CRISPR/Cas9-Mediated HY5 Gene Editing Reduces Growth Inhibition in Chinese Cabbage (Brassica rapa) under ER Stress.

Various stresses can affect the quality and yield of crops, including vegetables. In this study, CRISPR/Cas9 technology was employed to examine the role of the ELONGATED HYPOCOTYL 5 (HY5) gene in influencing the growth of Chinese cabbage (Brassica rapa). Single guide RNAs (sgRNAs) were designed to target the HY5 gene, and deep-sequencing analysis confirmed the induction of mutations in the bZIP domain of the gene. To investigate the response of Chinese cabbage to endoplasmic reticulum (ER) stress, plants were treated with tunicamycin (TM). Both wild-type and hy5 mutant plants showed increased growth inhibition with increasing TM concentration. However, the hy5 mutant plants displayed less severe growth inhibition compared to the wild type. Using nitroblue tetrazolium (NBT) and 3,3'-diaminobenzidine (DAB) staining methods, we determined the amount of reactive oxygen species (ROS) produced under ER stress conditions, and found that the hy5 mutant plants generated lower levels of ROS compared to the wild type. Under ER stress conditions, the hy5 mutant plants exhibited lower expression levels of UPR- and cell death-related genes than the wild type. These results indicate that CRISPR/Cas9-mediated editing of the HY5 gene can mitigate growth inhibition in Chinese cabbage under stresses, improving the quality and yield of crops.

High-performance optical phased array for LiDARs demonstrated by monolithic integration of polymer and SiN waveguides.

Optical phased array (OPA) beam scanners for light detection and ranging (LiDAR) are proposed by integrating polymer waveguides with superior thermo-optic effect and silicon nitride (SiN) waveguides exhibiting strong modal confinement along with high optical power capacity. A low connection loss of only 0.15 dB between the polymer and SiN waveguides was achieved in this work, enabling a low-loss OPA device. The polymer-SiN monolithic OPA demonstrates not only high optical throughput but also efficient beamforming and stable beam scanning. This novel integrative approach highlights the potential of leveraging heterogeneous photonic materials to develop advanced photonic integrated circuits with superior performance.

CRISPR/Cas9-mediated gene editing to confer turnip mosaic virus (TuMV) resistance in Chinese cabbage (Brassica rapa).

Genome editing approaches, particularly the CRISPR/Cas9 technology, are becoming state-of-the-art for trait development in numerous breeding programs. Significant advances in improving plant traits are enabled by this influential tool, especially for disease resistance, compared to traditional breeding. One of the potyviruses, the turnip mosaic virus (TuMV), is the most widespread and damaging virus that infects Brassica spp. worldwide. We generated the targeted mutation at the eIF(iso)4E gene in the TuMV-susceptible cultivar "Seoul" using CRISPR/Cas9 to develop TuMV-resistant Chinese cabbage. We detected several heritable indel mutations in the edited T0 plants and developed T1 through generational progression. It was indicated in the sequence analysis of the eIF(iso)4E-edited T1 plants that the mutations were transferred to succeeding generations. These edited T1 plants conferred resistance to TuMV. It was shown with ELISA analysis the lack of accumulation of viral particles. Furthermore, we found a strong negative correlation (r = -0.938) between TuMV resistance and the genome editing frequency of eIF(iso)4E. Consequently, it was revealed in this study that CRISPR/Cas9 technique can expedite the breeding process to improve traits in Chinese cabbage plants.

Monolithic integration of polymer waveguide phase modulators with silicon nitride waveguides using adiabatic transition tapers.

Polymer waveguide phase modulators (PMs) demonstrate high thermal confinement with outstanding thermo-optic properties and can provide stable low-power phase modulation in optical phased arrays (OPA). On the other hand, silicon nitride (SiN) waveguides produce stronger optical confinement with smaller waveguide core sizes than polymer waveguides and can handle high optical power without nonlinear effects. In this work, a high-performance PM was achieved by monolithic integration of a polymer waveguide and tapered SiN input and output waveguides. The integration of heterogeneous waveguide materials on a single substrate will enable the fabrication of efficient OPAs for advanced imaging, display, sensing, and communications applications.

Case report: Bilateral posterior ischemic optic neuropathy in a patient with atrial fibrillation and multifocal embolic stroke.

