Diverse Panel Research Articles

Genome-wide association of an organic naked barley diversity panel identified quantitative trait loci for disease resistance.

Foliar fungal diseases are a major limitation in organic naked barley (Hordeum vulgare L.) production. The lack of conventional fungicides in organic systems increases reliance on genetic resistance. We evaluated the severity of barley stripe rust (Puccinia striiformis f.sp. hordei Westend), leaf rust (Puccina hordei sp. hordei), spot blotch (Cochliobolus sativus, anamorph Bipolaris sorokiniana (S. Ito & Kurib.) Drechsler ex Dastur), and scald (Rhynchosporium commune Zaffarano, McDonald and Linde sp. November) on a naked barley diversity panel of 350 genotypes grown in 13 environments to identify quantitative trait loci associated with disease resistance. Genome-wide association analyses across and within environments found 10 marker trait associations for barley stripe rust, four marker trait associations for leaf rust, one marker trait association for scald, and five marker trait associations for spot blotch. Structure analysis identified six Ward groups based on genotypic diversity. Resistance to susceptible allele ratios were high for stripe rust and spot blotch, moderate for leaf rust, and low for scald. Combined phenotypic analysis values for each disease overlayed by a principal component analysis found distinct resistance and susceptibility patterns for barley stripe rust and scald. Most significant marker trait associations were previously identified in the literature, providing confirmation and potential new sources of disease resistance for genetic improvement of naked barley germplasm.

The Missing Voices, an exploration of what healthcare-related research would matter to Global Ethnic Majority Women in Aberdeenshire, Scotland

Abstract Introduction In multicultural communities, such as the UK, published evidence has indicated that patients from marginalised backgrounds experience healthcare inequality and inequity with regards to accessibility and safety.1 The lack of appropriate ethnic representation in healthcare-related research, has been identified as a potential causation of some of these disparities and poorer health outcomes.2,3 The focus of this project was the marginalised communities identified by the NIHR to have poorer health outcomes, such as Global Ethnic Majority (GEM) women. Aim To explore what healthcare research matters to marginalised communities with a focus on lived and perceived experiences on access to healthcare for GEM women in Aberdeen city and Aberdeenshire, Scotland. Methods This pilot project captured real world data through an inclusive community engagement approach of reaching within rather than reaching out. A framework of 5Cs (Connect, Collaborate, Consult, Co-create and Circulate) was used to establish a diverse panel of ten GEM women. All panel members had a passion for equality and wellbeing as well as diverse lived experiences. The method used to establish the panel is presented elsewhere. Based on a review of literature, open-ended, flexible, thought-provoking questions for the discussions were developed and circulated to all panel members for approval. These questions were used to guide both in-person and virtual open discussions with aforementioned stakeholders to capture narratives and perspectives around barriers and facilitators to equitable healthcare access in the area. As the public members were research partners and not participants, no ethical approval was required as advised by a professor of pharmacy research and the school’s ethics convenor. The project had three main objectives. This submission will only report on objective three that aimed to Identify and prioritise research questions relating to equitable access to healthcare and the needs of marginalised minority ethnic communities. Results The objective was met. A list of emergent themes from the pre-panel questions and a list of panel-approved research questions were devised with a focus on access to healthcare. The emergent themes were around accessibility and equity of maternal/reproductive healthcare, lack of early screening for high-risk GEM groups and culturally appropriate approaches to mental healthcare. Solution focused recommendations included the design of an inclusive healthcare curriculum, compulsory EDI and cultural competency training for healthcare professionals who practice in diverse communities, additional screening programmes tailored to specific GEM groups based on prevalence and risk factors and the development of localised culturally appropriate and inclusive community programmes, especially for those who support new immigrants. Mistrust and lack of inclusive language were mentioned as potential barriers to participating in research. Discussion / Conclusion This pilot offered the historically under-represented and usually silent communities an equal voice within a trusting and collaborative environment. Over ten years after the enaction of the UK Equality Act (2010) inequity in healthcare access and poor outcomes are still evident. The outcomes of this small pilot study highlight that GEM-specific projects should be driven by that community.

Fine mapping of QGPC.caas-7AL for grain protein content in bread wheat.

