Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages.

Rice (Oryza sativa) is an important staple crop to address the Hidden Hunger problem not only in Asia but also in Africa where rice is fast becoming an important source of calories. The brown rice (whole grain with bran) is known to be more nutritious due to elevated mineral composition. The genetics underlying brown rice ionome (sum total of such mineral composition) remains largely unexplored. Hence, we conducted a comprehensive study to dissect the genetic architecture of the brown rice ionome. We used genome-wide association studies, gene set analysis, and targeted association analysis for 12 micronutrients in the brown rice grains. A diverse panel of 300 resequenced indica accessions, with more than 1.02 million single nucleotide polymorphisms, was used. We identified 109 candidate genes with 5-20% phenotypic variation explained for the 12 micronutrients and identified epistatic interactions with multiple micronutrients. Pooling all candidate genes per micronutrient exhibited phenotypic variation explained values ranging from 11% to almost 40%. The key donor lines with larger concentrations for most of the micronutrients possessed superior alleles, which were absent in the breeding lines. Through gene regulatory networks we identified enriched functional pathways for central regulators that were detected as key candidate genes through genome-wide association studies. This study provided important insights on the ionome variations in rice, on the genetic basis of the genome-ionome relationships and on the molecular mechanisms underlying micronutrient signatures.

Natural variation of OsML1, a mitochondrial transcription termination factor, contributes to mesocotyl length variation in rice.

Mesocotyl length (ML) is a crucial factor in determining the establishment and yield of rice planted through dry direct seeding, a practice that is increasingly popular in rice production worldwide. ML is determined by the endogenous and external environments, and inherits as a complex trait. To date, only a few genes have been cloned, and the mechanisms underlying mesocotyl elongation remain largely unknown. Here, through a genome-wide association study using sequenced germplasm, we reveal that natural allelic variations in a mitochondrial transcription termination factor, OsML1, predominantly determined the natural variation of ML in rice. Natural variants in the coding regions of OsML1 resulted in five major haplotypes with a clear differentiation between subspecies and subpopulations in cultivated rice. The much-reduced genetic diversity of cultivated rice compared to the common wild rice suggested that OsML1 underwent selection during domestication. Transgenic experiments and molecular analysis demonstrated that OsML1 contributes to ML by influencing cell elongation primarily determined by H2 O2 homeostasis. Overexpression of OsML1 promoted mesocotyl elongation and thus improved the emergence rate under deep direct seeding. Taken together, our results suggested that OsML1 is a key positive regulator of ML, and is useful in developing varieties for deep direct seeding by conventional and transgenic approaches.

SpeedFlower: a comprehensive speed breeding protocol for indica and japonica rice.

To increase rice yields and feed billions of people, it is essential to enhance genetic gains. However, the development of new varieties is hindered by longer generation times and seasonal constraints. To address these limitations, a speed breeding facility has been established and a robust speed breeding protocol, SpeedFlower is developed that allows growing 4-5 generations of indica and/or japonica rice in a year. Our findings reveal that a high red-to-blue (2R > 1B) spectrum ratio, followed by green, yellow and far-red (FR) light, along with a 24-h long day (LD) photoperiod for the initial 15 days of the vegetative phase, facilitated early flowering. This is further enhanced by 10-h short day (SD) photoperiod in the later stage and day and night temperatures of 32/30 °C, along with 65% humidity facilitated early flowering ranging from 52 to 60 days at high light intensity (800 µmol m-2 s-1). Additionally, the use of prematurely harvested seeds and gibberellic acid treatment reduced the maturity duration by 50%. Further, SpeedFlower was validated on a diverse subset of 198 rice accessions from 3K RGP panel encompassing all 12 distinct groups of Oryza sativa L. classes. Our results confirmed that using SpeedFlower one generation can be achieved within 58-71 days resulting in 5.1-6.3 generations per year across the 12 sub-groups. This breakthrough enables us to enhance genetic gain, which could feed half of the world's population dependent on rice.

Steady agronomic and genetic interventions are essential for sustaining productivity in intensive rice cropping.

