUND: Exposure to ultraviolet (UV) light from the sun is known to have a deleterious effect on the skin. Repeated insults to the dermal matrix from UV radiation result in the clinical signs of photodamage, including changes in skin elasticity, color, and texture. UV radiation also leads to the accumulation of DNA mutations and promotes tumor development, resulting in the formation of cutaneous precancerous and cancerous lesions. Continuous-wave incoherent blue light, intense pulsed light (IPL), and pulsed dye laser (PDL) are safe and efficacious light sources commonly used for aminolevulinic acid photodynamic therapy (PDT). The aim of this study was to prospectively evaluate the efficacy of PDT for the treatment of photodamage and actinic keratoses using four different combinations of light sources: PDL, PDL + blue light, IPL, and IPL + blue light. STUDY: A total of 220 patients with either photodamage or actinic keratosis (AK) were recruited from the Miami Dermatology Laser Institute (Miami, FL) and were assigned prospectively to undergo one PDT treatment with one of the four light options: PDL, PDL + blue light, IPL or IPL + blue light. Of the 220 patients enrolled in treatment groups, 214 patients completed the study. Of the 214 patients, 88 received treatment for AK, and 126 received treatment for photodamage. All patients gave their consent to participate in the study and to allow their photographs to be utilized for the purpose of scientific presentations. RESULTS: Treatment with IPL resulted in a 70.8% reduction of actinic keratoses at a 1-month follow-up. Treatment with IPL and blue light 84.4% reduction of actinic keratoses at 1 month follow up. Treatment with PDL 70.5% reduction of actinic keratoses at 1 month follow up. Treatment with PDL and blue light 69.3% reduction of actinic keratoses at 1 month follow up. Treatment with IPL resulted in an improvement score of 2.9. Treatment with IPL and blue light resulted in an improvement score of 3.0. Treatment PDL resulted in an improvement score of 1.5. Treatment with PDL and blue light resulted in an improvement score of 1.8. CONCLUSION: Although all four treatment groups led to some improvement in signs of photoaging, IPL + blue light again demonstrated increased efficacy when compared to IPL, PDL, and PDL + blue light treatment groups. Results from our study were limited by an unequal distribution between treatment groups and a lack of follow-up beyond a 1-month period and warrant further research.

Medical and aesthetic improvement of photodamaged skin by the combination of intense pulsed light and photodynamic therapy with 10% aminolevulinic acid hydrochloride gel.

OBJECTIVE: To evaluate the efficacy and safety of photodynamic therapy (PDT) with the novel 10% aminolevulinic acid (ALA) hydrochloride gel (10% ALA gel) and BF-RhodoLED® light (635 nm; 37 J/cm2 ) in combination with intense pulsed light (IPL) to augment the medical and aesthetic improvement of photodamaged skin of the décolleté. METHODS: This was a single-site prospective, randomized, intraindividual split chest pilot study with 20 female subjects with moderate to severe photodamage of the décolleté. Subjects were randomized to ALA-PDT + IPL to one split-side of the chest and ALA-PDT only to the contralateral side. Three blinded raters assessed aesthetic improvement using the global aesthetic improvement scale (GAIS). RESULTS: Eighteen subjects completed the study. Superior GAIS results were achieved on the ALA-PDT + IPL treatment side than on the ALA-PDT only treatment side (p < 0.001) after 24 weeks of follow-up. CONCLUSIONS: ALA-PDT using 10% ALA hydrochloride gel and BF-RhodoLED® light had superior rejuvenation effects on the décolleté when combined with IPL compared to ALA-PDT alone.

Analysis of port-wine birthmark vascular characteristics by location: Utility of optical coherence tomography mapping.

