Genetic Variation Research Articles

Cytogenetic and molecular identification of novel wheat-Elymus sibiricus addition lines with resistance to leaf rust and the presence of leaf pubescence trait

IntroductionEmerging new races of leaf rust (Puccinia triticina Eriks) are threatening global wheat (Triticum aestivum L.) production. Identifying additional resistance genes from all available gene pools is crucial to expanding wheat resistance to these virulent leaf rust races. Siberian wild rye (Elymus sibiricus L.) possesses numerous beneficial traits that can be valuable in wheat improvement. Three new wheat-E. sibiricus addition lines, O27-2 (BC8), O27-3 (BC12) and O193-3 (BC12), were developed through a backcrossing scheme in this study, using leaf rust field evaluations, molecular marker assays and cytogenetic analysis. MethodsThese three lines were derived from progeny of the bread wheat cultivar ‘Obriy’ (2n = 6x = 42, AABBDD) and partial octoploid amphiploid wheat-E. sibiricus (2n = 8x = 56, AABBDDStSt). Results and discussionThe lines (O27-2, O27-3 and O193-3) demonstrated strong specific leaf pubescence (hairiness) and resistance at the adult stage to a local population of leaf rust races. The response to leaf rust in these three lines significantly differed from that of the Lr24 gene, providing evidence for a distinct resistance mechanism associated with the 3St chromosome. This study is the first to report the transfer of an E. sibiricus chromosome into wheat that confers leaf rust resistance. Molecular marker analysis and genomic in situ hybridization confirmed that lines O27-2, O27-3 and O193-3 each possess one pair of E. sibiricus 3St chromosomes. The resistance gene was determined to be on the additional alien chromosome in these lines. Molecular markers (Xwmc221, Lr29F18, Sr24/Lr24) confirmed that the lines O27-2, O27-3, and O193-3 each contain a pair of E. sibiricus 3St chromosomes carrying leaf rust resistance genes. These findings demonstrate that the E. sibiricus 3St chromosome carries the leaf rust resistance gene and that the O27-2, O27-3, and O193-3 lines can serve as novel germplasm sources for introducing this resistance into wheat breeding programs. This study contributes to broadening the genetic diversity of resistance genes available for combating leaf rust in wheat.

Genetic Variability in Fusarium Wilt Resistant BC2F1 Lines of Yard Long Bean (Vigna unguiculata subsp. sesquipedalis (L.) Verdcourt) Variety Githika for Yield and its Related Traits

Yardlong bean is a highly popular and profitable vegetable traditionally cultivated in the humid tropics of Kerala and is an inexpensive source of vegetable protein. Developing sustainable host plant resistance mechanisms, such as using the backcross method to introduce single-gene resistance into susceptible crop varieties, is crucial for reducing losses due to Fusarium wilt. In the present study Thirty-five resistant backcross progenies (BC2F1) of Yardlong Bean (Vigna unguiculata subsp. sesquipedalis (L.) Verdcourt) variety Githika were evaluated for various genetic parameters for yield and its related traits using Completely Randomized Design at Department of Genetics and Plant Breeding, College of Agriculture, Vellayani, Trivandrum. High phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) were observed for traits such as the number of pods per plant, pod weight, pod yield per plant, crude protein content. High Heritability(H) and High Genetic advance as percent mean (GAM) were observed for traits such as Number of pods per plant, Pod weight, Pod length, Number of seeds per pod, Pod Yield per plant, Crude fibre and Crude protein content. This significantly suggest that additive gene action is predominant in these traits and low reliance by environmental factors on these traits, making such character a good candidate for direct selection. The study helps in assessing genetic variability to identify traits as well as lines with maximum similarity with recurrent parent which could be used for further crop improvement program.

Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations.

The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations.