An 80-year-old female with a history of diabetes mellitus (DM) and hypertension presented with sudden onset of sequential bilateral visual loss. The best visual acuity was light perception in the right eye and finger counting in the left eye, however, bilateral fundus did not reveal optic disc edema. Diffusion-weighted magnetic resonance imaging (MRI) of the brain revealed acute embolic stroke and diffusion restriction in the posterior portion of both optic nerves. The 24-h Holter monitor showed persistent atrial fibrillation (AF) with rapid ventricular response. The presence of painless and severe visual loss at onset unaccompanied by optic disc edema in the patient with newly detected uncontrolled AF and multiple embolic infarctions favored a diagnosis of non-arteritic posterior ischemic optic neuropathy (PION). The current case contributes to better understanding of PION pathophysiology and associated risk factors, indicating a possible relationship between non-arteritic PION and uncontrolled AF and embolic cerebral infarction.

Frequency Response of Thermo-Optic Phase Modulators Based on Fluorinated Polyimide Polymer Waveguide.

Polymer waveguide phase modulators exhibit stable low-power phase modulation owing to their exceptional thermal confinement and high thermo-optic effect, and thus, have the merit of thermal isolation between channels, which is crucial for an optical phased array (OPA) beam scanner device. In this work, a waveguide phase modulator was designed and fabricated based on a high-refractive-index fluorinated polyimide. The propagation loss of the polyimide waveguide and the temporal response of the phase modulator were characterized. Moreover, the transfer function of the phase modulator including multiple poles and zeros was obtained from the measured frequency response. The polyimide waveguide modulator device demonstrated a fast response time of 117 µs for 1 kHz input signal, however, for 1 mHz step-function input, it exhibited an additional 5% phase change in 5 s.

Recurrent Cerebral Artery Dissection Associated with Seronegative Antiphospholipid Antibody Syndrome.

Stroke in young patients requires thorough evaluation as they often lack risk factors. Antiphospholipid syndrome can cause arterial thrombosis and pregnancy loss; hence, differential diagnoses should include seronegative antiphospholipid syndrome. We report a case of recurrent ischemic stroke caused by recurrent dissection in a patient with a history of pregnancy loss. A 33-year-old woman was admitted with global aphasia and right hemiparesis. During intra-arterial thrombectomy, a left middle cerebral artery dissection was detected. After 5.5 years, she was re-admitted for dysarthria, left facial palsy, subtle left hemiparesis, and right middle cerebral artery dissection. She tested negative for autoimmune diseases and vasculitis. However, underlying pathologic conditions could not be excluded because of the unique disease course. Finally, she was diagnosed with seronegative antiphospholipid syndrome. The concept of seronegative antiphospholipid syndrome has been proposed for patients with clinical features suggestive of antiphospholipid syndrome but with negative titers. However, this syndrome can only be diagnosed by exclusion. Furthermore, arterial dissection should be considered to be its main pathology. Antiphospholipid syndrome itself can be a risk factor for arterial dissection because it weakens the vessel walls. Therefore, diagnosis is important to prevent future complications in young patients with recurrent cerebral artery dissection, especially those associated with pregnancy-related morbidities.

Fast-running beamforming algorithm for optical phased array beam scanners comprised of polymeric waveguide devices.

The phase error imposed in optical phased arrays (OPAs) for beam scanning LiDAR is unavoidable due to minute dimensional fluctuations that occur during the waveguide manufacturing process. To compensate for the phase error, in this study, a fast-running beamforming algorithm is developed based on the rotating element vector method. The proposed algorithm is highly suitable for OPA devices comprised of polymer waveguides, where thermal crosstalk between phase modulators is suppressed effectively, allowing for each phase modulator to be controlled independently. The beamforming speed is determined by the number of phase adjustments. Hence, by using the least square approximation for a 32-channel polymer waveguide OPA device the number of phase adjustments needed to complete beamforming was reduced and the beamforming time was shortened to 16 seconds.

A vicious cycle of health (in)equity: Migrant inclusion in light of COVID-19.

