Homology-independent targeted insertion-mediated derivation of M1-biased macrophages harbouring Megf10 and CD3ζ from human pluripotent stem cells.

BACKGROUND: Macrophages engineered with chimeric antigen receptors (CAR) are suitable for immunotherapy based on their immunomodulatory activity and ability to infiltrate solid tumours. However, the production and application of genetically edited, highly effective, and mass-produced CAR-modified macrophages (CAR-Ms) are challenging. METHODS: Here, we used homology-independent targeted insertion (HITI) for site-directed CAR integration into the safe-harbour region of human pluripotent stem cells (hPSCs). This approach, together with a simple differentiation protocol, produced stable and highly effective CAR-Ms without heterogeneity. FINDINGS: These engineered cells phagocytosed cancer cells, leading to significant inhibition of cancer-cell proliferation in vitro and in vivo. Furthermore, the engineered CARs, which incorporated a combination of CD3ζ and Megf10 (referred to as FRP5Mζ), markedly enhanced the antitumour effect of CAR-Ms by promoting M1, but not M2, polarisation. FRP5Mζ promoted M1 polarisation via nuclear factor kappa B (NF-κB), ERK, and STAT1 signalling, and concurrently inhibited STAT3 signalling even under M2 conditions. These features of CAR-Ms modulated the tumour microenvironment by activating inflammatory signalling, inducing M1 polarisation of bystander non-CAR macrophages, and enhancing the infiltration of T cells in cancer spheroids. INTERPRETATION: Our findings suggest that CAR-Ms have promise as immunotherapeutics. In conclusion, the guided insertion of CAR containing CD3ζ and Megf10 domains is an effective strategy for the immunotherapy of solid tumours. FUNDING: This work was supported by KRIBB Research Initiative Program Grant (KGM4562431, KGM5282423) and a Korean Fund for Regenerative Medicine (KFRM) grant funded by the Korean government (Ministry of Science and ICT,Ministry of Health and Welfare) (22A0304L1-01).

Skin Hydration Measurement: Comparison Between Devices and Clinical Evaluations.

BACKGROUND: The need for an objective method for measuring skin hydration levels is becoming increasingly important. Various devices with different measuring principles for assessing skin hydration have been developed and are widely used. OBJECTIVE: This study aimed to investigate the reproducibility and correlation between clinical evaluation and skin hydration measurement devices that are the most widely used in the field. METHODS: A prospective comparative clinical trial was conducted on 184 healthy volunteers. Skin hydration levels were measured using the Corneometer (CM820) and hydration probe (HP: DermaLab Combo) at 3 points: the ventral forearm, the dorsal forearm, and the shin. We used the intraclass correlation coefficient (ICC) to evaluate the reproducibility and Pearson's correlation coefficient (PCC) to evaluate the correlation of each measurement. Simple linear regression was used to analyze the Corneometer and HP skin hydration value changes according to changes in xerosis severity scale (XSS) values, which were evaluated by clinicians. RESULTS: Both the Corneometer and HP showed significant, excellent reproducibility (ICC for Corneometer: 0.954-0.971, ICC for HP: 0.980-0.986) and significant high positive correlations (PCC: 0.708-0.737) regardless of the measurement site. Both devices showed negative regression coefficients in all measurement sites in XSS analysis, but this was not statistically significant. CONCLUSION: The Corneometer and HP were both accurate and objective skin hydration measuring devices, regardless of the measurement site. Using reliable and objective devices such as the Corneometer or HP can aid in understanding an individual's skin condition and making more informed decisions for skin care. TRIAL REGISTRATION: Clinical Research Information Service Identifier: KCT0005146.

Rice rhizobiome engineering for climate change mitigation.

The year 2023 was the warmest year since 1850. Greenhouse gases, including CO2 and methane, played a significant role in increasing global warming. Among these gases, methane has a 25-fold greater impact on global warming than CO2. Methane is emitted during rice cultivation by a group of rice rhizosphere microbes, termed methanogens, in low oxygen (hypoxic) conditions. To reduce methane emissions, it is crucial to decrease the methane production capacity of methanogens through water and fertilizer management, breeding of new rice cultivars, regulating root exudation, and manipulating rhizosphere microbiota. In this opinion article we review the recent developments in hypoxia ecology and methane emission mitigation and propose potential solutions based on the manipulation of microbiota and methanogens for the mitigation of methane emissions.