Intensive systems with two or three rice (Oryza sativa L.) crops per year account for about 50% of the harvested area for irrigated rice in Asia. Any reduction in productivity or sustainability of these systems has serious implications for global food security. Rice yield trends in the world's longest-running long-term continuous cropping experiment (LTCCE) were evaluated to investigate consequences of intensive cropping and to draw lessons for sustaining production in Asia. Annual production was sustained at a steady level over the 50-y period in the LTCCE through continuous adjustment of management practices and regular cultivar replacement. Within each of the three annual cropping seasons (dry, early wet, and late wet), yield decline was observed during the first phase, from 1968 to 1990. Agronomic improvements in 1991 to 1995 helped to reverse this yield decline, but yield increases did not continue thereafter from 1996 to 2017. Regular genetic and agronomic improvements were sufficient to maintain yields at steady levels in dry and early wet seasons despite a reduction in the yield potential due to changing climate. Yield declines resumed in the late wet season. Slower growth in genetic gain after the first 20 y was associated with slower breeding cycle advancement as indicated by pedigree depth. Our findings demonstrate that through adjustment of management practices and regular cultivar replacement, it is possible to sustain a high level of annual production in irrigated systems under a changing climate. However, the system was unable to achieve further increases in yield required to keep pace with the growing global rice demand.

Deep learning generated lower extremity radiographic measurements are adequate for quick assessment of knee angular alignment and leg length determination.

PURPOSE: Angular and longitudinal deformities of leg alignment create excessive stresses across joints, leading to pain and impaired function. Multiple measurements are used to assess these deformities on anteroposterior (AP) full-length radiographs. An artificial intelligence (AI) software automatically locates anatomical landmarks on AP full-length radiographs and performs 13 measurements to assess knee angular alignment and leg length. The primary aim of this study was to evaluate the agreements in LLD and knee alignment measurements between an AI software and two board-certified radiologists in patients without metal implants. The secondary aim was to assess time savings achieved by AI. METHODS: The measurements assessed in the study were hip-knee-angle (HKA), anatomical-tibiofemoral angle (aTFA), anatomical-mechanical-axis angle (AMA), joint-line-convergence angle (JLCA), mechanical-lateral-proximal-femur-angle (mLPFA), mechanical-lateral-distal-femur-angle (mLDFA), mechanical-medial-proximal-tibia-angle (mMPTA), mechanical-lateral-distal-tibia- angle (mLDTA), femur length, tibia length, full leg length, leg length discrepancy (LLD), and mechanical axis deviation (MAD). These measurements were performed by two radiologists and the AI software on 164 legs. Intraclass-correlation-coefficients (ICC) and Bland-Altman analyses were used to assess the AI's performance. RESULTS: The AI software set incorrect landmarks for 11/164 legs. Excluding these cases, ICCs between the software and radiologists were excellent for 12/13 variables (11/13 with outliers included), and the AI software met performance targets for 11/13 variables (9/13 with outliers included). The mean reading time for the AI algorithm and two readers, respectively, was 38.3, 435.0, and 625.0 s. CONCLUSION: This study demonstrated that, with few exceptions, this AI-based software reliably generated measurements for most variables in the study and provided substantial time savings.

Lost genome segments associate with trait diversity during rice domestication.

BACKGROUND: DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. RESULTS: In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. CONCLUSIONS: We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Unearthing old rice germplasm, illuminating a new way to improvement.

Rice germplasm collections contain vast reserves of genetic diversity but remain understudied. This Commentary highlights the effectiveness of mining genetic resources from germplasm as a means to overcome current yield constraints, using clustered-spikelet rice as an example.

Functional outcomes are preserved in adult acetabular dysplasia with radiographic evidence of lumbosacral spine anomalies: an investigation in hip-spine syndrome.

PURPOSE: Acetabular dysplasia (AD) is a debilitating condition which results in impaired hip function, leading to hip-spine syndrome with anomalies identifiable on plain radiographs. However, no study to date has investigated the association between radiographic spine anomalies and functional outcomes in AD. We hypothesize that AD patients with radiographic evidence of lumbar spine anomalies are associated with decreased function in comparison to those without such radiographic findings. PATIENTS AND METHODS: One hundred thirty-five hips underwent a full four-view hip radiograph series, and two observers analyzed hip and spine variables using standard radiographs and obtained Castellvi grade, assessment of spondylolisthesis, and L4-S1 interpedicular distance. A comprehensive hip questionnaire was administered which included Harris Hip Score (HHS) and Hip Disability and Osteoarthritis Outcome Score (HOOS) to assess patient function. Correlations between HHS and HOOS and radiographic spinal measurements were calculated, and p-values were corrected for multiple comparison using the Holm's method. RESULTS: Out of 135 patients, 119 were female (88.1%) and 16 were male (11.9%). Average age of presentation was 34.2 years, and average BMI was 26. There was no statistically significant correlation between Castellvi grade, presence of spondylolisthesis, or L4-S1 interpedicular distance and the patient-reported outcome measures HHS or HOOS. Conversely, a significant correlation was observed between Femoro-Epiphyseal Acetabular Roof (FEAR) index and HOOS of the contralateral hip (correlation coefficient = 0.38, adjusted p = 0.03) and Tönnis angle of AD severity and HHS of the contralateral hip (correlation coefficient = - 0.33, adjusted p = 0.04). CONCLUSION: Severity of spinal anomalies measured by Castellvi grade and spondylolisthesis in patients with AD was not associated with decreased patient function in the ipsilateral diseased hip. To our knowledge, this is the first study to date to report the relationship between radiographically identifiable lumbosacral abnormalities and hip function in AD.