A major stable QTL, QGPC.caas-7AL, for grain protein content of wheat, was narrowed down to a 1.82-Mb inter on chromosome 7AL, and four candidate genes were predicated. Wheat grain protein content (GPC) is important for end-use quality. Identification of genetic loci for GPC is helpful to create new varieties with good processing quality and nutrients. Zhongmai 578 (ZM578) and Jimai 22 (JM22) are two elite wheat varieties with different contents of GPC. In the present study, 262 recombinant inbred lines (RILs) derived from a cross between ZM578 and JM22 were used to map the GPC with high-density wheat Illumina iSelect 50K single-nucleotide polymorphism (SNP) array. Seven quantitative trait loci (QTLs) were identified for GPC on chromosomes 3AS, 3AL, 3BS, 4AL, 5BS, 5DL and 7AL by inclusive composite interval mapping, designated as QGPC.caas-3AS, QGPC.caas-3AL, QGPC.caas-3BS, QGPC.caas-4AL, QGPC.caas-5BS, QGPC.caas-5DL and QGPC.caas-7AL, respectively. Among these, alleles for increasing GPC at QGPC.caas-3AS, QGPC.caas-3BS, QGPC.caas-4AL and QGPC.caas-7AL loci were contributed by ZM578, whereas those at the other three loci were from JM22. The stable QTL QGPC.caas-7AL was fine mapped to a 1.82-Mb physical interval using secondary populations from six heterozygous recombinant plants obtained by selfing a residual RIL. Four genes were predicted as candidates of QGPC.caas-7AL based on sequence polymorphism and expression patterns. The near-isogenic lines (NILs) with the favorable allele at the QGPC.caas-7AL locus increased Farinograph stability time, Extensograph extension area, extensibility and maximum resistance by 19.6%, 6.3%, 6.0% and 20.3%, respectively. Kompetitive allele-specific PCR (KASP) marker for QGPC.caas-7AL was developed and validated in a diverse panel of 166 Chinese wheat cultivars. These results provide further insight into the genetic basis of GPC, and the fine-mapped QGPC.caas-7AL will be an attractive target for map-based cloning and marker-assisted selection in wheat breeding programs.

Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa).

This study aimed to broaden applicability of KASP for Oryza sativa across diverse genotypes through incorporation of ambiguous (degenerate) bases into their primer designs and to validate 4000 of them for genotyping applications. A bioinformatics pipeline was used to compare 129 rice genomes from 89 countries with the indica reference genome R498 and generate ∼1.6 million KASP designs for the more common variants between R498 and the other genomes. Of the designs, 98,238 were for predicted functional markers. Up to five KASP each for 1024 breeder-selected loci were assayed in a panel of 178 diverse rice varieties, generating 3366 validated KASP. The 84% success rate was within the normal range for KASP demonstrating that the ambiguous bases do not compromise efficacy. The 3366-trait-specific marker panel was applied for population structure analysis in the diversity panel and resolved them into four expected groups. Target variations in thirteen of the genome sequences used for designs were compared with the corresponding KASP genotypes of other accessions of the same thirteen varieties in the diversity panel. There was agreement across 12 varieties for 79% of markers. Ten varieties had high agreement (>88%) but a variety selected from a landrace had only 46.5% agreement. Breeders can now search for the validated KASP and >1 million so-far untested designs across three alternative reference genomes (including Niponbare MSU7), search for designs proximal to previously published SSR markers and retrieve the target variations in 129 rice genomes plus their genomic locations with +/-25 bp flanking sequences.

The sugary enhancer1 (se1) Allele Is Associated with Significant Decreases in Carotenoids and Tocotrienols in Yellow (Y1) sugary1 (su1) Sweet Corn

A distinctive phenotype of homozygous sugary enhancer1 (se1) sweet corn (Zea mays) inbreds and hybrids is a light-yellow color in mature kernels. Carotenoid pigments contribute to yellow endosperm color in maize and are of nutritional importance in the human diet along with the related tocochromanols, the E vitamins. Tocochromanols, including both tocopherols and tocotrienols, are antioxidants important in human nutrition and cardiovascular health. Effects of the presence of sugary enhancer1 allele on carotenoid and tocochromanol levels in homozygous su1, Y1 endosperm were evaluated in the Wisconsin Sweet Corn Diversity Panel. Although population structure was present in the panel, the majority of variation in carotenoid levels was explained by genotype at the se1 locus. se1 was associated with significant decreases in the amount of lutein (34%) and zeaxanthin (36%) and decreases of tocotrienols by 12% to 65%. There were no significant differences in β-carotene and tocopherol levels between the two groups. Given that the biosynthesis pathways for carotenoids and tocochromanols are well defined, these differences in carotenoids and tocotrienols between su1Se1 and su1se1 inbreds point to a broader role of se1 alleles in metabolic pathways beyond endosperm starch production.