Why some ‘inbreeder’ species among mostly outbreeders? conifer examples, a postulate, and research agenda

AbstractBreeding systems vary widely in plants, but mostly cluster towards outbreeding or inbreeding extremes. Conifers, which are woody and generally long-lived perennials, are almost all classical outbreeders, but include occasional species characterised as inbreeders. The latter include some very narrow endemics, but narrow endemics include outbreeders. The inbreeders show high self-fertility, minimal inbreeding depression, typically low DNA polymorphism, and modest functional genetic variation, but self-fertilisation rates can be low. Seven such species are reviewed. It is widely (if often tacitly) assumed that inbreeders arise through severe population bottlenecks. It is proposed, more specifically, that inbreeders could arise through recessive resistance alleles of large effects being expressed, during biotic crises, through some inbreeding in the typically mixed mating systems of outbreeders. Such a crisis might produce not only a population bottleneck but also the conditions for recessive alleles to operate beneficially to make inbreeding advantageous. Avenues for probing the recessive-alleles hypothesis are: quantitative modelling to identify what are plausible conditions, examining genomic signatures of inbreeders, and empirical observation. Appropriate modelling appears challenging, as does seeking informative genomic signatures. Empirical observation, however, may be facilitated by biotic crises promoted by current global migration of pathogens and animal pests.

Abstract 4137846: Smooth muscle expression of RNA editing enzyme ADAR1 controls vascular integrity and progression of atherosclerosis

Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 ( IFIH1 ) and stimulation of an interferon stimulated gene (ISG) response. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing to be an important mechanism of coronary artery disease (CAD) risk. Here, we provide a crucial link between observations in human genetics and mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that ISG induction occurs in SMC phenotypic modulation, implicating MDA5 activation. Through culture of human coronary artery SMCs, generation of a conditional SMC specific Adar1 deletion mouse model on a pro-atherosclerosis background, and with incorporation of single cell RNA sequencing cellular profiling, we further show that Adar1 controls SMC phenotypic state, is required to maintain vascular integrity, and controls progression of atherosclerosis and vascular calcification. Our data implicates MDA5 activation to occur in SMC phenotypic modulation and accelerates formation of chondromyocytes in a distinct cellular lineage trajectory — indicating a cell type and context specific requirement of RNA editing. Through this work, we describe a fundamental new mechanism of CAD, where RNA editing and sensing of dsRNA in a cell type and context specific mechanism mediates disease progression, bridging our understanding of human genetics and disease causality.

CYP2C gene polymorphisms in North African populations.

Cytochrome P450 is a superfamily of genes generating hemoproteins that metabolize foreign chemicals as well as endogenous compounds, such as steroids. The human CYP2C genes (CYP2C8, CYP2C9, CYP2C18, CYP2C19) cluster on chromosome 10 and metabolize many clinically useful drugs. CYP2C19 and CYP2C9 have been the most studied while CYP2C8 has been studied less frequently. CYP2C18 has been relatively ignored until recently but its importance has begun to be recognized. We studied the genotypes of 7 pharmacogenetic markers in 3 CYP2C genes: CYP2C19 (rs12248560), CYP2C9 (rs4918758, rs1799853), and CYP2C8 (rs10509681, rs11572103, rs1058930, rs11572080), in one Libyan population and 7 Tunisian populations. Five of the 7 SNPs are in exons and have functional consequences while one intronic SNP is considered to be in close proximity to a regulatory region because of the many studies that report associations with metabolic effects. We carried out principal component analysis (PCA) on the North African populations and 83 other populations from the 1000 Genomes Project and Kidd Laboratory. The geographic clustering observed via PCA was more pronounced when considering multi-SNP haplotype frequencies. This studyreveals the intermediate position of North Africans between Europeans and Asians and the varied dissimilarities with other world regions. The genetic variation observed within and between geographic regions have implications for drug metabolism and adverse individual responses to medical treatments.

Functional and Practical Insights Into the Genetic Basis of Takayasu Arteritis.