Synergizing breeding strategies via combining speed breeding, phenotypic selection, and marker-assisted backcrossing for the introgression of Glu-B1i in wheat.

Wheat is a major food crop that plays a crucial role in the human diet. Various breeding technologies have been developed and refined to meet the increasing global wheat demand. Several studies have suggested breeding strategies that combine generation acceleration systems and molecular breeding methods to maximize breeding efficiency. However, real-world examples demonstrating the effective utilization of these strategies in breeding programs are lacking. In this study, we designed and demonstrated a synergized breeding strategy (SBS) that combines rapid and efficient breeding techniques, including speed breeding, speed vernalization, phenotypic selection, backcrossing, and marker-assisted selection. These breeding techniques were tailored to the specific characteristics of the breeding materials and objectives. Using the SBS approach, from artificial crossing to the initial observed yield trial under field conditions only took 3.5 years, resulting in a 53% reduction in the time required to develop a BC2 near-isogenic line (NIL) and achieving a higher recurrent genome recovery of 91.5% compared to traditional field conditions. We developed a new wheat NIL derived from cv. Jokyoung, a leading cultivar in Korea. Milyang56 exhibited improved protein content, sodium dodecyl sulfate-sedimentation value, and loaf volume compared to Jokyoung, which were attributed to introgression of the Glu-B1i allele from the donor parent, cv. Garnet. SBS represents a flexible breeding model that can be applied by breeders for developing breeding materials and mapping populations, as well as analyzing the environmental effects of specific genes or loci and for trait stacking.

Artificial Rainfall on Grain Quality and Baking Characteristics of Winter Wheat Cultivars in Korea.

Wheat (Triticum aestivum L.) stands as a significant cereal crop globally, including in Korea, where its consumption reached 35.7 kg per capita in 2023. In the southern regions of Korea, wheat cultivation follows paddy rice, with harvesting typically occurring during the rainy season in mid-June. This timing, coupled with the high humidity and unpredictable rainfall, often leads to pre-harvest sprouting and subsequent deterioration in flour quality. To assess the impact of rain on flour quality, an artificial rain treatment was administered 45 days after heading in an open field greenhouse, followed by flour quality analysis. The color measurement revealed an increase in the L* parameter, indicative of enhanced kernel vitreousness, attributed to endosperm starch degradation via alpha-amylase activation induced by water absorption. Moreover, significant changes were observed in ash content and the gluten index within the wetted group, resulting in decreased dough strength and stability, ultimately leading to a reduction in loaf volume. Consequently, it is recommended that wheat be harvested 4-7 days after reaching the physiological maturity stage to avoid the rainy season and ensure the production of high-quality wheat.

Self-Powered Electrical Bandage Based on Body-Coupled Energy Harvesting.

Self-powered electrical bandages (SEBs), integrated with wearable energy harvesters, can provide an effective and autonomous electrical stimulation (ES) solution for rapid and scarless wound healing. A continuously operating, wireless, and applicable-to-comprehensive-wound ES device is essential for the quick restoration of wounds and convenience. This work illustrates a SEB powered by body-coupled energy harvesting. The SEB continuously treats the wound with 60-Hz sinusoidal electrical potential gained from the coupling of the human body and ambient electrical waves. It is demonstrated that enough level of electrical potential can be applied to the wound, further enhanced by strong capacitive coupling arising from the use of high-permittivity poly(vinylidene fluoride-trifluoroethylene):CaCu3Ti4O12 (P(VDF-TrFE):CCTO) nanocomposite. The potential clinical efficacy of the SEB is illustrated by preclinical analysis of human fibroblasts and mouse wound model, thus confirming the successful expedition of wound recovery. This work suggests a new class of wearable devices to provide ES events and its potential for extension to other conventional wound care materials and device technology.

Employment of diverse in vitro systems for analyzing multiple aspects of disease, hereditary hemorrhagic telangiectasia (HHT).