4CMenB Breadth of Immune Response, Immunogenicity, and Safety: Results from a Phase 3 Randomized, Controlled, Observer Blind Study in Adolescents and Young Adults

Abstract Background Meningococcal serogroup B (MenB) strains are highly diverse. Breadth of immune response for the MenB vaccine, 4CMenB, administered at 0-2, 0-6, or 0-2-6 months, was demonstrated by endogenous complement-human serum bactericidal antibody (enc-hSBA) assay against an epidemiologically-relevant panel of 110 MenB strains. Methods In a phase 3 trial, 3651 healthy 10–25 year-old participants were randomized 5:5:9:1 to receive 4CMenB (0-6 schedule), 4CMenB (0-2-6 schedule), investigational MenABCWY vaccine, or control MenACWY-CRM vaccine. The primary objectives were to evaluate safety and demonstrate breadth of immune response by enc-hSBA assay against the MenB strain panel using test-based (percentage of samples without bactericidal activity against strains after 4CMenB versus control vaccination) and responder-based (percentage of participants whose post-vaccination sera kill ≥70% strains) approaches. Success was demonstrated with two-sided 97.5% confidence interval (CI) lower limit >65%. Immunogenicity was assessed by traditional hSBA assay against four indicator strains. Results Breadth of immune response (test-based) was 78.7% (97.5% CI 77.2%–80.1%), 81.8% (80.4%–83.1%), 83.2% (81.9%–84.4%) for the 0-2, 0-6, and 0-2-6 schedules, respectively, and (responder-based) 84.8% (81.8%–87.5%), 89.8% (87.2%–92.0%), and 93.4% (91.2%–95.2%), respectively. No clinically relevant differences in immunogenicity were observed across schedules. 4CMenB was well tolerated. Conclusions The two-dose (0-2, 0-6) 4CMenB schedules met pre-defined criteria for success for both breadth of immune response endpoints against a diverse MenB strain panel, had comparable immunogenicity, and safety in line with the established 4CMenB safety profile. The three-dose schedule provided no additional immunological benefit, supporting use of the 4CMenB 0-2 schedule. Clinical Trial Registration NCT04502693.

Biochemical analysis of EGFR exon20 insertion variants insASV and insSVD and their inhibitor sensitivity

Somatic mutations in the epidermal growth factor receptor (EGFR) are a major cause of non-small cell lung cancer. Among these structurally diverse alterations, exon 20 insertions represent a unique subset that rarely respond to EGFR tyrosine kinase inhibitors (TKIs). Therefore, there is a significant need to develop inhibitors that are active against this class of activating mutations. Here, we conducted biochemical analysis of the two most frequent exon 20 insertion variants, V769_D770insASV (insASV) and D770_N771insSVD (insSVD) to better understand their drug sensitivity and resistance. From kinetic studies, we found that EGFR insASV and insSVD are similarly active, but have lower Km, ATP values compared to the L858R variant, which contributes to their lack of sensitivity to 1st-3rd generation EGFR TKIs. Biochemical, structural, and cellular studies of a diverse panel of EGFR inhibitors revealed that the more recently developed compounds BAY-568, TAS6417, and TAK-788 inhibit EGFR insASV and insSVD in a mutant-selective manner, with BAY-568 being the most potent and selective versus wild-type (WT) EGFR. Cocrystal structures with WT EGFR reveal the binding modes of each of these inhibitors and of poziotinib, a potent but not mutantselective inhibitor, and together they define interactions shared by the mutant-selective agents. Collectively, our results show that these exon20 insertion variants are not inherently inhibitor resistant, rather they differ in their drug sensitivity from WT EGFR. However, they are similar to each other, indicating that a single inhibitor should be effective for several of the diverse exon 20 insertion variants.

GWAS for identification of genomic regions and candidate genes in vegetable crops.