Takayasu arteritis (TAK) is a rare vasculitis characterized by inflammation of large arteries. Although the exact etiology of TAK remains unclear, a genetic predisposition to the disease has been established. Large-scale genetic studies have significantly contributed to the identification of genetic variation associated with immune-mediated diseases. To date, five genome-wide association studies (GWAS) have been performed in TAK, identifying multiple genetic susceptibility loci across the genome. Here, we summarize the major findings from GWAS in TAK and provide an in silico functional evaluation of the associated loci (P < 5 × 10-8) and variants in high linkage disequilibrium with them (r2 > 0.8). By exploring gene expression and chromatin interaction data, we identified candidate causal genes in TAK, some of them with well-known functional implications. The analysis of transcription factor motifs within TAK-associated loci revealed enrichment of the STAT and RUNX families, both characterized by their role in immune functions and inflammatory responses. The enrichment in biological processes in susceptibility loci confirmed the involvement of specific immune-related pathways in TAK. Further, we devised and calculated a cumulative genetic risk score for TAK and confirmed differences in genetic risk for the disease among ancestries. Finally, we provide a practical guide to communicate genetic information for TAK to patients and families.

Multimodal scanning of genetic variants with base and prime editing.

Mutational scanning connects genetic variants to phenotype, enabling the interrogation of protein functions, interactions and variant pathogenicity. However, current methodologies cannot efficiently engineer customizable sets of diverse genetic variants in endogenous loci across cellular contexts in high throughput. Here, we combine cytosine and adenine base editors and a prime editor to assess the pathogenicity of a broad spectrum of variants in the epithelial growth factor receptor gene (EGFR). Using pooled base editing and prime editing guide RNA libraries, we install tens of thousands of variants spanning the full coding sequence of EGFR in multiple cell lines and assess the role of these variants in tumorigenesis and resistance to tyrosine kinase inhibitors. Our EGFR variant scan identifies important hits, supporting the robustness of the approach and revealing underappreciated routes to EGFR activation and drug response. We anticipate that multimodal precision mutational scanning can be applied broadly to characterize genetic variation in any genetic element of interest at high and single-nucleotide resolution.

Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a poxvirus substrate mimic

Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that mimic the natural substrate, eIF2α, and inhibit PKR activity. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface’s critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3, encoded by the vaccinia virus gene K3L. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.

Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a poxvirus substrate mimic.

Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that mimic the natural substrate, eIF2α, and inhibit PKR activity. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface's critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3, encoded by the vaccinia virus gene K3L. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.

Hereditary alpha tryptasemia: elevated tryptase, female sex, thyroid disorders, and anaphylaxis

IntroductionThe clinical significance of elevated baseline serum tryptase (BST) in the absence of mast cell disorders or allergic reactions has long been unclear. Recently, a genetic variation of the TPSAB1 gene, which among others encodes for alpha tryptase, has been reported and named hereditary alpha tryptasemia (HaT). HaT has been linked to various manifestations, including severe allergic reactions. However, clinical studies are limited. In this study, we aimed to determine HaT prevalence and characterize its clinical manifestations in patients at a specialized allergy center.MethodsFrom January 2022 to December 2023, patients with elevated BST at least once were screened for HaT at the outpatient clinic. A control group included patients with a history of anaphylaxis undergoing specific Hymenoptera immunotherapy. TPSAB1 copy numbers, BST levels, and clinical parameters were assessed and analyzed.ResultsOf 47 patients with elevated BST (≥11.4 µg/L), 93% showed increased TPSAB1 copy numbers. Individuals diagnosed with HaT displayed a BST range between 12.3 and 28.4 µg/L, with 84.1% associated with TPSAB1 duplication and 15.9% with triplication. HaT predominated in women (86.4%) and was associated with thyroid disease (27.3%). Over half had a history of anaphylaxis (54.5%), which was mainly low-grade.DiscussionIn patients with elevated BST but no mastocytosis, the most likely cause of elevated BST was an increase in the copy number of the TPSAB1 gene. A heightened risk of anaphylaxis should be considered. Further research is needed to explore the predominance of women and the emerging link with thyroid disease.

