Multitrait engineering of Hassawi red rice for sustainable cultivation.

Sustainable agriculture requires locally adapted varieties that produce nutritious food with limited agricultural inputs. Genome engineering represents a viable approach to develop cultivars that fulfill these criteria. For example, the red Hassawi rice, a native landrace of Saudi Arabia, tolerates local drought and high-salinity conditions and produces grain with diverse health-promoting phytochemicals. However, Hassawi has a long growth cycle, high cultivation costs, low productivity, and susceptibility to lodging. Here, to improve these undesirable traits via genome editing, we established efficient regeneration and Agrobacterium-mediated transformation protocols for Hassawi. In addition, we generated the first high-quality reference genome and targeted the key flowering repressor gene, Hd4, thus shortening the plant's lifecycle and height. Using CRISPR/Cas9 multiplexing, we simultaneously disrupted negative regulators of flowering time (Hd2, Hd4, and Hd5), grain size (GS3), grain number (GN1a), and plant height (Sd1). The resulting homozygous mutant lines flowered extremely early (∼56 days) and had shorter stems (approximately 107 cm), longer grains (by 5.1%), and more grains per plant (by 50.2%), thereby enhancing overall productivity. Furthermore, the awns of grains were 86.4% shorter compared to unedited plants. Moreover, the modified rice grain displayed improved nutritional attributes. As a result, the modified Hassawi rice combines several desirable traits that can incentivize large-scale cultivation and reduce malnutrition.

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.

The gyrfalcon (Falco rusticolus) genome.

High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.193 Gbp, including 8,064 complete Benchmarking Universal Single-Copy Orthologs (BUSCOs) of the total 8,338 BUSCO groups present in the library aves_odb10. Of these BUSCO genes, 96.7% were complete, 96.1% were present as a single copy, and 0.6% were duplicated. Furthermore, 0.8% of BUSCO genes were fragmented and 2.5% (210) were missing. A de novo search for transposable elements (TEs) identified 5,716 TEs that masked 7.61% of the F. rusticolus genome assembly when combined with publicly available TE collections. Long interspersed nuclear elements, in particular, the element Chicken-repeat 1 (CR1), were the most abundant TEs in the F. rusticolus genome. A de novo first-pass gene annotation was performed using 293,349 PacBio Iso-Seq transcripts and 496,195 transcripts derived from the assembly of 42,429,525 Illumina PE RNA-seq reads. In all, 19,602 putative genes, of which 59.31% were functionally characterized and associated with Gene Ontology terms, were annotated. A comparison of the gyrfalcon genome assembly with the publicly available assemblies of the domestic chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and hummingbird (Calypte anna) revealed several genome rearrangements. In particular, nine putative chromosome fusions were identified in the gyrfalcon genome assembly compared with those in the G. gallus genome assembly. This genome assembly, its annotation for TEs and genes, and the comparative analyses presented, complement and strength the base of high-quality genome assemblies and associated resources available for comparative studies focusing on the evolution, ecology, and conservation of Aves.

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.

Combined Blood Indexes of Systemic Inflammation as a Mirror to Admission to Intensive Care Unit in COVID-19 Patients: A Multicentric Study.