Genome-wide association Studies (GWAS), initially developed for human genetics, have been highly effective in plant research, particularly for vegetable crops. GWAS is a robust tool for identifying genes associated with key traits such as yield, nutritional value, disease resistance, adaptability, and bioactive compound biosynthesis. Unlike traditional methods, GWAS does not require prior biological knowledge and can accurately pinpoint loci, minimizing false positives. The process involves developing a diverse panel, rigorous phenotyping and genotyping, and sophisticated statistical analysis using various models and software tools. By scanning the entire genome, GWAS identifies specific loci or single nucleotide polymorphisms (SNPs) linked to target traits. When a causal SNP variant is not directly genotyped, GWAS identifies SNPs in linkage disequilibrium (LD) with the causal variant, mapping the genetic interval. The method begins with careful panel selection, phenotyping, and genotyping, controlling for environmental effects and utilizing Best Linear Unbiased Prediction (BLUP). High-correlation, high-heritability traits are prioritized. Various genotyping methods address confounders like population structure and kinship. Bonferroni correction (BC) prevents false positives, and significant associations are shown in Manhattan plots. Candidate genes are identified through LD analysis and fine mapping, followed by functional validation. GWAS offers critical insights for enhancing vegetable crop breeding efficiency and precision, driving breakthroughs through advanced methods.

Autosomal recessive VWA1-related disorder: comprehensive analysis of phenotypic variability and genetic mutations.

A newly identified subtype of hereditary axonal motor neuropathy, characterized by early proximal limb involvement, has been discovered in a cohort of 34 individuals with biallelic variants in von Willebrand factor A domain-containing 1 (VWA1). This study further delineates the disease characteristics in a cohort of 20 individuals diagnosed through genome or exome sequencing, incorporating neurophysiological, laboratory and imaging data, along with data from previously reported cases across three different studies. Newly reported clinical features include hypermobility/hyperlaxity, axial weakness, dysmorphic signs, asymmetric presentation, dystonic features and, notably, upper motor neuron signs. Foot drop, foot deformities and distal leg weakness followed by early proximal leg weakness are confirmed to be initial manifestations. Additionally, this study identified 11 novel VWA1 variants, reaffirming the 10 bp insertion-induced p.Gly25ArgfsTer74 as the most prevalent disease-causing allele, with a carrier frequency of ∼1 in 441 in the UK and Western European population. Importantly, VWA1-related pathology may mimic various neuromuscular conditions, advocating for its inclusion in diverse gene panels spanning hereditary neuropathies to muscular dystrophies. The study highlights the potential of lower quality control filters in exome analysis to enhance diagnostic yield of VWA1 disease that may account for up to 1% of unexplained hereditary neuropathies.

The collaborative cross mouse for studying the effect of host genetic background on memory impairments due to obesity and diabetes.

Over the past few decades, a threefold increase in obesity and type 2 diabetes (T2D) has placed a heavy burden on the health-care system and society. Previous studies have shown correlations between obesity, T2D, and neurodegenerative diseases, including dementia. It is imperative to further understand the relationship between obesity, T2D, and cognitive deficits. This investigation tested and evaluated the cognitive impact of obesity and T2D induced by high-fat diet (HFD) and the effect of the host genetic background on the severity of cognitive decline caused by obesity and T2D in collaborative cross (CC) mice. The CC mice are a genetically diverse panel derived from eight inbred strains. Our findings demonstrated significant variations in the recorded phenotypes across different CC lines compared to the reference mouse line, C57BL/6J. CC037 line exhibited a substantial increase in body weight on HFD, whereas line CC005 exhibited differing responses based on sex. Glucose tolerance tests revealed significant variations, with some lines like CC005 showing a marked increase in area under the curve (AUC) values on HFD. Organ weights, including brain, spleen, liver, and kidney, varied significantly among the lines and sexes in response to HFD. Behavioral tests using the Morris water maze indicated that cognitive performance was differentially affected by diet and genetic background. Our study establishes a foundation for future quantitative trait loci mapping using CC lines and identifying genes underlying the comorbidity of Alzheimer's disease (AD), caused by obesity and T2D. The genetic components may offer new tools for early prediction and prevention.

Genetic loci associated with sorghum drought tolerance in multiple environments and their sensitivity to environmental covariables.