Abstract 4127792: Age-stratified Monogenic and Polygenic Contributions for Atrial Fibrillation in the All of Us Research Program

Background: Rare and common genetic variation both contribute to atrial fibrillation (AF), but the effects may not be uniform across ages. The All of Us Research Program contains whole-genome sequencing of 100,574 adult participants with electronic health records. Hypothesis: Rare genetic variants are associated with early-onset AF; common genetic variants are associated with late-onset AF. Aims: To quantify the diagnostic yield provided by rare and common genetic variation in AF across age. Methods: The clinical, monogenic, and polygenic contributions to AF were assessed in a cross-sectional group of participants in the NIH-funded All of Us Research Program, stratified by three age groups: &lt;45 years (n=22,290), 45-60 years (n= 26,805), &gt;60 years (n=51,659). Variant discovery was performed for pathogenic or likely pathogenic (P/LP) variants among 145 candidate cardiac genes with dominant inheritance for cardiomyopathy and arrhythmia. A previously established polygenic risk score (PRS) was calculated. After adjusting for known clinical factors, multivariable analysis quantified the associations between monogenic and polygenic factors versus AF status in each age group. Results: There were 100,574 participants: 7,811 with AF and 92,763 without AF. The presence of ≥1 P/LP variant(s) were associated with AF across all age groups, with stronger associations in the age &lt;45 group (OR 2.3 [95% CI 1.4-4.1]) compared older groups (OR 1.5 [95% CI 1.1-2.1] in age 45-60, and OR 1.4 [95% CI 1.2-1.7] in age &gt;60). In contrast, PRS was not associated with AF in participants &lt;45 years (OR 1.02 [95% CI 0.88-1.17]) but was associated with AF in the older groups: OR 1.54 [95% CI 1.31-1.80] in age 45-60 and OR 1.49 [95% CI 1.40-1.59] for age &gt;60. Overall, clinical risk factors are highly associated with AF (AUC 0.84 [0.83-0.85]); adding polygenic and monogenic factors contribute only marginal improvement (AUC 0.86 [0.85-0.87]). Conclusion: In this cross-sectional dataset, monogenic and polygenic factors have opposite associations with AF. Monogenic variants are associated with early-onset AF, whereas PRS has no association with AF at younger ages. Clinical risk factors continue to explain the majority of the variation in AF status.

Quantifying the impact of vaccination on transmission and diversity of influenza A variants in pigs.

Global evolutionary dynamics of influenza A virus (IAV) are fundamentally driven by the extent of virus diversity generated, transmitted, and shaped in individual hosts. How vaccination affects the degree of IAV genetic diversity that can be transmitted and expanded in pigs is unknown. To evaluate the effect of vaccination on the transmission of genetically distinct IAV variants and their diversity after transmission in pigs, we examined the whole genome of IAV recovered from the nasal cavities of pigs vaccinated with different influenza immunization regimens after being infected simultaneously by H1N1 and H3N2 IAVs using a seeder pig model. We found that the seeder pigs harbored more diversified virus populations than the contact pigs. Among contact pigs, H3N2 and H1N1 viruses recovered from pigs vaccinated with a single dose of an unmatched modified live vaccine generally accumulated more extensive genetic mutations than non-vaccinated pigs. Furthermore, the non-sterilizing immunity elicited by the single-dose-modified live vaccine may have exerted positive selection on H1 antigenic regions as we detected significantly higher nonsynonymous but lower synonymous evolutionary rates in H1 antigenic regions than non-antigenic regions. In addition, we observed that the vaccinated pigs shared significantly less proportion of H3N2 variants with seeder pigs than unvaccinated pigs. These results indicated that vaccination might reduce the impact of transmitted influenza variants on the overall diversity of IAV populations harbored in recipient pigs and that within-host genetic selection of IAV is more likely to occur in pigs vaccinated with improperly matched vaccines.IMPORTANCEUnderstanding how vaccination shapes the diversity of influenza variants that transmit and propagate among pigs is essential for designing effective IAV surveillance and control programs. Current knowledge about the transmission of IAV variants has primarily been explored in humans during natural infection. However, how immunity elicited by improperly matched vaccines affects the degree of IAV genetic diversity that can be transmitted and expanded in pigs at the whole-genome level is unknown. We analyzed IAV sequences from samples collected daily from experimentally infected pigs vaccinated with various protocols in a field-represented IAV co-infection model. We found that vaccine-induced non-sterilizing immunity might promote genetic variation on the IAV genome and drive positive selection at antigenic sites during infection. In addition, a smaller proportion of H3N2 viral variants were shared between seeder pigs and vaccinated pigs, suggesting the influence of vaccination on shaping the virus genomic diversity in recipient pigs during the transmission events.