BACKGROUND: In vitro disease modeling enables translational research by providing insight into disease pathophysiology and molecular mechanisms, leading to the development of novel therapeutics. Nevertheless, in vitro systems have limitations for recapitulating the complexity of tissues, and a single model system is insufficient to gain a comprehensive understanding of a disease. RESULTS: Here we explored the potential of using several models in combination to provide mechanistic insight into hereditary hemorrhagic telangiectasia (HHT), a genetic vascular disorder. Genome editing was performed to establish hPSCs (H9) with ENG haploinsufficiency and several in vitro models were used to recapitulate the functional aspects of the cells that constitute blood vessels. In a 2D culture system, endothelial cells showed early senescence, reduced viability, and heightened susceptibility to apoptotic insults, and smooth muscle cells (SMCs) exhibited similar behavior to their wild-type counterparts. Features of HHT were evident in 3D blood-vessel organoid systems, including thickening of capillary structures, decreased interaction between ECs and surrounding SMCs, and reduced cell viability. Features of ENG haploinsufficiency were observed in arterial and venous EC subtypes, with arterial ECs showing significant impairments. Molecular biological approaches confirmed the significant downregulation of Notch signaling in HHT-ECs. CONCLUSIONS: Overall, we demonstrated refined research strategies to enhance our comprehension of HHT, providing valuable insights for pathogenic analysis and the exploration of innovative therapeutic interventions. Additionally, these results underscore the importance of employing diverse in vitro systems to assess multiple aspects of disease, which is challenging using a single in vitro system.

Revealing the pathogenesis of keloids based on the status: Active vs inactive.

Recently, the pathomechanisms of keloids have been extensively researched using transcriptomic analysis, but most studies did not consider the activity of keloids. We aimed to profile the transcriptomics of keloids according to their clinical activity and location within the keloid lesion, compared with normal and mature scars. Tissue samples were collected (keloid based on its activity (active and inactive), mature scar from keloid patients and normal scar (NS) from non-keloid patients). To reduce possible bias, all keloids assessed in this study had no treatment history and their location was limited to the upper chest or back. Multiomics assessment was performed by using single-cell RNA sequencing and multiplex immunofluorescence. Increased mesenchymal fibroblasts (FBs) was the main feature in keloid patients. Noticeably, the proportion of pro-inflammatory FBs was significantly increased in active keloids compared to inactive ones. To explore the nature of proinflammatory FBs, trajectory analysis was conducted and CCN family associated with mechanical stretch exhibited higher expression in active keloids. For vascular endothelial cells (VECs), the proportion of tip and immature cells increased in keloids compared to NS, especially at the periphery of active keloids. Also, keloid VECs highly expressed genes with characteristics of mesenchymal activation compared to NS, especially those from the active keloid center. Multiomics analysis demonstrated the distinct expression profile of active keloids. Clinically, these findings may provide the future appropriate directions for development of treatment modalities of keloids. Prevention of keloids could be possible by the suppression of mesenchymal activation between FBs and VECs and modulation of proinflammatory FBs may be the key to the control of active keloids.

Blood vessel organoids generated by base editing and harboring single nucleotide variation in Notch3 effectively recapitulate CADASIL-related pathogenesis.

Human blood vessel organoids (hBVOs) offer a promising platform for investigating vascular diseases and identifying therapeutic targets. In this study, we focused on in vitro modeling and therapeutic target finding of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), the most common form of hereditary stroke disorder caused by mutations in the NOTCH3 gene. Despite the identification of these mutations, the underlying pathological mechanism is elusive, and effective therapeutic approaches are lacking. CADASIL primarily affects the blood vessels in the brain, leading to ischemic strokes, migraines, and dementia. By employing CRISPR/Cas9 base-editing technology, we generated human induced pluripotent stem cells (hiPSCs) carrying Notch3 mutations. These mutant hiPSCs were differentiated into hBVOs. The NOTCH3 mutated hBVOs exhibited CADASIL-like pathology, characterized by a reduced vessel diameter and degeneration of mural cells. Furthermore, we observed an accumulation of Notch3 extracellular domain (Notch3ECD), increased apoptosis, and cytoskeletal alterations in the NOTCH3 mutant hBVOs. Notably, treatment with ROCK inhibitors partially restored the disconnection between endothelial cells and mural cells in the mutant hBVOs. These findings shed light on the pathogenesis of CADASIL and highlight the potential of hBVOs for studying and developing therapeutic interventions for this debilitating human vascular disorder.

Temperature impact on microbial and metabolic profiles in kimchi fermentation.

Kimchi is a traditional Korean fermented food and harbors diverse bacteria. Therefore, proper temperature management contributes to the fermentation and preservation of kimchi. In this study, we explored fermentation temperature influences the bacterial composition and metabolite variations in kimchi, employing pyrosequencing for bacterial community analysis and mass spectrometry for metabolite profiling. Elevated temperatures within the range of 10-15 °C had a significant impact on the community of lactic acid bacteria (LAB) compared to 4 °C, leading to increased bacterial diversity and richness. We observed a significant increase in Lactiplantibacillus plantarum and Latilactobacillus sakei, alongside a reduction in Lactococcus lactis, during fermentation at 10-15 °C. These changes occurred within a similar pH range across different kimchi fermentation periods. We performed a liquid extraction via the acetonitrile method, which involved the collection of kimchi samples, and performed LC-MS analysis. Our analysis revealed approximately 5000 metabolites. Notably, we observed a significant increase in metabolite counts, with 3048 metabolites increasing at 10 °C and 2853 metabolites exhibiting a similar trend at 15 °C. Metabolite analysis showed an increase in lactic and succinic acid with increased glucose and sucrose consumption at 10 and 15 °C. These results indicated that elevated temperatures significantly influenced the glycolysis and tricarboxylic acid cycle, leading to increased acidity during the fermentation process. These findings show the crucial role played by temperature in controlling the fermentation process, thereby influencing the bacterial succession and the resulting flavor and taste of the product. Therefore, proper temperature management can effectively control kimchi fermentation and yield the desired sensory properties.

Revisiting roles of mast cells and neural cells in keloid: exploring their connection to disease activity.

Background: Mast cells (MCs) and neural cells (NCs) are important in a keloid microenvironment. They might contribute to fibrosis and pain sensation within the keloid. However, their involvement in pathological excessive scarring has not been adequately explored. Objectives: To elucidate roles of MCs and NCs in keloid pathogenesis and their correlation with disease activity. Methods: Keloid samples from chest and back regions were analyzed. Single-cell RNA sequencing (scRNA-seq) was conducted for six active keloids (AK) samples, four inactive keloids (IK) samples, and three mature scar (MS) samples from patients with keloids. Results: The scRNA-seq analysis demonstrated notable enrichment of MCs, lymphocytes, and macrophages in AKs, which exhibited continuous growth at the excision site when compared to IK and MS samples (P = 0.042). Expression levels of marker genes associated with activated and degranulated MCs, including FCER1G, BTK, and GATA2, were specifically elevated in keloid lesions. Notably, MCs within AK lesions exhibited elevated expression of genes such as NTRK1, S1PR1, and S1PR2 associated with neuropeptide receptors. Neural progenitor cell and non-myelinating Schwann cell (nmSC) genes were highly expressed in keloids, whereas myelinating Schwann cell (mSC) genes were specific to MS samples. Conclusions: scRNA-seq analyses of AK, IK, and MS samples unveiled substantial microenvironmental heterogeneity. Such heterogeneity might be linked to disease activity. These findings suggest the potential contribution of MCs and NCs to keloid pathogenesis. Histopathological and molecular features observed in AK and IK samples provide valuable insights into the mechanisms underlying pain and pruritus in keloid lesions.

Effects of Baclofen on Central Paroxysmal Positional Downbeat Nystagmus.

Paroxysmal positional nystagmus frequently occurs in lesions involving the cerebellum, and has been ascribed to disinhibition and enhanced canal signals during positioning due to cerebellar dysfunction. This study aims to elucidate the mechanism of central positional nystagmus (CPN) by determining the effects of baclofen on the intensity of paroxysmal positional downbeat nystagmus due to central lesions. Fifteen patients with paroxysmal downbeat CPN were subjected to manual straight head-hanging before administration of baclofen, while taking baclofen 30 mg per day for at least one week, and two weeks after discontinuation of baclofen. The maximum slow phase velocity (SPV) and time constant (TC) of the induced paroxysmal downbeat CPN were analyzed. The positional vertigo was evaluated using an 11-point numerical rating scale (0 to 10) in 9 patients. After treatment with baclofen, the median of the maximum SPV of paroxysmal downbeat CPN decreased from 30.1°/s [interquartile range (IQR) = 19.6-39.0°/s] to 15.2°/s (IQR = 11.2-22.0°/s, Wilcoxon signed rank test, p < 0.001) with the median decrement ratio at 40.2% (IQR = 28.2-50.6%). After discontinuation of baclofen, the maximum SPV re-increased to 24.6°/s (IQR = 13.1-34.4°/s, Wilcoxon signed rank test, p = 0.001) with the median increment ratio at 23.5% (IQR = 5.2-87.9%). In contrast, the TCs of paroxysmal downbeat CPN remained unchanged at approximately 3.0 s throughout the evaluation. The positional vertigo also decreased with the medication (Wilcoxon signed rank test, p = 0.020), and remained unchanged even after discontinuation of medication (Wilcoxon signed rank test, p = 0.737). The results of this study support the prior presumption that paroxysmal CPN is caused by enhanced responses of the semicircular canals during positioning due to cerebellar disinhibition. Baclofen may be tried in symptomatic patients with paroxysmal CPN.