BACKGROUND: The Coronavirus 2019 is a pandemic that has spread worldwide, threatening human health. The main cause of death in patients with COVID-19 is a systemic pro-inflammatory mechanism that quickly progresses to acute respiratory distress syndrome. Hematological ratios as affordable indicators of inflammatory response were studied in COVID-19 patients. The study aimed to study the importance of the blood cell indexes of the systemic inflammatory response, as the Aggregate Index of Systemic Inflammation (AISI), neutrophils lymphocyte to platelet ratio (NLPR), systemic immune-inflammation index (SII) and, systemic inflammation response index (SIRI) in predicting intensive care unit (ICU) admission of COVID-19 patients. METHODS: 495 COVID-19 patients managed in four tertiary centers; divided into non-ICU and ICU groups. RESULTS: Total leucocyte count (TLC), AISI, NLPR, SII, and SIRI were more elevated in the ICU group (P < 0.001 for all except AMC P = 0.006), while this group had less absolute lymphocyte count (ALC) (P = 0.047). We estimated the optimal cut-off values of the hematological ratio; AISI (729), NLPR (0.0195), SII (1346), and SIRI (2.5). SII had the highest specificity (95.6%), while NLPR had the highest sensitivity (61.3%). Age, AISI, CRP, D-dimer, and oxygen aid were the independent predictors for ICU admission in COVID-19 in multivariate logistic regression. CONCLUSION: AISI is a predictor for severity and ICU admission in COVID-19 patients, SII is a predictor of survival, while NLPR and SIRI have an additive role that needs further evaluation.

Determinants of Obtaining COVID-19 Vaccination among Health Care Workers with Access to Free COVID-19 Vaccination: A Cross-Sectional Study.

INTRODUCTION: Despite global efforts to contain the illness, COVID-19 continues to have severe health, life, and economic repercussions; thus, maintaining vaccine development is mandatory. Different directions concerning COVID-19 vaccines have emerged as a result of the vaccine's unpredictability. AIMS: To study the determinants of the attitudes of healthcare workers (HCWs) to receiving or refusing to receive the vaccine. METHODS: The current study adopted an interviewed questionnaire between June and August 2021. A total of 341 HCWs currently working at Assiut University hospitals offered to receive the vaccine were included. RESULTS: Only half of the HCWs (42%) accepted the COVID-19 vaccine. The most common reason that motivated the HCWs was being more susceptible than others to infection (71.8%). On other hand, the common reasons for refusing included: previously contracted the virus (64.8%); did not have time (58.8%); warned by a doctor not to take it (53.8%). Nearly one-third of nonaccepting HCWs depended on television, the Internet, and friends who refused the vaccine for information (p < 0.05). In the final multivariate regression model, there were six significant predictors: sex, job category, chronic disease, being vaccinated for influenza, and using Assiut University hospital staff and the Ministry of Health as sources of information (p < 0.05). CONCLUSION: Misinformation and negative conceptions are still barriers against achieving the desired rate of vaccination, especially for vulnerable groups such as HCWs.

A platinum standard pan-genome resource that represents the population structure of Asian rice.

As the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated Asian rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to map resequencing data to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice.

Telemedicine for diabetic retinopathy screening using an ultra-widefield fundus camera.

OBJECTIVE: Telemedicine reporting of diabetic retinopathy (DR) screening using ultra-widefield (UWF) fundus camera. MATERIALS AND METHODS: Cross-sectional study of diabetic patients who visited the endocrinology department of a private multi-specialty hospital in United Arab Emirates between April 2015 and January 2017 who underwent UWF fundus imaging. Fundus pictures are then accessed at the Retina Clinic in the Department of Ophthalmology. Primary outcome measure was incidence of any form of DR detected. The secondary outcome measure was failure to take good image and inability to grade. RESULTS: A total of 1,024 diabetic individuals were screened for DR from April 2015 to January 2017 in the department of Endocrinology. Rate of DR was 9.27%; 165 eyes of 95 individuals were diagnosed to have some form of DR. Mild non-proliferative DR (NPDR) was seen in 114 of 165 eyes (69.09%), moderate NPDR in 32 eyes (19.39%), severe NPDR in six eyes (3.64%), and proliferative DR (PDR) in 13 eyes (7.88%). The secondary outcome measure of poor image acquisition was seen in one individual who had an image acquired in one eye that could not be graded due to bad picture quality. CONCLUSIONS: The present study has shown the effectiveness of DR screening using UWF fundus camera. It has shown the effectiveness of trained nursing personnel taking fundus images. This model can be replicated in any private multi-specialty hospital and reduce the burden of DR screening in the retina clinic and enhance early detection of treatable DR.