Genetic variability for growth and yield traits of Ethiopian highland barley landraces on acid soils, in the choke water shade, Ethiopia

Genetic variability for growth and yield traits of Ethiopian highland barley landraces on acid soils, in the choke water shade, Ethiopia

Morphological and agronomic evaluation of short-cycle native maize varieties (Zea mays L.)

Objective: The objective of this study was to analyze the morphological composition and agronomic behavior of five varieties of Zea mays L. Two Zapalote Chico, two Zapalote Grande and an improved variety (V-424) which are characterized by having a short vegetative cycle Desing/methodology/approach: The maize varieties evaluated were sourced from various locations within the municipality, with explicit consent from the producers, who provided the seeds for the study. Four native cultivars (treatments) were selected from the Zapalote Chico and Zapalote Grande races and one improved and open-pollinated maize variety (V-424 or Tuxpeño Precoz) as a control, released by INIFAP. The local farmers assigned the common names to the evaluated maize varieties, except for V-424. The varieties were distributed in a randomized block design with four replications, resulting in a total of 20 experimental units. Each unit consisted of four furrows, each measuring 4 meters in length. Results: The findings of this study on native short-cycle maize varieties in Chiapas have significant implications at the genetic, social, cultural, economic, and environmental levels. Each of these aspects provides crucial guidance for decision-making related to the utilization, management, and conservation of local maize varieties. A key outcome of this study is the recognition of native maize as a repository of essential genes for food security in rural areas. Short-cycle landraces exhibit unique genetic adaptations that enable them to thrive under the specific agroclimatic conditions of the Frailesca region in Chiapas. Limitations on study/implications: none Findings/conclusions: The native maize varieties exhibited significant genetic variability across the variables under consideration. The Zapalote Chico race is characterized by its favourable characteristics, as recognized by farmers, including early maturity, drought resistance, lodging resistance, and resistance to the fall armyworm. These qualities make it a promising candidate for future research and for inclusion in genetic improvement programs, whether conventional or participatory. It is crucial to continue promoting agroecological inputs with the goal of fostering the development of resilient agroecosystems and, consequently, enhancing the well-being of farmers and the conservation of native maize reservoirs.

An Examination of Ethiopian Data on the Coffee Value Chain from a Systemic Perspective

Ethiopia&amp;apos;s principal export crop is coffee. Currently, one of the most profitable exports for nations in East Africa, including Ethiopia, Uganda, Kenya, and Tanzania, is coffee. Ethiopia is recognized as the source and major hub of Arabica coffee varietal. Global coffee production is insignificant, with over 70 nations and approximately 25 million growers producing coffee. Seventeen percent of coffee producers worldwide are from Ethiopia. Ethiopia, which produces 4.46 percent of the world&amp;apos;s coffee, is the world&amp;apos;s fifth-largest producer, behind only Brazil, Vietnam, Colombia, and Indonesia. the biggest and most prolific grower in Africa, making up around 43.15% of the continent. Ethiopian coffee varieties vary greatly in terms of genetic variety. The nation has also captured the attention of the world because of its inherent. More than 60% of the world&amp;apos;s coffee is produced by the top three countries—Brazil, Vietnam, and Colombia together. Ethiopia is the eighth-largest supplier of coffee to the world market, accounting for 3–3.7 percent. Sixty countries import coffee from Ethiopia. The top 10 countries to import Ethiopian coffee, in terms of value, were Italy, Germany, Saudi Arabia, Japan, Belgium, South Korea, China, the United Arab Emirates, and Taiwan. They make up 84% of the whole. Japan moved up from sixth place in 2020–2021 to fourth place in the world for coffee imports in 2021–2022.

Coffee consumption with different additives and types, genetic variation in caffeine metabolism and new-onset acute kidney injury.