Climate change can limit yields of naturally resilient crops, like sorghum, challenging global food security. Agriculture under an erratic climate requires tapping into a reservoir of flexible adaptive loci that can lead to lasting yield stability under multiple abiotic stress conditions. Domesticated in the hot and dry regions of Africa, sorghum is considered a harsh crop, which is adapted to important stress factors closely related to climate change. To investigate the genetic basis of drought stress adaptation in sorghum, we used a multi-environment multi-locus genome-wide association study (MEML-GWAS) in a subset of a diverse sorghum association panel (SAP) phenotyped for performance both under well-watered and water stress conditions. We selected environments in Brazil that foreshadow agriculture where both drought and temperature stresses coincide as in many tropical agricultural frontiers. Drought reduced average grain yield (Gy) by up to 50% and also affected flowering time (Ft) and plant height (Ph). We found 15 markers associated with Gy on all sorghum chromosomes except for chromosomes 7 and 9, in addition to loci associated with phenology traits. Loci associated with Gy strongly interacted with the environment in a complex way, while loci associated with phenology traits were less affected by G × E. Studying environmental covariables potentially underpinning G × E, increases in relative humidity and evapotranspiration favored and disfavored grain yield, respectively. High temperatures influenced G × E and reduced sorghum yields, with a ~ 100kgha-1 average decrease in grain yield for each unit increase in maximum temperature between 29 and 38°C. Extreme G × E for sorghum stress resilience poses an additional challenge to breed crops for moving, erratic weather conditions.

Characterization of Collaborative Cross mouse founder strain CAST/EiJ as a novel model for lethal COVID-19

Mutations in SARS-CoV-2 variants of concern (VOCs) have expanded the viral host range beyond primates, and a few other mammals, to mice, affording the opportunity to exploit genetically diverse mouse panels to model the broad spectrum of responses to infection in patient populations. Here we surveyed responses to VOC infection in genetically diverse Collaborative Cross (CC) founder strains. Infection of wild-derived CC founder strains produced a broad range of viral burden, disease susceptibility and survival, whereas most other strains were resistant to disease despite measurable lung viral titers. In particular, CAST/EiJ, a wild-derived strain, developed high lung viral burdens, more severe lung pathology than seen in other CC strains, and a dysregulated cytokine profile resulting in morbidity and mortality. These inbred mouse strains may serve as a valuable platform to evaluate therapeutic countermeasures against severe COVID-19 and other coronavirus pandemics in the future.

Genomic prediction of cereal crop architectural traits using models informed by gene regulatory circuitries from maize.

Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well positioned to expedite genetic gain of plant architectural traits since they are typically highly heritable. Additionally, the adaptation of genomic prediction models to query predictive abilities of markers tagging certain genomic regions could shed light on the genetic architecture of these traits. Here, we leveraged transcriptional networks from a prior study that contextually described developmental progression during tassel and leaf organogenesis in maize (Zea mays) to inform genomic prediction models for architectural traits. Since these developmental processes underlie tassel branching and leaf angle, 2 important agronomic architectural traits, we tested whether genes prioritized from these networks quantitatively contribute to the genetic architecture of these traits. We used genomic prediction models to evaluate the ability of markers in the vicinity of prioritized network genes to predict breeding values of tassel branching and leaf angle traits for 2 diversity panels in maize and diversity panels from sorghum (Sorghum bicolor) and rice (Oryza sativa). Predictive abilities of markers near these prioritized network genes were similar to those using whole-genome marker sets. Notably, markers near highly connected transcription factors from core network motifs in maize yielded predictive abilities that were significantly greater than expected by chance in not only maize but also closely related sorghum. We expect that these highly connected regulators are key drivers of architectural variation that are conserved across closely related cereal crop species.

Genetic architecture of phosphorus-use-efficiency across diverse environmental conditions: Insights from maize elite and landrace lines.

Phosphorus is an essential nutrient for all crops. Thus, a better understanding of the genetic control of phosphorus-use-efficiency reflected in physiological, developmental, and morphological traits and its environmental plasticity is required to establish the basis for maintaining or enhancing yield while making agriculture more sustainable. In this study, we utilized a diverse panel of maize (Zea mays L.), including 398 elite and landrace lines, phenotyped across three environments and two phosphorus fertilization treatments. We performed genome-wide association mapping for 13 traits, including phosphorus uptake and allocation, that showed a strong environment-dependency in their expression. Our results highlight the complex genetic architecture of phosphorus-use-efficiency as well as the substantial differences between the evaluated genetic backgrounds. Despite harboring more of the identified QTL, almost all of the favourable alleles from landraces were found to be present in at least one of the two elite heterotic groups. Notably, we also observed trait-specific genetic control even among biologically related characteristics, as well as a substantial plasticity of the genetic architecture of several traits in response to the environment and P fertilization. Collectively, our work illustrates the difficulties in improving phosphorus-use-efficiency but also presents possible solutions for the future contribution of plant breeding to improve the phosphorus cycle.