Objectives: Whilst mass vaccination is suggested as an important means to contain COVID-19 pandemic, vaccination policies across many countries have systematically excluded some groups of population, especially migrants. This study aims to document the impact of diversified vaccination strategies as a preventative and control measure for the health and safety of the wider population within a country. Methods: We selected five countries that have experienced the changes in migrant inflows to the most extreme among OECD countries in 2020: The United States, Australia, Canada, Japan, and South Korea. We conducted an extensive qualitative documentary analysis focused on policies and interventions implemented in these countries since January 2020 till the end of September 2021. We also analyzed publicly available epidemiological data (released by the governments and other international organizations). Results: We find that achieving migrants' health and vaccination equity is not without challenges, and a failure to address those multiplicity of concerns may result in a vicious cycle for the vulnerable population at the fringes of our economy. Migrants continue to face extenuating circumstances with higher risks to their health and safety, when they are excluded or disadvantaged in vaccination policies. The more inclusive and proactive the governments are in consideration of diversity of migrant populations, the better they can manage the pandemic, which leads to overall societal benefit of ensuring public health. Conclusions: Equity-based policies can mitigate disparities in access to vaccination and healthcare, thereby reducing the spread of COVID-19 in the community.

Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.).

Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line '16P118' and inbred line 'Sweet Green' through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07-11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.

Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry.

The genus Fragaria encompass fruits with diverse colors influenced by the distribution and accumulation of anthocyanin. Particularly, the fruit colors of strawberries with different ploidy levels are determined by expression and natural variations in the vital structural and regulatory genes involved in the anthocyanin pathway. Among the regulatory genes, MYB10 transcription factor is crucial for the expression of structural genes in the anthocyanin pathway. In the present study, we performed a genome wide investigation of MYB10 in the diploid and octoploid Fragaria species. Further, we identified seven quantitative trait loci (QTLs) associated with fruit color in octoploid strawberry. In addition, we predicted 20 candidate genes primarily influencing the fruit color based on the QTL results and transcriptome analysis of fruit skin and flesh tissues of light pink, red, and dark red strawberries. Moreover, the computational and transcriptome analysis of MYB10 in octoploid strawberry suggests that the difference in fruit colors could be predominantly influenced by the expression of MYB10 from the F. iinumae subgenome. The outcomes of the present endeavor will provide a platform for the understanding and tailoring of anthocyanin pathway in strawberry for the production of fruits with aesthetic colors.

Chromosome Level Assembly of Homozygous Inbred Line 'Wongyo 3115' Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa).

Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line 'Wongyo 3115', using long- and short-read sequencing technologies. The assembly of 'Wongyo 3115' produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the 'Wongyo 3115' reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the 'BS F2' populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the 'Wongyo 3115' genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of 'BS F2' obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.

Compact solid-state optical phased array beam scanners based on polymeric photonic integrated circuits.

Optical phased array (OPA) devices are being actively investigated to develop compact solid-state beam scanners, which are essential in fields such as LiDAR, free-space optical links, biophotonics, etc. Based on the unique nature of perfluorinated polymers, we propose a polymer waveguide OPA with the advantages of low driving power and high optical throughput. Unlike silicon photonic OPAs, the polymer OPAs enable sustainable phase distribution control during beam scanning, which reduces the burden of beamforming. Moreover, by incorporating a tunable wavelength laser comprising a polymer waveguide Bragg reflector, two-dimensional beam scanning is demonstrated, which facilitates the development of laser-integrated polymeric OPA beam scanners.

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

Powdery mildew (PM) is a common fungal disease infecting pepper plants worldwide. Molecular breeding of pepper cultivars with powdery mildew resistance is desirable for the economic improvement of pepper cultivation. In the present study, 188 F5 population derived from AR1 (PM resistant) and TF68 (PM sensitive) parents were subjected to high-throughput genotyping by sequencing (GBS) for the identification of single nucleotide polymorphism (SNP) markers. Further, the identified SNP markers were utilized for the construction of genetic linkage map and QTL analysis. Overall read mapping percentage of 87.29% was achieved in this study with the total length of mapped region ranging from 2,956,730 to 25,537,525 bp. A total of 41,111 polymorphic SNPs were identified, and a final of 1,841 SNPs were filtered for the construction of a linkage map. A total of 12 linkage groups were constructed corresponding to each chromosome with 1,308 SNP markers with the map length of 2506.8 cM. Further, two QTLs such as Pm-2.1 and Pm-5.1 were identified in chromosomes 2 and 5, respectively, for the PM resistance. Overall, the outcomes of the present endeavor can be utilized for the marker-assisted selection of pepper with powdery mildew-resistant trait.

QTL Mapping for Gummy Stem Blight Resistance in Watermelon (Citrullus spp.).

Watermelon (Citrulluslanatus) is an economically important fruit crop worldwide. Gummy stem blight (GSB) is one of the most damaging diseases encountered during watermelon cultivation. In the present study, we identified quantitative trait loci (QTLs) associated with GSB resistance in an F2 population derived from a cross between maternal-susceptible line '920533' (C. lanatus) and the paternal-resistant line 'PI 189225' (C. amarus). The resistance of 178 F2 plants was assessed by two different evaluation methods, including leaf lesion (LL) and stem blight (SB). To analyze the QTLs associated with GSB resistance, a linkage map was constructed covering a total genetic distance of 1070.2 cM. QTL analysis detected three QTLs associated with GSB resistance on chromosome 8 and 6. Among them, two QTLs, qLL8.1 and qSB8.1 on chromosome 8 identified as major QTLs, explaining 10.5 and 10.0% of the phenotypic variations localizing at same area and sharing the same top markers for both LL and SB traits, respectively. A minor QTL, qSB6.1, explains 9.7% of phenotypic variations detected on chromosome 6 only for the SB trait. High-throughput markers were developed and validated for the selection of resistant QTLs using watermelon accessions, and commercial cultivars. Four potential candidate genes were predicted associated with GSB resistance based on the physical location of flanking markers on chromosome 8. These findings will be helpful for the development of watermelon cultivars resistant to GSB.

Versatile Nutraceutical Potentials of Watermelon-A Modest Fruit Loaded with Pharmaceutically Valuable Phytochemicals.

Watermelon (Citrulus lantus) is an important horticultural crop which belongs to the Curcubitaceae family. The nutraceutical potential of watermelon has been illustrated by several researchers, which makes it a better choice of functional food. Watermelon has been used to treat various ailments, such as cardio-vascular diseases, aging related ailments, obesity, diabetes, ulcers, and various types of cancers. The medicinal properties of watermelon are attributed by the presence of important phytochemicals with pharmaceutical values such as lycopene, citrulline, and other polyphenolic compounds. Watermelon acts as vital source of l-citrulline, a neutral-alpha amino acid which is the precursor of l-arginine, an essential amino acid necessary for protein synthesis. Supplementation of l-citrulline and lycopene displayed numerous health benefits in in vitro and in vivo studies. Similarly, the dietary intake of watermelon has proven benefits as functional food in humans for weight management. Apart from the fruits, the extracts prepared from the seeds, sprouts, and leaves also evidenced medicinal properties. The present review provides a comprehensive overview of benefits of watermelon for the treatment of various ailments.

Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding.

The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic importance. In order to accelerate the genomics assisted breeding and genetic selection, transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic (SNP) markers. The sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC (%) of 47.80-49.34 and phred quality score (Q30) of 96.47-97.54%. A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding (MAB) markers were generated from the polymorphic SNPs. Further, functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering process. The SNPs were predominantly associated with the four major flowering related transcription factors such as MYB, MADS box (AG), AP2/EREB, and bHLH. In addition, SNPs in the vital flowering integrator gene (FT) and floral repressors (EMBRYONIC FLOWER 1, 2, and FRIGIDA) were identified among the radish inbred lines. Further, 50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system (KASP) in 102 radish inbred lines. The homozygosity of the inbred lines varied from 56 to 96% and the phylogenetic analysis resulted in the clustering of inbred lines into three subgroups. Taken together, the SNP markers identified in the present study can be utilized for the discrimination, seed purity test, and adjusting parental combinations for breeding in radish.

Deciphering the Nutraceutical Potential of Raphanus sativus-A Comprehensive Overview.

Raphanus sativus (Radish) belongs to the Brassicaceae family and is a widely consumed root vegetable all around the world. The nutritional and medicinal values of radishes have been proven by several researches. Extracts prepared from the aerial and underground parts of radishes have been used in the treatment of stomach disorders, urinary infections, hepatic inflammation, cardiac disorders and ulcers in folk medicine since the ancient times. The pharmaceutical potential of radishes is attributed to the presence of its beneficial secondary metabolites, such as glucosinolates, polyphenols and isothiocyanates. The present review has focused on the impact of radish extract administration under pathological complications, such as cancer, diabetes, hepatic inflammation and oxidative stress. In addition, a comprehensive view of molecular mechanism behind the regulation of molecular drug targets associated with different types of cancers and diabetes by the bioactive compounds present in the radish extracts have been discussed in detail.

Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper.

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance.

The present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F4 populations and correlated with the phenotypic disease index.