Image quality improvement and motion degradation reduction in shoulder MR imaging: comparison of BLADE and rectilinear techniques at 3-Tesla scanning.

OBJECTIVE: MR imaging of joints, particularly shoulder, requires a high degree of spatial resolution to ascertain anatomy and pathology. Unfortunately, motion artifacts can reduce the clinical quality of the examinations. BLADE sequence reduces motion degradation improving overall diagnostic imaging quality. The objective was to compare standard, rectilinear k-space coverage turbo spin echo (TSE), and BLADE sequences. MATERIAL AND METHODS: Over a 4-month period, fifty-seven consecutive patients (22 males, 35 females; mean age: 48.5 years, range: 23-64 years) were scanned using traditional intermediate-weighted spin echo and BLADE sequences. Qualitative evaluation was performed by three musculoskeletal fellowship trained radiologists, each with more than 5 years of experience. Image sequences were evaluated using a Likert scale for each of the following five categories: motion degradation, ghosting/phase misregistration artifacts, star/radial encoding artifacts, fat suppression quality, and overall diagnostic quality. Additionally, image sequences were evaluated for signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) using manually drawn regions of interest (ROI) analysis. RESULTS: Ghosting and phase artifacts were lower within BLADE sequence while streak artifacts were higher (p < 0.001). Image fat suppression, tendon and labral appearances, and the overall SNR and CNR were comparable on both sequences (p > 0.05). CONCLUSION: Addition of BLADE reduces motion degradation and improves overall diagnostic imaging quality. Application of BLADE in patient scans suspected of motion artifacts can reduce the frequency of repeat imaging in patients with claustrophobia or those where motion is a concern. By reducing overall imaging time and call backs, it could reduce the cost burden to patients and healthcare system.

Does Preoperative Activity Level Affect Postoperative Outcomes Following Total Hip Arthroplasty?

BACKGROUND: Many patients electing to undergo total hip arthroplasty (THA) value continuing active lifestyles when considering treatment options. Addressing these concerns requires evaluating the effect of preoperative activity level on patient-reported outcomes and improvement following THA. METHODS: Three hundred thirty-five patients (368 hips) who underwent THA with a minimum 6-month (mean 533 ± 271 days) follow-up completed preoperative and postoperative University of California, Los Angeles (UCLA) activity score along with various patient-reported measures of function, pain, and mental state. Preoperative UCLA score divided patients into inactive, mild, and active groups. Analysis of covariance controlling for age, sex, body mass index, surgical approach, implant, bilateral cases, conversions, and follow-up time evaluated differences among groups for postoperative outcomes with subsequent Tukey-Kramer pairwise comparisons. RESULTS: Mildly active patients (73:139 male:female) had better postoperative outcomes than inactive patients (40:70 male:female) for UCLA score, EuroQol Visual Analog Scale (EQVAS), Hip Outcome Score (HOS), 12-item Short-Form (SF-12) Physical, and Visual Analog Pain Scale (average/now/worst) (P values <0.001/<0.001/<0.001/<0.001/0.003/<0.001/<0.001). Active patients (32:14 male:female) had better postoperative outcomes than inactive patients for UCLA score, EQVAS, HOS, SF-12 Physical, and Visual Analog Pain Scale Worst (P values <0.001/0.024/0.001/0.001/0.017). No postoperative outcome differences existed between active and mild patients. Inactive patients displayed greater outcome improvements than mildly active patients for UCLA score, Harris Hip Score, and International Hip Outcome Tool (P values <0.001/<0.001/0.013) and active patients for UCLA score, EQVAS, HOS, International Hip Outcome Tool, and SF-12 Physical (P values <0.001/0.008/0.013/0.022/0.004). CONCLUSIONS: Inactive patients achieve greater measure improvements following THA. Active patients achieve better absolute outcomes than inactive patients; however, increasing activity levels do not incrementally improve patient-reported outcome measures. Patients similarly improve pain and mental health regardless of activity level.