INTRODUCTION: Port-wine birthmarks (PWBs) are congenital capillary malformations that can be located on any area of the body. Vascular features include vessel size, depth, and density, which can greatly differ between patients, individual lesions, and even sites within the same lesion. Previous studies have determined that the location of PWB lesions has impacted their clinical response to laser treatment. OBJECTIVE: We utilized dynamic optical coherence tomography (D-OCT) to measure in vivo vessel diameter, density, and superficial plexus depth in patients of all ages with PWB on various sites of the body. We hypothesized that these vascular characteristics would differ according to body location. MATERIALS AND METHODS: Patients who had a PWB and presented to clinic at three sites for treatment with the pulsed dye laser (PDL) were enrolled into the study. A D-OCT scanner was utilized for noninvasive, in vivo imaging of PWB lesions. The depth of the top portion of the superficial vascular plexus was estimated as the depth at which the vessel density reaches 50% of the maximum. Vessel diameter and density were calculated by incorporated software algorithm. RESULTS: A total of 108 patients were enrolled into the study. There was a total of 204 measurements of PWB lesions. Of all patients, 56.5% (n = 61) reported having a previous treatment with PDL. Of all D-OCT scans, 62.3% (n = 127) were located on the head, 14.2% (n = 29) the upper extremities, 8.3% (n = 17) the lower extremities, 7.8% (n = 16) the trunk, and 7.8% (n = 15) the neck. All locations were compared for each vascular characteristic. For superficial plexus depth, lesions on the head were significantly shallower than those on the upper extremities (217 vs. 284 µm; p < 0.001) and lower extremities (217 vs. 309 µm; p < 0.001). For vessel diameter, lesions on the head had significantly larger vessels than those on the upper extremities (100 vs. 72 µm; p = 0.001). For vessel density, lesions on the head had significantly denser vessels than those on the trunk (19% vs. 9.6%; p = 0.039) and upper extremities (19% vs. 9.3%; p < 0.001) CONCLUSIONS: PWB lesions have distinct vascular characteristics, which can be associated with their body location. This includes superficial vascular plexus depth as well as vessel diameter and density.

Vascular characteristics of port wine birthmarks as measured by dynamic optical coherence tomography.

BACKGROUND: Port wine birthmarks (PWBs) are congenital capillary malformations. Vessel characteristics, such as diameter and depth, may impact presentation and outcomes. They can be imaged using dynamic optical coherence tomography, a high-resolution, noninvasive imaging method. PURPOSE: We conducted a cross-sectional observational study to measure in vivo vascular characteristics as a function of PWB color. METHODS: Patients undergoing treatment for PWB were recruited from 3 sites. PWBs were classified by color. Dynamic optical coherence tomography images with calculations were obtained. RESULTS: One hundred eight patients were enrolled. Mean age correlated with PWB color, with birthmarks being lighter in younger patients and darker in older patients (P < .01). Mean superficial plexus depth was significantly shallower in purple PWBs than in pink PWBs. Color was not associated with significant differences in mean superficial vessel density or diameter. Among pink PWBs, each 10-year increase in age was associated with a 10.6-µm increase in superficial plexus depth. Among purple PWBs, each 10-year increase in age was associated with a 16.2-µm reduction in superficial plexus depth. In lesions without prior treatment, vessel density was 12.7% lower in purple PWBs than in pink PWBs. CONCLUSION: Superficial vessels of purple PWBs were significantly closer to the epidermis than those of pink PWBs, which might impact optimal laser parameters.

Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences.

Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning.

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color.

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

US Dermatology Resident Responses about the COVID-19 Pandemic: Results from a Nationwide Survey.

OBJECTIVES: The coronavirus disease 2019 (COVID-19) pandemic has drastically changed resident training in the United States. Here, we explore the early perceived effects of COVID-19 on dermatology residents through an electronic sample survey and identify possible areas for targeted improvement in lieu of a possible second wave of COVID-19 cases. METHODS: On April 3, 2020, a survey of link with 25 questions was sent to dermatology program coordinators to be disseminated among dermatology residents in the United States. The survey was closed on April 13, 2020. All of the questions were optional and no personal identifiers were collected. RESULTS: A total of 140 dermatology residents from 50 different residency programs across 26 states responded to the survey. The majority of respondents (85%) reported negative effects of COVID-19 on their overall wellness. Despite the majority of residents (92%) speculating that COVID-19 will have negative long-term effects on the US economy, only 33% agreed or strongly agreed that it will affect their job prospects. Teledermatology was widely implemented following the declaration of a national emergency (96% of represented residencies compared with only 30% before the pandemic), with heavy resident involvement. The majority of residents (99%) reported having virtual didactics and that they found them to be beneficial. Most residents were uncomfortable with the prospect of being reassigned to a nondermatology specialty during the pandemic. In addition, 22% of residents believed that their leadership were not transparent and prompt in addressing changes relating to COVID-19. CONCLUSIONS: Dermatology residents were affected negatively by COVID-19 in regard to their well-being, clinical training, and education. Several areas of improvement were identified that could improve our preparedness for a second wave of the virus.