Genetic Variation In Response Research Articles

Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize

BackgroundHeterosis has successfully enhanced maize productivity and quality. Although significant progress has been made in delineating the genetic basis of heterosis, the molecular mechanisms underlying its genetic components remain less explored. Allele-specific expression (ASE), the imbalanced expression between two parental alleles in hybrids, is increasingly being recognized as a factor contributing to heterosis. ASE is a complex process regulated by both epigenetic and genetic variations in response to developmental and environmental conditions.ResultsIn this study, we explored the differential characteristics of ASE by analyzing the transcriptome data of two maize hybrids and their parents under four light conditions. On the basis of allele expression patterns in different hybrids under various conditions, ASE genes were divided into three categories: bias-consistent genes involved in basal metabolic processes in a functionally complementary manner, bias-reversal genes adapting to the light environment, and bias-specific genes maintaining cell homeostasis. We observed that 758 ASE genes (ASEGs) were significantly overlapped with heterosis quantitative trait loci (QTLs), and high-frequency variations in the promoter regions of heterosis-related ASEGs were identified between parents. In addition, 10 heterosis-related ASEGs participating in yield heterosis were selected during domestication.ConclusionsThe comprehensive analysis of ASEGs offers a distinctive perspective on how light quality influences gene expression patterns and gene-environment interactions, with implications for the identification of heterosis-related ASEGs to enhance maize yield.

Toward Ecologically Relevant Genetics of Interactions Between Host Plants and Plant Growth‐Promoting Bacteria

AbstractThe social movement to reduce reliance on pesticides and synthesized fertilizers and the growing global demand for sustainable food supplies require the development of eco‐friendly and sustainable agricultural practices. In line, plant growth‐promoting bacteria (PGPB) can participate in creating innovative agroecological systems. While the effectiveness of PGPB is highly influenced by abiotic conditions and microbe–microbe interactions, beneficial plant–PGPB interactions can also highly depend on both host and PGPB genotype. Here, the state of the art on the extent of natural genetic variation of plant–PGPB interactions and the underlying genetic architecture, in particular in Arabidopsis thaliana is reviewed. Extensive natural plant genetic variation in response to PGPB is associated with a polygenic architecture and genetic pathways rarely mentioned as being involved in the response to PGPB. To date, natural genetic variation within PGPB is little explored, which may in turn allow the identification of new genetic pathways underlying benefits to plants. Accordingly, several avenues to better understand the genomic and molecular landscape of plant–PGPB interactions are introduced. Finally, the need for establishing thorough functional studies of candidate genes underlying Quantitative Trait Loci and estimating the extent of genotype‐by‐genotype‐by‐environment interactions within the context of realistic (agro‐)ecological conditions is advocated.

The effects of multifactorial stress combination on rice and maize.

The complexity of environmental factors affecting crops in the field is gradually increasing due to climate change-associated weather events, such as droughts or floods combined with heat waves, coupled with the accumulation of different environmental and agricultural pollutants. The impact of multiple stress conditions on plants was recently termed "multifactorial stress combination" (MFSC) and defined as the occurrence of 3 or more stressors that impact plants simultaneously or sequentially. We recently reported that with the increased number and complexity of different MFSC stressors, the growth and survival of Arabidopsis (Arabidopsis thaliana) seedlings declines, even if the level of each individual stress is low enough to have no significant effect on plants. However, whether MFSC would impact commercial crop cultivars is largely unknown. Here, we reveal that a MFSC of 5 different low-level abiotic stresses (salinity, heat, the herbicide paraquat, phosphorus deficiency, and the heavy metal cadmium), applied in an increasing level of complexity, has a significant negative impact on the growth and biomass of a commercial rice (Oryza sativa) cultivar and a maize (Zea mays) hybrid. Proteomics, element content, and mixOmics analyses of MFSC in rice identified proteins that correlate with the impact of MFSC on rice seedlings, and analysis of 42 different rice genotypes subjected to MFSC revealed substantial genetic variability in responses to this unique state of stress combination. Taken together, our findings reveal that the impacts of MFSC on 2 different crop species are severe and that MFSC may substantially affect agricultural productivity.

Unraveling Psychedelic Responses: Targeted Protein Degradation and Genetic Diversity.

This Viewpoint discusses the intersection of targeted protein degradation (TPD) technologies and psychedelic research. The resurgence in interest in psychedelics for treating mental disorders and the known genetic variability in responses require new strategies. TPD technologies might address this variability, modulating protein expressions based on genetic profiles. The discussion includes potential challenges in implementing TPD technologies in psychedelic research and potential strategies to address these issues. It considers lessons from COVID-19 research on genetic variability, proposing integration of TPD technologies into psychedelic research as a promising field despite these challenges, possibly leading to personalized treatments and improved patient outcomes.

Edaphic ecotypic divergence in Senecio vulgaris and the evolutionary potential of predominantly self-fertilising species

ABSTRACT Background There is continued interest in ecotypic divergence because it is informative of local adaptation and can be an important step in speciation. Aim To investigate ecotypic divergence in a predominantly self-fertilising species, Senecio vulgaris, in response to variation in soil nitrogen (N) and phosphorus (P) concentrations. Methods Responses to increased N and P were compared among populations sampled from sand dune, bird sanctuary and garden habitats, containing soils of low, high and intermediate fertility, respectively. Responses were measured in terms of growth, with capitulum production and days to seed set recorded in some experiments. Results Population differences in response to increased N and P were detected and linked to differences in soil fertility among habitats. Thus, the sand dune population exhibited the lowest growth response to increased N and P concentrations, while a bird sanctuary population showed the greatest response to increased N supplied as either NaNO3, NH4NO3 or urea. Genetic variation in response to increased N was present in both of these populations. Conclusions The results indicate the presence of edaphic ecotypes in S. vulgaris, providing further evidence that questions the premise that self-fertilisation limits adaptation to environmental change and thus is an evolutionary dead-end.

A Bayesian approach to differential edges with probabilistic interactions: applications in association and classification

AbstractMotivationDifferential network (D-Net) analysis has attracted great attention in systems biology for its ability to identify genetic variations in response to different conditions. Current approaches either estimate the condition-specific networks separately followed by post-procedures to determine the differential edges or estimate the D-Net directly. Both types of analysis overlook the probabilistic inference and can only provide deterministic inference of the edges.ResultsHere, we propose a Bayesian solution and translate the probabilistic estimation in the regression model to an inferential D-Net analysis for genetic association and classification studies. The proposed PRobabilistic Interaction for Differential Edges (PRIDE) focuses on inferring the D-Net with uncertainty so that the existence of the differential edges can be evaluated with probability and even prioritized if comparison among these edges is of interest. The performance of the proposed model is compared with state-of-the-art methods in simulations and is demonstrated in glioblastoma and breast cancer studies. The proposed PRIDE performs comparably to or outperforms most existing tools under deterministic evaluation criteria. Additionally, it offers the unique advantages, including prioritizing the differential edges with probabilities, highlighting the relative importance of hub nodes, and identifying potential sub-networks in a D-Net.Availability and implementationAll the data analyzed in this research can be downloaded at https://xenabrowser.net/datapages/. The R code for implementing PRIDE is available at https://github.com/YJGene0806/PRIDE_Code.

Factors affecting in vitro regeneration in the model tree Populus trichocarpa: II. Heritability estimates, correlations among explant types, and genetic interactions with treatments among wild genotypes

To enhance the sensitivity of an ongoing Genome Wide Association Study (GWAS) for in vitro shoot regeneration and genetic transformation, a wide range of factors that can affect regeneration rate and, therefore, expression of genetic diversity were studied. Included were explant types and sources; direct versus indirect regeneration; nitrogen salts and micronutrient levels in basal medium; sucrose, auxin, and cytokinin types and levels; light intensity and quality; melatonin and serotonin; antibiotics (to exogenously control contaminants); antioxidants; and the ethylene-mitigating agent silver nitrate. Genotype was a statistically significant source of variance in response to nearly every treatment and for every measure of regeneration noted in shoots and roots, and initial generation of callus. Nonetheless, broad-sense heritability estimates varied widely as a result of variable degrees of environmental modification and statistical interactions with genotype. Compared to leaves, stem and petiole explants were highly correlated in their expression of genetic variation in response to treatments, a likely result of their functional similarity. Based on literature review, this study appears to be the most intensive analysis of plant natural genetic variation in response to in vitro manipulations published. It should help to guide development of improved and highly heritable treatments in other plant species that employ organogenic regeneration systems.

Physiological Responses of Chickpea Genotypes to Cold and Heat Stress in Flowering Stage

Due to climate change, more temperature extremes are expected in the future, potentially endangering agricultural production. Chickpea (Cicer arietinum L.) is an important cool-season food legume grown worldwide; however, cold and heat episodes are major threats in chickpea production that cause considerable yield losses especially at the flowering stage. The aim of this study was to evaluate the physiological performance of contrasting chickpea genotypes during the flowering phase under cold and heat. Four chickpea genotypes (Desi, Eldorado, Acc#2 and Acc#7) with different temperature susceptibilities were treated for 3 days under cold (9/4 °C) and heat (38/33 °C). The results showed that cold stress reduced the maximum quantum efficiency of photosystem II (Fv/Fm) by 5%, net photosynthetic rate (PN) by 74%, and chlorophyll a+b content by 31% on average in all tested genotypes. Up to a 9-fold increase in the amount of starch was found in the leaves of plants under cold stress, indicating that carbohydrates strongly accumulated in chickpeas under cold stress. This helps to maintain the vegetative and generative organs and enable fast recovery. Under heat stress, chickpeas maintained Fv/Fm and PN, although chlorophyll a+b content decreased by 39% on average. Carbohydrates did not accumulate under heat in chickpeas; thereby, a reduction in biomass and reproductive organs took place. Genetic variation in response to cold and heat stress was detected among the tested flowering chickpea genotypes. Desi and Acc#2 were cold-sensitive candidates, and Eldorado was a cold-tolerant candidate, whereas Acc#7 and Acc#2 were heat-sensitive candidates, while Desi and Eldorado were heat-tolerant candidates. This study provides important knowledge on the physiological response of flowering chickpeas under cold and heat stress. This will benefit the identification of stress-tolerant chickpea genotypes to ensure high yields in the future climate.

Estimating Genetic Variance in Life-Span Response to Diet: Insights From Statistical Simulation.

Several studies demonstrate genetic variation in response to dietary restriction (DR) by replicating treatments across isogenic lines/strains from genetic reference panels. These studies typically quantify the response to DR as an effect size, estimated for each strain separately (eg, the difference in mean life span between groups). Such "no-pooling" analyses are expected to systematically overestimate variation in response DR, principally by overlooking sampling variance. In contrast, "partial-pooling" analyses using mixed-effects models are less prone to this bias. I demonstrate these issues using simulations, which also show that partial-pooling analyses can improve replicability among studies. Regardless of the analyses used, estimates of among-strain variation will have low precision when sample sizes are small. A worked example using survival data in mice is given. Life-span studies using genetic reference panels always have to trade-off within- and among-strain replication owing to logistical challenges. The simulation presented can also be used to help design such studies through power analysis.

Genetic Variation in Responses to Salt Stress in Tunisian Populations of Medicago ciliaris

Soil salinity is one of the most serious environmental factors affecting crop productivity around the world. We used a morpho-physiological approach to investigate the salt responses of four Tunisian natural populations of Medicago ciliaris. Forty-six lines of M. ciliaris were grown under a control treatment and 100 mM NaCl. We measured 11 quantitative traits of shoot and root growth during harvest. An analysis of variance showed that the variations in salt response can be explained by the effects of the population, line, treatment, and interactions between the population and treatment and the line and treatment. Most of the measured traits showed significant differences between the studied populations under the control treatment and salt stress. High to moderate broad-sense heritabilities (H2) were noted for most of the parameters under the control treatment and salt stress, implying that salt tolerance is highly heritable. Most correlations between the measured traits under the two treatments were positive, of which the strongest correlations were recorded between characteristics related to development. The 46 studied lines formed three groups in both conditions, while their genetic structure was dependent on the treatment factor. The results from this study can provide a basis for identifying and breeding salt-tolerant lines of M. ciliaris.

Overview of Research on Germline Genetic Variation in Immune Genes and Cancer Outcomes

Abstract Since the late 19th century, the immune system has been known to play a role in cancer risk, initiation, and progression. Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for autoimmune and inflammatory diseases, yet the connection between human genetic variation and immune-mediated response to cancer treatments remains less well-explored. Understanding inherited genetic variation, with respect to germline genetic polymorphisms that affect immune system pathways, could lead to greater insights about how these processes may best be harnessed to successfully treat cancer. Our goal in this manuscript was to understand progress and challenges in assessing the role of inherited genetic variation in response to cancer treatments. Overall, the 39 studies reviewed here suggest that germline genetic variation in immune system–related genes may potentially affect responses to cancer treatments. Although further research is needed, considering information on germline immune genetic variation may help, in some cases, to optimize cancer treatment.

Physiological and transcriptomic analyses reveal novel insights into the cultivar-specific response to alkaline stress in alfalfa (Medicago sativa L.)

Soil alkalization severely limits plant growth and development, however, the mechanisms of alkaline response in plants remain largely unknown. In this study, we performed physiological and transcriptomic analyses using two alfalfa cultivars (Medicago sativa L.) with different sensitivities to alkaline conditions. The chlorophyll content and shoot fresh mass drastically declined in the alkaline-sensitive cultivar Algonquin (AG) following alkaline treatment (0–25 mM Na2CO3 solution), while the alkaline-tolerant cultivar Gongnong NO.1 (GN) maintained relatively stable growth and chlorophyll content. Compared with AG, GN had higher contents of Ca2+ and Mg2+; the ratios of Ca2+ and Mg2+ to Na+, proline and soluble sugar, as well as higher enzyme activities of peroxidase (POD) and catalase (CAT) under the alkaline conditions. Furthermore, transcriptomic analysis identified three categories of alkaline-responsive differentially expressed genes (DEGs) between the two cultivars: 48 genes commonly induced in both the cultivars (CAR), 574 genes from the tolerant cultivar (TAR), and 493 genes from the sensitive cultivar (SAR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that CAR genes were mostly involved in phenylpropanoid biosynthesis, lipid metabolism, and DNA replication and repair; TAR genes were significantly enriched in metabolic pathways, such as biosynthesis of amino acids and secondary metabolites including flavonoids, and the MAPK signaling pathway; SAR genes were specifically enriched in vitamin B6 metabolism. Taken together, the results identified candidate pathways associated with genetic variation in response to alkaline stress, providing novel insights into the mechanisms underlying alkaline tolerance in alfalfa.

Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS.

Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish

The adaptive genetic variation in response to heterogeneous habitats of the Indian Ocean was investigated in the Indian oil sardine using ddRAD sequencing to understand the subpopulation structure, stock complexity, mechanisms of resilience, and vulnerability in the face of climate change. Samples were collected from different ecoregions of the Indian ocean and ddRAD sequencing was carried out. Population genetic analyses revealed that samples from the Gulf of Oman significantly diverged from other Indian Ocean samples. SNP allele-environment correlation revealed the presence of candidate loci correlated with the environmental variables like annual sea surface temperature, chlorophyll-a, and dissolved oxygen concentration which might represent genomic regions allegedly diverging as a result of local adaptation. Larval dispersal modelling along the southwest coast of India indicated a high dispersal rate. The two major subpopulations (Gulf of Oman and Indian) need to be managed regionally to ensure the preservation of genetic diversity, which is crucial for climatic resilience.

Different cultivation media conditions affecting behavior and genetic stability of <i>Lepidium sativum</i> L.

<i>Lepidium sativum</i> is an edible medicinal plant from the family Brassicaceae. It holds many uses in folk medicine, and the bioactivities activities originate from its constituents. So, it is essential to estimate the different physiological compounds in this plant. It is also essential to determine which organ in the plant could contain these active compounds. So, it is necessary to evaluate the growth conditions of this plant. In this study,<i> L. sativum</i> is grown in different conditions (with water only in Petri-dish, in pots with peat-moss soil and on jars with Murashige and Skoog (MS) medium with tissue culture technique). From the results obtained, it was clear that cultivation in peat-moss soil supplement the plant with more pigmentation concentration (but not for a long time) and much protein content. In comparison, cultivation on MS media provides much protein content. In all parameters, seeds germinated with water only have the lowest value. Genetically, RAPD-PCR molecular marker illustrates that there is no genetic stability in <i>L. sativum</i> grew on different cultivation conditions. The polymorphism percentage was 54.71%. So, there is genetic variation in response to different cultivation conditions.

Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium.

Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because—like many studies of organism-environment interaction—it is primarily informed by experiments considering performance at two discrete levels—wet and dry—rather than as a continuously varying environmental gradient. Here, we used experimental and statistical methods based on function-valued traits to explore genetic variation in responses to a continuous soil moisture gradient in physiological and morphological traits among 10 genotypes across two species of the model grass genus Brachypodium. We find that most traits exhibit significant genetic variation and nonlinear responses to soil moisture variability. We also observe differences in the shape of these nonlinear responses between traits and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. Our results point to the importance of considering diversity in nonlinear organism-environment relationships to understand plastic and evolutionary responses to changing climates.

GxEsum: a novel approach to estimate the phenotypic variance explained by genome-wide GxE interaction based on GWAS summary statistics for biobank-scale data

Genetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. However, existing methods are computationally demanding and infeasible to handle biobank-scale data. Here, we introduce GxEsum, a method for estimating the phenotypic variance explained by genome-wide GxE based on GWAS summary statistics. Through comprehensive simulations and analysis of UK Biobank with 288,837 individuals, we show that GxEsum can handle a large-scale biobank dataset with controlled type I error rates and unbiased GxE estimates, and its computational efficiency can be hundreds of times higher than existing GxE methods.

Genetically determined variations of selenoprotein P are associated with antioxidant, muscular, and lipid biomarkers in response to Brazil nut consumption by patients using statins

Several single nucleotide polymorphisms (SNPs) could indirectly, as well directly, influence metabolic parameters related to health effects in response to selenium (Se)supplementation. This study aimed to investigate whether the selenoprotein SNPs were associated with the response of Se status biomarkers to the Brazil nut consumption in patients using statins and if the variation in Se homoeostasis could affect antioxidant protection, lipid profile, muscle homoeostasis and selenoproteins mRNA. The study was performed in the Ribeirão Preto Medical School University Hospital. Thirty-two patients using statins received one unit of Brazil nut daily for 3 months. Body composition, blood Se concentrations, erythrocyte glutathione peroxidase (GPX) activity, total cholesterol, low-density lipoprotein(LDL), high-density lipoprotein (HDL), triacylglycerol (TAG), creatine kinase (CK) activity and gene expression of GPX1 and selenoprotein P (SELENOP) were evaluated before and after Brazil nut consumption. The volunteers were genotyped for SNP in GPX1 (rs1050450) and SELENOP (rs3877899 and rs7579). SNPs in selenoproteins were not associated with plasma and erythrocyte Se, but SNPs in SELENOP influenced the response of erythrocyte GPX activity and CK activity, TAG and LDL after Brazil nut consumption. Also, Brazil nut consumption increased GPX1 mRNA expression only in subjects with rs1050450 CC genotype. SELENOP mRNA expression was significantly lower in subjects with rs7579 GG genotype before and after the intervention. Thus, SNP in SELENOP could be associated with interindividual differences in Se homeostasis after Brazil nut consumption, emphasising the involvement of genetic variability in response to Se consumption towards health maintenance and disease prevention.

The association between MDR1 C3435T genetic polymorphism and the risk of multidrug-resistant epilepsy in Egyptian children

BackgroundEpilepsy is a chronic disease affecting about 2% of the population and is considered a serious neurological disease. Despite its good prognosis, 20–30% of epileptic patients were not cured of their seizures even with the many trials of antiepileptic drug (AED) therapy. The resistance mechanism is still unclear, maybe due to the effect of the genetic factors on the bioavailability of the drugs. Consequently, the association between therapy resistance and the presence of a gene called “multidrug resistance 1 (MDR1)” had been proposed. Thus, the present study aimed to understand the relationship between the genetic polymorphism of MDR1C3435T and the resistance to AEDs.ResultA non-significant association was found between MDR1 C3435T single-nucleotide polymorphism (SNP) and drug-resistant epilepsy. However, there was statistical significance in the association between the drug type and the genotype distribution, in cases that were maintained on sodium valproate and MDR1C3435T genotype.ConclusionPossible involvement of the MDR1 gene C 3435T polymorphism with sodium valproate resistance clarifies the importance of genetic variability in response to the drug and may help to find novel genetic therapy for epilepsy, by targeting the biological mechanisms responsible for epilepsy in each specific individual. Future studies with bigger sample sizes and in other racial populations will be necessary.

Yield and photosynthetic rate of wheat under continuously high temperature

In tropical regions high temperature occurs throughout wheat growth cycle and is a major factor influencing growth and yield in this area. The aim of this work is to describe the responses to continuously-high temperatures on growth, photosynthesis and yield of wheat, under controlled conditions. Nias and Dewata (Indonesian wheat varieties) and Axe and Gladius (Australian varieties) were tested in growth room experiment with temperature and photoperiod chosen to simulate conditions on Lombok Island, at lowland (32/23°C) and highland (28/20°C) sites. The third temperature (25/15°C) was selected to represent temperature in a more temperate wheat-producing area. High temperature reduced yield and dry matter accumulation which was associated with a reduction in photosynthetic rate and stomata conductance and an increase in respiration rate. The reduction in photosynthetic rate at high temperature was not only due to lower stomatal conductance but also non-stomatal effects as mesophyll conductance and quantum yield were lower. Genetic variability in response to heat stress was evident with the Indonesian varieties being more tolerant to high temperatures than Australian varieties. Nias and Dewata produced higher yield and biomass and maintaining higher rates of photosynthesis. Maintaining high photosynthetic rate and high stomata conductance, are important characters in adapting wheat into tropical environment such as Lombok Island.