This study aimed to evaluate the association of consumption of coffee with different additives, including milk and/or sweetener (sugar and/or artificial sweetener), and consumption of different types of coffee, including instant, ground, and decaffeinated coffee, with new-onset acute kidney injury (AKI), and examine the modifying effects of genetic variation in caffeine metabolism. 194,324 participants without AKI at baseline in the UK Biobank were included. The study outcome was new-onset AKI. During a median follow-up of 11.6 years, 5,864 participants developed new-onset AKI. Compared with coffee non-consumers, a significantly lower risk of new-onset AKI was found in coffee consumers adding neither milk nor sugar to coffee (HR, 0.86; 95%CI, 0.78-0.94) and adding only milk to coffee (HR,0.83; 95%CI, 0.78-0.89), but not in coffee consumers adding only sweetener (HR,1.14; 95%CI, 0.99-1.31) and both milk and sweetener to coffee (HR,0.96; 95%CI, 0.89-1.03). Moreover, there was a U-shaped association of coffee consumption with new-onset AKI, with the lowest risk at 2-3 drinks/d, in unsweetened coffee (no additives or milk only to coffee), but no association was found in sweetened coffee (sweetener only or both milk and sweetener to coffee). Genetic variation in caffeine metabolism didn't significantly modify the association. A similar U-shaped association was found for instant, ground, and decaffeinated coffee consumption in unsweetened coffee consumers, but not in sweetened coffee consumers. In conclusion, moderate consumption (2-3 drinks/d) of unsweetened coffee with or without milk was associated with a lower risk of new-onset AKI, irrespective of coffee type and genetic variation in caffeine metabolism.

Downy mildew of millets - An overview

Amidst global food insecurity, malnutrition, agricultural challenges, and climate change, millet farming is emerging as a viable alternativedue to its high nutritional value, resilience to extreme weather conditions, and adaptability to marginal soils. Often referred to as “super-crops”, millets gained international recognition in March 2021 during the 75th session of the United Nations General Assembly. Millets rank among the most important crops globally, following rice, wheat, maize, and sorghum. However, they are susceptible to more than fifty diseases, with the most destructive being ‘Downy Mildew’. This disease is caused by oomycete pathogens such as Sclerospora graminicola, Peronosclerospora sorghi and Sclerophthora macrospora, posing a significant threat to millet production, with yield losses ranging from 50% to 100%. This review emphasizes the importance of millet and the devastating effects of downy mildew on its yields. It explores the physiological and histological changes induced by the disease, the characterization of effector protein, and the genetic variability in millet populations. Additionally, various management techniques for combating downy mildew are examined, including chemical treatments, induced resistance, organic-based approaches, cultural practices, resistant genotypes, and advancements in nanotechnology. By compiling current knowledge on millet disease and effective management strategies, this review aims to serve as a comprehensive resource for researchers and farmers, supporting sustainable millet farming and improving global food security.

Successful Invasion Into New Environments Without Evidence of Rapid Adaptation by a Predatory Marine Gastropod.

Invasive species with native ranges spanning strong environmental gradients are well suited for examining the roles of selection and population history in rapid adaptation to new habitats, providing insight into potential evolutionary responses to climate change. The Atlantic oyster drill (Urosalpinx cinerea) is a marine snail whose native range spans the strongest coastal latitudinal temperature gradient in the world, with invasive populations established on the US Pacific coast. Here, we leverage this system using genome-wide SNPs and environmental data to examine invasion history and identify genotype-environment associations indicative of local adaptation across the native range, and then assess evidence for allelic frequency shifts that would signal rapid adaptation within invasive populations. We demonstrate strong genetic structuring among native regions which aligns with life history expectations, identifying southern New England as the source of invasive populations. Then, we identify putatively thermally adaptive loci across the native range but find no evidence of allele frequency shifts in invasive populations that suggest rapid adaptation to new environments. Our results indicate that while these loci may underpin local thermal adaptation in their native range, selection is relaxed in invasive populations, perhaps due to complex polygenic architecture underlying thermal traits and/or standing capacity for phenotypic plasticity. Given the prolific invasion of Urosalpinx, our study suggests population success in new environments is influenced by factors other than selection on standing genetic variation that underlies local adaptation in the native range and highlights the importance of considering population history and environmental selection pressures when evaluating adaptive capacity.

Genome-wide assessment of genetic variation and population structure in cultivated vanilla from Madagascar

Genome-wide assessment of genetic variation and population structure in cultivated vanilla from Madagascar