Exploring the influence of garlic on microbial diversity and metabolite dynamics during kimchi fermentation.

Garlic (Allium sativum) is a key ingredient in Korean cuisine, particularly in the preparation of kimchi, contributing to its flavor and taste. Garlic has been a potential resource for lactic acid bacteria (LAB) in kimchi. However, the mechanism by which it influences microbial diversity and metabolite production is unclear. This study investigated the effect of garlic on the bacterial composition of and metabolite changes in kimchi. To achieve this, four separate batches of kimchi were prepared with varying garlic concentrations (w/w): 0 %, 1 %, 2 %, and 4 %, and the bacterial communities and metabolite production were monitored. In the early stages of fermentation, the count of LAB, operational taxonomic units (OTUs), and Shannon index increased linearly with the increase in garlic content. This indicated that garlic is a rich resource and contributes to the diversity of LAB during kimchi fermentation. Compared with the kimchi samples with a lower garlic content, those with a high garlic content (≥2 %) exhibited increased abundance of Lactobacillus and Leuconostoc as well as noticeable differences in functional diversity, including carbohydrate, amino acid, and energy metabolisms. Correlation analysis between sugars, organic acids, and predominant LAB in the garlic-containing kimchi samples suggested that in kimchi samples with high garlic content, LAB played a significant role in the fermentation process by metabolizing sugars and producing organic acids. Overall, this study demonstrated that the addition of garlic has a positive impact on the bacterial diversity and metabolite production during kimchi fermentation, potentially affecting the fermentation process and flavor profile of kimchi.

Association between dairy-rich dietary pattern and metabolic dysfunction-associated steatotic liver disease: Findings from the Korean Genome and Epidemiology Study.

BACKGROUNDS: Dietary components and the development of metabolic dysfunction-associated liver disease (MASLD) are closely linked, but large-scale studies on dietary patterns and MASLD are scarce, most previous studies having focused on individual nutrients or foods rather than overall dietary patterns. Therefore, we aimed to investigate the association between dietary patterns and MASLD in Koreans. METHODS: A total of 6,052 participants from the Korean Genome and Epidemiology Study. Dietary intake was assessed using a validated Korean semiquantitative food frequency questionnaire comprising 106 food items. Principal component analysis was used to determine the major dietary patterns. Cox proportional hazard regression analysis was performed to assess the association between the incidence of MASLD and dietary patterns. RESULTS: Four major dietary patterns, namely carnivore, plant-based, dairy-rich, and starch-rich diet patterns, were identified. The carnivore, plant-based, and starch-rich diet patterns showed no significant association with incident MASLD, while the dairy-rich diet pattern was associated with a lower risk of MASLD, also showing significantly lower cumulative incidence of MASLD in the higher adherence to dairy-rich diet pattern. CONCLUSION: The dairy-rich diet pattern was significantly associated with a lower risk of MASLD in Koreans. Appropriate dietary guidance based on dietary patterns is crucial for preventing MASLD.

Knowledge and the behavioral patterns of photoprotection among Koreans with skin disease.

BACKGROUND: Photoprotection is crucial in preventing the development and progression of various skin diseases. However, patients with skin disease have limited awareness of photoprotection. We evaluated the knowledge and behavioral patterns of photoprotection among Koreans with skin diseases. METHODS: A cross-sectional study was conducted in 11 general hospitals across South Korea. The study population consisted of patients aged 19 years or older who visited dermatologic clinics for their skin diseases. A self-administered questionnaire was used to collect patient demographics, knowledge of photoprotection, and photoprotective habits. RESULTS: In this study, 1173 patients with skin cancer, hyperpigmentary disorders, hypopigmentary disorders, or other skin diseases participated. Females scored significantly higher in knowledge of photoprotection compared to males (mean score 8.4 vs. 7.8; p < .001), and younger patients (<50 years) scored higher than older patients (mean score 8.7 vs. 7.5; p < .001). Males also reported longer sun exposure times and lower usage of photoprotective measures (both p < .001). Patients with skin cancer had the lowest mean knowledge score (7.1 ± 2.6) and were less likely to use photoprotective measures compared to other groups (p < .001). In contrast, patients with hyperpigmentation actively avoided sun exposure compared with other groups (p < 0.001). CONCLUSIONS: Knowledge of photoprotection among Korean patients with skin diseases varied depending on the gender, age, and type of skin disease. Their photoprotective behaviors were inadequate, especially among males and those with skin cancer. These findings emphasize the importance of educating and tailoring photoprotection strategies for patients with skin diseases.

Assessment of hair loss and skin changes during treatment in Asian breast cancer patients: A prospective cohort study.

With the increasing number of young breast cancer (BC) patients worldwide, concerns about hair loss and skin change persist among BC survivors. This study aimed to evaluate the hair loss and skin changes in Asian BC patients and to compare them according to the treatment regimens. This study enrolled 322 patients scheduled to undergo BC surgery. Hair loss and skin changes were assessed at the following two time points: one day before surgery and 6 months after surgery. Patients who had received systemic anticancer treatment before surgery were assigned to the neoadjuvant treatment group, while patients who were scheduled to receive systemic anticancer treatment were assigned to the adjuvant treatment group. In the adjuvant treatment group, patients with taxane-based chemotherapy had significantly higher odds of increased hair loss, a higher melanin index, and an increased volume of wrinkles (p < 0.0001, p = 0.0110, and p = 0.0371, respectively). In the neoadjuvant treatment group, hair loss was reversed in most patients at 6 months after surgery. Clinicians should inform BC patients about the potential for hair loss and skin changes and provide supportive care to mitigate the effects on the patients' quality of life.

Pleomorphic dermal sarcoma presenting in a child with Li-Fraumeni syndrome: A case report and review of the literature.

Pleomorphic dermal sarcoma (PDS) is an uncommon malignant soft-tissue tumor that occurs mostly in elderly patients, with only 5% of cases occurring in children. However, pediatric patients with Li-Fraumeni syndrome (LFS) can develop several types of cancer, particularly sarcomas. Here, we describe a young LFS patient who presented with early-onset PDS and review the literature.

Cognitive dysfunction following finasteride use: a disproportionality analysis of the global pharmacovigilance database.

BACKGROUND: Finasteride is commonly prescribed for androgenic alopecia and benign prostatic hyperplasia. However, concerns regarding its safety have been growing as cases of cognitive dysfunction have been reported. METHODS: A disproportionality analysis was conducted on data collected between 1967 and 2022 to explore the potential association. Cases of cognitive dysfunction associated with finasteride use were identified, and the reporting odds ratio (rOR) was calculated with 95% confidence intervals to determine the strength of the association between the two variables. Sensitivity analyses were conducted to account for confounding by indication. RESULTS: Among the 54,766 cases of adverse events reported for finasteride use, 1,624 (2.97%) were associated with cognitive dysfunction. The study found a significant disproportionality for cognitive dysfunction related to finasteride use (rOR 5.43, 95% CI 5.17-5.71). Most cases were considered serious (65.83%), with no signs of recovery (58.37%). Sensitivity analyses showed that patients younger than 45 years (rOR 7.30, 95% CI 6.39-8.35) and those with alopecia (rOR 5.52, 95% CI 5.15-5.91) reported more cognitive dysfunctions than their counterparts. CONCLUSION: This study showed an increased reporting of cognitive dysfunction associated with finasteride use, especially among younger alopecia patients. Finasteride should be prescribed with caution, especially to younger alopecia patients.

Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice (Oryza sativa L.) using multiple GAPIT models.