Know your way around acute unenhanced CT during global iodinated contrast crisis: a refresher to ED radiologists.

Due to a contrast shortage crisis resulting from the decreased supply of iodinated contrast agents, the American College of Radiology (ACR) has issued a guidance statement followed by memoranda from various hospitals to preserve and prioritize the limited supply of contrast. The vast majority of iodinated contrast is used by CT, with a minority used by vascular and intervention radiology, fluoroscopy, and other services. A direct consequence is a paradigm shift to large volume unenhanced CT scans being utilized for acute and post traumatic patients in EDs, an uncharted territory for most radiologists and trainees. This article provides radiological diagnostic guidance and a pictorial example through systematic review of common unenhanced CT findings in the acute setting.

OsTPR boosts the superior grains through increase in upper secondary rachis branches without incurring a grain quality penalty.

To address the future food security in Asia, we need to improve the genetic gain of grain yield while ensuring the consumer acceptance. This study aimed to identify novel genes influencing the number of upper secondary rachis branches (USRB) to elevate superior grains without compromising grain quality by studying the genetic variance of 310 diverse O. sativa var. indica panel using single- and multi-locus genome-wide association studies (GWAS), gene set analyses and gene regulatory network analysis. GWAS of USRB identified 230 significant (q-value < 0.05) SNPs from chromosomes 1 and 2. GWAS targets narrowed down using gene set analyses identified large effect association on an important locus LOC_Os02g50790/LOC_Os02g50799 encoding a nuclear-pore anchor protein (OsTPR). The superior haplotype derived from non-synonymous SNPs identified in OsTPR was specifically associated with increase in USRB with superior grains being low chalk. Through haplotype mining, we further demonstrated the synergy of offering added yield advantage due to superior allele of OsTPR in elite materials with low glycaemic index (GI) property. We further validated the importance of OsTPR using recombinant inbred lines (RILs) population by introgressing a superior allele of OsTPR into elite materials resulted in raise in productivity in high amylose background. This confirmed a critical role for OsTPR in influencing yield while maintaining grain and nutritional quality.

A drought-responsive rice amidohydrolase is the elusive plant guanine deaminase with the potential to modulate the epigenome.

Drought stress in plants causes differential expression of numerous genes. One of these differentially expressed genes in rice is a specific amidohydrolase. We characterized this amidohydrolase gene on the rice chromosome 12 as the first plant guanine deaminase (OsGDA1). The biochemical activity of GDA is known from tea and coffee plants where its catalytic product, xanthine, is the precursor for theine and caffeine. However, no plant gene that is coding for GDA is known so far. Recombinant OsGDA1 converted guanine to xanthine in vitro. Measurement of guanine and xanthine contents in the OsGDA1 knockout (KO) line and in the wild type Tainung 67 rice plants also suggested GDA activity in vivo. The content of cellular xanthine is important because of its catabolic products allantoin, ureides, and urea which play roles in water and nitrogen stress tolerance among others. The identification of OsGDA1 fills a critical gap in the S-adenosyl-methionine (SAM) to xanthine pathway. SAM is converted to S-adenosyl-homocysteine (SAH) and finally to xanthine. SAH is a potent inhibitor of DNA methyltransferases, the reduction of which leads to increased DNA methylation and gene silencing in Arabidopsis. We report that the OsGDA1 KO line exhibited a decrease in SAM, SAH and adenosine and an increase in rice genome methylation. The OsGDA1 protein phylogeny combined with mutational protein destabilization analysis suggested artificial selection for null mutants, which could affect genome methylation as in the KO line. Limited information on genes that may affect epigenetics indirectly requires deeper insights into such a role and effect of purine catabolism and related genetic networks.

Systems-based rice improvement approaches for sustainable food and nutritional security.

KEY MESSAGE: An integrated research approach to ensure sustainable rice yield increase of a crop grown by 25% of the world's farmers in 10% of cropland is essential for global food security. Rice, being a global staple crop, feeds about 56% of the world population and sustains 40% of the world's poor. At ~ $200 billion, it also accounts for 13% of the annual crop value. With hunger and malnutrition rampant among the poor, rice research for development is unique in global food and nutrition security. A systems-based, sustainable increase in rice quantity and quality is imperative for environmental and biodiversity benefits. Upstream 'discovery' through biotechnology, midstream 'development' through breeding and agronomy, downstream 'dissemination and deployment' must be 'demand-driven' for 'distinct socio-economic transformational impacts'. Local agro-ecology and livelihood nexus must drive the research agenda for targeted benefits. This necessitates sustained long-term investments by government, non-government and private sectors to secure the future food, nutrition, environment, prosperity and equity status.

Structured Reporting in Musculoskeletal Radiology.

Musculoskeletal (MSK) radiologists are predominantly consultants in the service departments of health care. Unlike the manufacturing industry, quality controls are difficult to institute in a service industry and more variability is expected. Structured reporting is a unique way to institute quality standards, and by using the checklist approach with uniform terminology, it can lead to more homogeneity and consistency of reporting, concise lexicon use within and across practices, minimization of errors, enhancement of divisional and departmental branding, improvement of interdisciplinary communications, and future data mining. We share our experience from more than a decade of structured reporting in the domain of MSK radiology, our practice standards, and how reporting has evolved in our MSK practice. Further discussions include future directions aided by machine learning approaches with augmented reality and the possibility of virtual fellowship and training using consistent lexicons and structured reporting.

Photosynthesis research: a model to bridge fundamental science, translational products, and socio-economic considerations in agriculture.

Despite impressive success in molecular physiological understanding of photosynthesis, and preliminary evidence on its potential for quantum shifts in agricultural productivity, the question remains of whether increased photosynthesis, without parallel fine-tuning of the associated processes, is enough. There is a distinct lack of formal socio-economic impact studies that address the critical questions of product profiling, cost-benefit analysis, environmental trade-offs, and technological and market forces in product acceptability. When a relatively well understood process gains enough traction for translational value, its broader scientific and technical gap assessment, in conjunction with its socio-economic impact assessment for success, should be a prerequisite. The successes in the upstream basic understanding of photosynthesis should be integrated with a gap analysis for downstream translational applications to impact the farmers' and customers' lifestyles and livelihoods. The purpose of this review is to assess how the laboratory, the field, and the societal demands from photosynthesis could generate a transformative product. Two crucial recommendations from the analysis of the state of knowledge and potential ways forward are (i) the formulation of integrative mega-projects, which span the multistakeholder spectrum, to ensure rapid success in harnessing the transformative power of photosynthesis; and (ii) stipulating spatiotemporal, labour, and economic criteria to stage-gate deliverables.

Concepts in U.S. Food and Drug Administration Regulation of Artificial Intelligence for Medical Imaging.

OBJECTIVE. Although extensive attention has been focused on the enormous potential of artificial intelligence (AI) technology, a major question remains: how should this fundamentally new technology be regulated? The purpose of this article is to provide an overview of the pathways developed by the U.S. Food and Drug Administration to regulate the incorporation of AI in medical imaging. CONCLUSION. AI is the new wave of innovation in health care. The technology holds promising applications to revolutionize all aspects of medicine.

A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues.

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.

RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.

BACKGROUND: As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources. RESULTS: We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs. CONCLUSIONS: RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.

Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome.

Identifying high-impact, rare genetic variants associated with specific traits is crucial for crop improvement. The 3,010 rice genome (3K RG) dataset offers a valuable resource for discovering genomic regions with potential applications in crop breeding. We used Extreme Trait GWAS (Et-GWAS), employing bulk pooling and allele frequency measurement to efficiently extract rare variants from the 3K RG. This innovative approach facilitates the detection of associations between genetic variants and target traits, concentrating and quantifying rare alleles. In our study, on grain yield under drought stress, Et-GWAS successfully identified five key genes (OsPP2C11, OsK5.2, OsIRO2, OsPEX1, and OsPWA1) known for enhancing yield under drought. In addition, we examined the overlap of our results with previously reported qDTY-QTLs and observed that OsUCH1 and OsUCH2 genes were located within qDTY2.2 We compared Et-GWAS with conventional GWAS, finding it effectively capturing most candidate genes associated with the target trait. Validation with resistant starch showed similar results. To enhance user-friendliness, we developed a GUI for Et-GWAS; https://et-gwas.shinyapps.io/Et-GWAS/.