Guidance for unbiased predictive information for healthcare decision-making and equity (GUIDE): considerations when race may be a prognostic factor.

Clinical prediction models (CPMs) are tools that compute the risk of an outcome given a set of patient characteristics and are routinely used to inform patients, guide treatment decision-making, and resource allocation. Although much hope has been placed on CPMs to mitigate human biases, CPMs may potentially contribute to racial disparities in decision-making and resource allocation. While some policymakers, professional organizations, and scholars have called for eliminating race as a variable from CPMs, others raise concerns that excluding race may exacerbate healthcare disparities and this controversy remains unresolved. The Guidance for Unbiased predictive Information for healthcare Decision-making and Equity (GUIDE) provides expert guidelines for model developers and health system administrators on the transparent use of race in CPMs and mitigation of algorithmic bias across contexts developed through a 5-round, modified Delphi process from a diverse 14-person technical expert panel (TEP). Deliberations affirmed that race is a social construct and that the goals of prediction are distinct from those of causal inference, and emphasized: the importance of decisional context (e.g., shared decision-making versus healthcare rationing); the conflicting nature of different anti-discrimination principles (e.g., anticlassification versus antisubordination principles); and the importance of identifying and balancing trade-offs in achieving equity-related goals with race-aware versus race-unaware CPMs for conditions where racial identity is prognostically informative. The GUIDE, comprising 31 key items in the development and use of CPMs in healthcare, outlines foundational principles, distinguishes between bias and fairness, and offers guidance for examining subgroup invalidity and using race as a variable in CPMs. This GUIDE presents a living document that supports appraisal and reporting of bias in CPMs to support best practice in CPM development and use.

Genetic architecture of Cercospora leaf spot response in table beet with implications for other Beta vulgaris crop types

AbstractTable beet (Beta vulgaris subsp. vulgaris) production is threatened by the fungal disease Cercospora leaf spot (CLS). Infections are common across table beet's closest relatives, including Swiss chard, sugar beet, and fodder beet (all B. v. subsp. vulgaris). This study was conducted to characterize the genetic architecture underlying CLS response in table beet. A secondary objective was to test whether CLS‐associated loci in table beet perform similarly across B. vulgaris crops. A diversity panel comprised of 168 table beet accessions and with an additional 70 accessions from all close relatives of table beet was screened for CLS response in replicated and inoculated field trials. Results from a genome‐wide association study of additive effects revealed seven quantitative trait loci mapped to chromosomes 1, 3, 7, and 9 to explain 30% of the phenotypic variation for CLS response in table beet. When the performance of these loci was compared between a table beet background and a background of Swiss chard, sugar beet, and fodder beet, two loci exhibited significantly different responses. Among the B. vulgaris crops, these loci may be unique to table beet germplasm and could be useful for the improvement of CLS resistance in other crop types. For the improvement of CLS resistance in table beet, this study identified the cultivar Winter Keeper as a potentially valuable source of resistance. The architecture of CLS response points to recurrent selection and backcross methods as effective strategies for the improvement of CLS resistance in table beet.

AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software.

Admixture is a fundamental process that has shaped levels and patterns of genetic variation in human populations. RFMIX version 2 (RFMIX2) utilizes a robust modeling approach to identify the genetic ancestries in admixed populations. However, this software does not have a built-in method to visually summarize the results of analyses. Here, we introduce the AncestryGrapher toolkit, which converts the numerical output of RFMIX2 into graphical representations of global and local ancestry (i.e., the per-individual ancestry components and the genetic ancestry along chromosomes, respectively). To demonstrate the utility of our methods, we applied the AncestryGrapher toolkit to visualize the global and local ancestry of individuals in the North African Mozabite Berber population from the Human Genome Diversity Panel (HGDP). Our results showed that the Mozabite Berbers derived their ancestry from the Middle East, Europe, and sub-Saharan Africa (global ancestry). We also found that the population origin of ancestry varied considerably along chromosomes (local ancestry). For example, we observed variance in local ancestry in the genomic region on chromosome 2 containing the regulatory sequence in the MCM6 gene associated with lactase persistence (LP), a human adaptive trait tied to the cultural development of adult milk consumption. Overall, the AncestryGrapher toolkit facilitates the exploration, interpretation, and reporting of ancestry patterns in human populations. The AncestryGrapher toolkit is free and open source on https://github.com/alisi1989/RFmix2-Pipeline-to-plot. Supplementary data are available at Bioinformatics online.