This study employed a joint strategy high-density SNP Chip DNA markers and multiple Genome Association and Prediction Integrated Tool (GAPIT) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and random model Circulating Probability Uniform (FarmCPU), General Linear Model (GLM), and Settlement of Mixed Linear Model (MLM) Under Progressively Exclusive Relationship (SUPER)], to investigate novel genetic factors controlling mesocotyl elongation and seedling emergence for direct-seeded rice. Genotype data (230,526 SNP Chip DNA makers) of 117 doubled haploid lines (derived from a cross between 93-11 (Oryza sativa L. ssp. indica) and Milyang352 (O. sativa L. ssp. japonica) were used to perform a Genome-Wide Association Study (GWAS). Results revealed the association between five (5) topmost significant SNP markers, of which number two [AX-155741269, Chr2: 15422406 bp, and AX-155200917, Chr7: 23814085 bp, explaining 37.5% and 13.8% of the phenotypic variance explained (PVE)] are linked to the mesocotyl elongation loci, while three (AX-282097034 and AX-283652873, Chr9: 9882817 bp and 1023383 bp, PVE 64.5%, and 20.2%, respectively, and AX-154356231, Chr1: 17413989 bp, PVE 21.1%) are tightly linked to the loci controlling seedling emergence. The qMEL2-1 and qSEM9-1 are identified as major QTLs explaining 37.5% and 64.5% of the PVE for mesocotyl elongation and seedling emergence, respectively. The AX-282097034 (Chr9: 9882817 bp) was co-detected by four GAPIT models (BLINK, FarmCPU, SUPER, and GLM), while AX-155741269 was co-detected by BLINK and SUPER. Furthermore, a high estimated heritability (Mesocotyl elongation: h2 = 0.955; seedling emergence: h2 = 0.863; shoot length: h2 = 0.707) was observed. Genes harbored by qMEL2-1 and qSEM9-1 have interesting annotated molecular functions that could be investigated through functional studies to uncover their roles during mesocotyl elongation and seedling emergence events in rice. Furthermore, the presence of genes encoding transcription factors, growth- and stress response, or signaling-related genes would suggest that mesocotyl elongation and seedling emergence from deep direct-seeded rice might involve an active signaling cascade and transport of molecules, which could be elucidated through functional analysis. Likewise, genomic selection analysis suggested markers useful for downstream marker-assisted selection (MAS).

Rice (Oryza sativa L.) Grain Size, Shape, and Weight-Related QTLs Identified Using GWAS with Multiple GAPIT Models and High-Density SNP Chip DNA Markers.

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]-High-Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs). Data show that parental lines (Ilpum and Tung Tin Wan Hein 1, TTWH1, Oryza sativa L., ssp. japonica and indica, respectively) exhibited divergent phenotypes for all analyzed grain traits), which was reflected in their derived population. GWAS results revealed the association between seven SNP Chip makers and QTLs for grain length, co-detected by all GAPIT models on chromosomes (Chr) 1-3, 5, 7, and 11, were qGL1-1BFSG (AX-95918134, Chr1: 3,820,526 bp) explains 65.2-72.5% of the phenotypic variance explained (PVE). In addition, qGW1-1BFSG (AX-273945773, Chr1: 5,623,288 bp) for grain width explains 15.5-18.9% of PVE. Furthermore, BLINK or FarmCPU identified three QTLs for grain thickness independently, and explain 74.9% (qGT1Blink, AX-279261704, Chr1: 18,023,142 bp) and 54.9% (qGT2-1Farm, AX-154787777, Chr2: 2,118,477 bp) of the observed PVE. For the grain length-to-width ratio (LWR), the qLWR2BFSG (AX-274833045, Chr2: 10,000,097 bp) explains nearly 15.2-32% of the observed PVE. Likewise, the major QTL for thousand-grain weight (TGW) was detected on Chr6 (qTGW6BFSG, AX-115737727, 28,484,619 bp) and explains 32.8-54% of PVE. The qTGW6BFSG QTL coincides with qGW6-1Blink for grain width and explained 32.8-54% of PVE. Putative candidate genes pooled from major QTLs for each grain trait have interesting annotated functions that require functional studies to elucidate their function in the control of grain size, shape, or weight in rice. Genome selection analysis proposed makers useful for downstream marker-assisted selection based on genetic merit of RILs.