Allelic variants confer Arabidopsis adaptation to small regional environmental differences.

Natural populations of Arabidopsis thaliana provide powerful systems to study the adaptation of wild plant species. Previous research has predominantly focused on global populations or accessions collected from regions with diverse climates. However, little is known about the genetics underlying adaptation in regions with mild environmental clines. We have examined a diversity panel consisting of 192 A. thaliana accessions collected from the Netherlands, a region with limited climatic variation. Despite the relatively uniform climate, we identified evidence of local adaptation within this population. Notably, semidwarf accessions, due to mutation of the GIBBERELLIC ACID REQUIRING 5 (GA5) gene, occur at a relatively high frequency near the coast and these displayed enhanced tolerance to high wind velocities. Additionally, we evaluated the performance of the population under iron deficiency conditions and found that allelic variation in the FE SUPEROXIDE DISMUTASE 3 (FSD3) gene affects tolerance to low iron levels. Moreover, we explored patterns of local adaptation to environmental clines in temperature and precipitation, observing that allelic variation at LA RELATED PROTEIN 1C (LARP1c) likely affects drought tolerance. Not only is the genetic variation observed in a diversity panel of A. thaliana collected in a region with mild environmental clines comparable to that in collections sampled over larger geographic ranges but it is also sufficiently rich to elucidate the genetic and environmental factors underlying natural plant adaptation.

Optimizing Siglec-8-Directed Immunotherapy for Eosinophilic and Mast Cell Disorders

Background/Objective: Current treatments for eosinophilic and mast cell disorders are often ineffective. One promising target to improve outcomes is sialic acid-binding immunoglobulin-like lectin-8 (Siglec-8). As limitations, there are few Siglec-8 monoclonal antibodies (mAbs) available to date, and Siglec-8-directed treatments have so far primarily focused on unconjugated mAbs, which may be inadequate, especially against mast cells. Methods: Here, we used transgenic mice to raise a diverse panel of fully human mAbs that either recognize the V-set domain, membrane-distal C2-set domain, or membrane-proximal C2-set domain of full-length Siglec-8 as a basis for novel therapeutics. Results: All mAbs were efficiently internalized into Siglec-8-expressing cells, suggesting their potential to deliver cytotoxic payloads. Tool T cell-engaging bispecific antibodies (BiAbs) and chimeric antigen receptor (CAR)-modified natural killer (NK) cells using single-chain variable fragments from Siglec-8 mAbs showed highly potent cytolytic activity against Siglec-8-positive cells even in cases of very low target antigen abundance, whereas they elicited no cytolytic activity against Siglec-8-negative target cells. Siglec-8V-set-directed T cell-engaging BiAbs and Siglec-8V-set-directed CAR-modified NK cells induced substantially greater cytotoxicity against cells expressing an artificial smaller Siglec-8 variant containing only the V-set domain than cells expressing full-length Siglec-8, consistent with the notion that targeting membrane-proximal epitopes enhances effector functions of Siglec-8 antibody-based therapeutics. Indeed, unconjugated Siglec-8C2-set mAbs, Siglec-8C2-set-directed T cell-engaging BiAbs, and Siglec-8C2-set-directed CAR-modified NK cells showed high antigen-specific cytolytic activity against Siglec-8-positive human cell lines and primary patient eosinophils. Conclusions: Together, these data demonstrate Siglec-8-directed immunotherapies can be highly potent, supporting their further development for eosinophilic and mast cell disorders.

K-mer genome-wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel.

Access to broad genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) can facilitate development of improved varieties with increased yield, improved market quality traits, and enhanced disease resistance. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and bean common mosaic virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer (short nucleotide subsequence) GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results-albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers could be mapped to the reference genome. Thus, to determine the genetic context of cis-associated k-mers, we generated draft whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible.