Strong Genetic Effects Research Articles

Genetic diversity of the immunoglobulin heavy chain locus in cohorts of patients affected with SARS-CoV-2

BackgroundThe Immunoglobulin Heavy Chain (IGH) genomic region is responsible for the production of circulating antibodies and warrants careful investigation for its association with COVID-19 characteristics. Multiple allelic variants within and across different IGH gene segments form a limited set of haplotypes. Previous studies have shown associations between some of these haplotypes and clinical outcomes of COVID-19. We typed 445 individuals of European ancestry, stratified for gender, age, and clinical status for 4 SNPs, two of which result in amino acid substitutions in IGHA2 and IGHG4, respectively. We analyzed associations at the single-locus level and for 4-loci haplotypes, inferred by phasing, after stratifying the overall cohort by gender, age, and disease severity. ResultsOnly weak evidence of significant differences between subgroups was obtained at the level of a single SNP. However, when the haplotypic data were analyzed for the young and old subgroups separately, uneven partitioning was observed regarding the occurrence of severe cases and Resistors. We then examined the cross-tabulation of disease severity in males and females, based on the presence of each haplotype in the genotype. Two haplotypes were underrepresented in young severe cases compared to old severe ones. The same two haplotypes were overrepresented among young Resistors. These findings provide stronger support for, the weak associations observed at the single locus level.ConclusionsTwo haplotypes seem to act as protective factors specifically in young individuals, counteracting the general increase in vulnerability with age. This observation aligns with stronger genetic effects seen in young patients for other susceptibility genes. Our findings complement previous research identifying specific genetic variants that influence COVID-19 susceptibility and severity, emphasizing the complex interplay between host genetics and viral infection outcomes. Our results are consistent with a potential causative role of IGH regulatory regions (e.g. HS1.2), which are flanked by the SNP set here analyzed.

Abstract 4137682: Genome wide association study for residualized apolipoprotein B elucidates its role in coronary artery disease risk

Background: Recent studies have shown apolipoprotein B (ApoB), the principle atherogenic lipoproteins, to have greater predictive ability for coronary artery disease (CAD) risk over standard lipid parameters. Moreover, discordantly high ApoB relative to Low-density lipoprotein cholesterol (LDLC) has repeatedly been associated with increased CAD risk. Aim: Given the strong genetic effects of ApoB and LDLC, we sought to characterize the discordance between ApoB and LDLC by genetics to obtain mechanistic insights into this emerging risk factor. Method: We derived residualized-ApoB regressing ApoB on LDLC in European-like populations (N = 383,500) in the UK Biobank. Using residualized-ApoB as an outcome, we explored clinical associations and conducted genome wide association study (GWAS). Result: Residualized-ApoB only modestly correlated with ApoB and LDLC (Spearman’s rho = 0.248 and -0.0079 respectively). We observed increased residualized-ApoB in males and individuals with lipid lowering therapy. Increased residualized-ApoB was associated with increased risk for CAD [Odds Ratio; 1.25 (95% Confidence interval 1.23-1.27)] independent from LDLC, ApoB, and Triglycerides. By GWAS, we observed significant heritability for residualized-ApoB [h 2 = 12.3 (SE 0.012)] and 195 significantly associated genetic loci ( P < 5 × 10 -8 ). Only 59 of these lead variants were associated with ApoB or LDLC. We also found different effects in ApoB-related loci. For example, ApoB-increasing alleles at APOB (rs533617) and APOE (rs7412) loci increased residualized-ApoB but ApoB-increasing alleles at ABCG8 (rs4245791) and HAPLN4-TM6SF2 (rs150641967) loci decreased residualized-ApoB. Conclusions: Exploiting genetics, we determined significant heritability of residualized-ApoB which was partially correlated with ApoB/LDLC. We identified distinct effects of genetic variants on residualized-ApoB. Our results provide the clues for further precise understanding of regulatory mechanisms between ApoB and LDLC.

The genetics of spatiotemporal variation in cortical thickness in youth

Prior studies have shown strong genetic effects on cortical thickness (CT), structural covariance, and neurodevelopmental trajectories in childhood and adolescence. However, the importance of genetic factors on the induction of spatiotemporal variation during neurodevelopment remains poorly understood. Here, we explore the genetics of maturational coupling by examining 308 MRI-derived regional CT measures in a longitudinal sample of 677 twins and family members. We find dynamic inter-regional genetic covariation in youth, with the emergence of regional subnetworks in late childhood and early adolescence. Three critical neurodevelopmental epochs in genetically-mediated maturational coupling were identified, with dramatic network strengthening near eleven years of age. These changes are associated with statistically-significant (empirical p-value <0.0001) increases in network strength as measured by average clustering coefficient and assortativity. We then identify genes from the Allen Human Brain Atlas with similar co-expression patterns to genetically-mediated structural covariation in children. This set was enriched for genes involved in potassium transport and dendrite formation. Genetically-mediated CT-CT covariance was also strongly correlated with expression patterns for genes located in cells of neuronal origin.

Genetic and environmental determinants of bone quality: a cross-sectional analysis of the Hungarian Twin Registry.

There is abundant evidence that bone mineral content is highly heritable, while the heritability of bone quality (i.e. trabecular bone score [TBS] and quantitative ultrasound index [QUI]) is rarely investigated. We aimed to disentangle the role of genetic, shared and unique environmental factors on TBS and QUI among Hungarian twins. Our study includes 82 twin (48 monozygotic, 33 same-sex dizygotic) pairs from the Hungarian Twin Registry. TBS was determined by DXA, QUI by calcaneal bone ultrasound. To estimate the genetic and environmental effects, we utilized ACE-variance decomposition. For the unadjusted model of TBS, an AE model provided the best fit with > 80% additive genetic heritability. Adjustment for age, sex, BMI and smoking status improved model fit with 48.0% of total variance explained by independent variables. Furthermore, there was a strong dominant genetic effect (73.7%). In contrast, unadjusted and adjusted models for QUI showed an AE structure. Adjustments improved model fit and 25.7% of the total variance was explained by independent variables. Altogether 70-90% of the variance in QUI was related to additive genetic influences. We found a strong genetic heritability of bone quality in unadjusted models. Half of the variance of TBS was explained by age, sex and BMI. Furthermore, the adjusted model suggested that the genetic component of TBS could be dominant or an epistasis could be present. In contrast, independent variables explained only a quarter of the variance of QUI and the additive heritability explained more than half of all the variance.

Genetic susceptibility to neurodevelopmental conditions associates with neonatal DNA methylation patterns in the general population: an individual participant data meta-analysis.

Autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and schizophrenia (SCZ) are highly heritable and linked to disruptions in foetal (neuro)development. While epigenetic processes are considered an important underlying pathway between genetic susceptibility and neurodevelopmental conditions, it is unclear (i) whether genetic susceptibility to these conditions is associated with epigenetic patterns, specifically DNA methylation (DNAm), already at birth; (ii) to what extent DNAm patterns are unique or shared across conditions, and (iii) whether these neonatal DNAm patterns can be leveraged to enhance genetic prediction of (neuro)developmental outcomes. We conducted epigenome-wide meta-analyses of genetic susceptibility to ASD, ADHD, and schizophrenia, quantified using polygenic scores (PGSs) on cord blood DNAm, using four population-based cohorts (n pooled=5,802), all North European. Heterogeneity statistics were used to estimate overlap in DNAm patterns between PGSs. Subsequently, DNAm-based measures of PGSs were built in a target sample, and used as predictors to test incremental variance explained over PGS in 130 (neuro)developmental outcomes spanning birth to 14 years. In probe-level analyses, SCZ-PGS associated with neonatal DNAm at 246 loci (p<9×10-8), predominantly in the major histocompatibility complex. Functional characterization of these DNAm loci confirmed strong genetic effects, significant blood-brain concordance and enrichment for immune-related pathways. 8 loci were identified for ASD-PGS (mapping to FDFT1 and MFHAS1), and none for ADHD-PGS. Regional analyses indicated a large number of differentially methylated regions for all PGSs (SCZ-PGS: 157, ASD-PGS: 130, ADHD-PGS: 166). DNAm signals showed little overlap between PGSs. We found suggestive evidence that incorporating DNAm-based measures of genetic susceptibility at birth increases explained variance for several child cognitive and motor outcomes over and above PGS. Genetic susceptibility for neurodevelopmental conditions, particularly schizophrenia, is detectable in cord blood DNAm at birth in a population-based sample, with largely distinct DNAm patterns between PGSs. These findings support an early-origins perspective on schizophrenia. HorizonEurope; European Research Council.

Identification of the CNGC Gene Family in Rice and Mining of Alleles for Application in Rice Improvement.

Cyclic nucleotide-gated ion channel (CNGC) gene regulation plays important roles in plant immune and abiotic stress response. Here, we identified 16 CNGC genes in rice (Oryza sativa). Then, we analyzed their chromosomal location, physicochemical properties, subcellular localization, gene functional interaction network, cis-acting elements, phylogenetic relationships, collinearity, expression in tissues under normal conditions and abiotic stresses, and geng-cds-haplotype (gcHap) diversity in 3010 gcHaps. As a result, OsCNGC3 (Os06g0527300) was identified as a gene different from previous report, and OsCNGC genes were found to play important roles in rice population differentiation and rice improvement. Our results revealed their very strong differentiation between subspecies and populations, important roles in response to abiotic stresses, as well as strong genetic bottleneck effects and artificial selection of gcHap diversity in the modern breeding process of Xian (indica) and Geng (japonica) populations. The results also suggested that natural variations in most rice CNGC loci are potentially valuable for improving rice productivity and tolerance to abiotic stresses. The favorable alleles at the CNGC loci should be explored to facilitate their application in future rice improvement.

Digital Phenotyping Reveals Phenotype Diversity and Epistasis among White Spotting Alleles in the American Paint Horse.

White spotting is an iconic feature of the American Paint Horse. The American Paint Horse Association (APHA) is dedicated to recording pedigree and performance of this stock-type breed, while preserving its distinctive coat color and conformation. Here, the depigmented proportion of the coat (% white coat) was measured using digital photograph analysis of 1195 registered American Paint Horses. Genotypes for nine white-spotting polymorphisms commonly found in Paint Horses, and two pigment-producing loci MCIR and ASIP genes, were also provided by the APHA. White-coat percent significantly increased in horses with more white-spotting alleles present, regardless of the number of loci bearing those alleles, likely due to a strong additive genetic effect at each white-spotting locus, as well as an additive epistatic effect among white spotting loci. Paint Horses with a chestnut base coat color (genotype e/e at MC1R) possessed a significantly higher white coat percentage, suggesting confirming an epistatic interaction between pigmentation signaling genes and loci for white spotting. The APHA registry categories of Regular versus Solid Paint-Bred also differed in their median white coat percentage (p < 0.0001), but not in the overall ranges of this phenotype, reenforcing the importance of the regional patterns of the depigmentation in the definition of the desired APHA phenotype. Multi-locus phenotype prediction models for white-coat percentage performed only moderately well, and improvements in the sample size and the number of loci genotyped will likely be needed before such an approach could be used practically by APHA breeders. In the future, models that enable phenotype prediction based on genotypes, and automated phenotype assessment could increase the production of valuable visual traits in the American Paint Horse population and improve the APHA member experience during the registration process.

Functional characterization and allelic mining of OsGLR genes for potential uses in rice improvement.

Glutamate-like receptor (GLR) genes are a group of regulatory genes involved in many physiological processes of plants. With 26 members in the rice genome, the functionalities of most rice GLR genes remain unknown. To facilitate their potential uses in rice improvement, an integrated strategy involving CRISPR-Cas9 mediated knockouts, deep mining and analyses of transcriptomic responses to different abiotic stresses/hormone treatments and gene CDS haplotype (gcHap) diversity in 3,010 rice genomes was taken to understand the functionalities of the 26 rice GLR genes, which led us to two conclusions. First, the expansion of rice GLR genes into a large gene family during evolution had gone through repeated gene duplication events occurred primarily in two large GLR gene clusters on rice chromosomes 9 and 6, which was accompanied with considerable functional differentiation. Secondly, except for two extremely conserved ones (OsGLR6.2 and OsGLR6.3), rich gcHap diversity exists at the remaining GLR genes which played important roles in rice population differentiation and rice improvement, evidenced by their very strong sub-specific and population differentiation, by their differentiated responses to day-length and different abiotic stresses, by the large phenotypic effects of five GLR gene knockout mutants on rice yield traits, by the significant association of major gcHaps at most GLR loci with yield traits, and by the strong genetic bottleneck effects and artificial selection on the gcHap diversity in populations Xian (indica) and Geng (japonica) during modern breeding. Our results suggest the potential values of the natural variation at most rice GLR loci for improving the productivity and tolerances to abiotic stresses. Additional efforts are needed to determine the phenotypic effects of major gcHaps at these GLR loci in order to identify 'favorable' alleles at specific GLR loci specific target traits in specific environments to facilitate their application to rice improvement in future.

Genes That Extend Lifespan May Do So by Mitigating the Increased Risk of Death Posed by Having Hypertension.

Genetic factors influence lifespan. In humans, there appears to be a particularly strong genetic effect in those aged ≥ 90 years. An important contribution is nutrient sensing genes which confer cell resilience. Our research has been investigating the genetic factors by longitudinal studies of American men of Japanese descent living on the island of Oahu in Hawaii. This cohort began as the Honolulu Heart Program in the mid-1960s and most subjects are now deceased. We previously discovered various genes containing polymorphisms associated with longevity. In recent investigations of the mechanism involved we found that the longevity genotypes ameliorated the risk of mortality posed by having a cardiometabolic disease (CMD) - most prominently hypertension. For the gene FOXO3 the protective alleles mitigated the risk of hypertension, coronary heart disease (CHD) and diabetes. For the kinase MAP3K5 it was hypertension, CHD and diabetes, for the kinase receptor PIK3R1 hypertension, CHD and stroke, and for the growth hormone receptor gene (GHR) and vascular endothelial growth factor receptor 1 gene (FLT1), it was nullifying the higher mortality risk posed by hypertension. Subjects with a CMD who had a longevity genotype had similar survival as men without CMD. No variant protected against risk of death from cancer. We have postulated that the longevity-associated genotypes reduced mortality risk by effects on intracellular resilience mechanisms. In a proteomics study, 43 "stress" proteins and associated biological pathways were found to influence the association of FOXO3 genotype with reduced mortality. Our landmark findings indicate how heritable genetic components affect longevity.

Combining ability analysis of yield and biomass allocation related traits in newly developed wheat populations

Increasing biomass allocation to the root system may increase soil-organic carbon stocks and confer drought adaptation in water-limited environments. Understanding the genetic bases and inheritance of biomass allocation is fundamental for drought tolerance breeding and soil health. The objective of this study was to determine the general and specific combining ability, maternal effects and the mode of gene action controlling the major yield and biomass allocation related traits in wheat to identify good combiners for breeding and enhanced carbon sequestration. Ten selected wheat genotypes were crossed in a full diallel mating design, and 90 F2 families were generated and evaluated in the field and greenhouse under drought-stressed and non-stressed conditions. Significant differences were recorded among the tested families revealing substantial variation for plant height (PH), kernels per spike (KPS), root biomass (RB), shoot biomass (SB), total plant biomass (PB) and grain yield (GY). Additive gene effects conditioned PH, SB, PB and GY under drought, suggesting the polygenic inheritance for drought tolerance. Strong maternal and reciprocal genetic effects were recorded for RB across the testing sites under drought-stressed conditions. Line BW162 had high yield and biomass production and can be used to transfer favourable genes to its progeny. The parental line LM75 maintained the general combining ability (GCA) effects in a positive and desirable direction for SB, PB and GY. Early generation selection using PH, SB, PB and GY will improve drought tolerance by exploiting additive gene action under drought conditions. Higher RB production may be maintained by a positive selection of male and female parents to capture the significant maternal and reciprocal effects found in this study.

Gene-based association study reveals a distinct female genetic signal in primary hypertension.

Hypertension is a polygenic disease that affects over 1.2 billion adults aged 30-79 worldwide. It is a major risk factor for renal, cerebrovascular, and cardiovascular diseases. The heritability of hypertension is estimated to be high; nevertheless, our understanding of its underlying mechanisms remains scarce and incomplete. This study covered the entries from European ancestry from the UK-Biobank (UKB), with 74,090 cases diagnosed with essential (primary) hypertension and 200,734 controls. We compared the findings from large-scale genome-wide association studies (GWAS) to the gene-based method of proteome-wide association studies (PWAS). We focused on 70 statistically significant associated genes, most of which failed to reach significance in variant-based GWAS. A total of 30% of the PWAS-associated genes were validated against independent cohorts, including the Finnish Biobank. Furthermore, gene-based analyses that were performed on both sexes revealed sex-dependent genetics with a stronger genetic component associated with females. Analysis of systolic and diastolic blood pressure measurements confirms a strong genetic effect associated with females. We demonstrated that gene-based approaches provide insight into the underlying biology of hypertension. Specifically, the expression profiles of the identified genes exposed the enrichment of endothelial cells from multiple organs. Furthermore, females' top-ranked significant genes are involved in cellular immunity. We conclude that studying hypertension and blood pressure via gene-based association methods improves interpretability and exposes sex-dependent genetic effects, which enhances clinical utility.

Arc regulates a second-guessing cognitive bias during naturalistic foraging through effects on discrete behavior modules

Foraging in animals relies on innate decision-making heuristics that can result in suboptimal cognitive biases in some contexts. The mechanisms underlying these biases are not well understood, but likely involve strong genetic effects. To explore this, we studied fasted mice using a naturalistic foraging paradigm and discovered an innate cognitive bias called "second-guessing." This involves repeatedly investigating an empty former food patch instead of consuming available food, which hinders the mice from maximizing feeding benefits. The synaptic plasticity gene Arc is revealed to play a role in this bias, as Arc-deficient mice did not exhibit second-guessing and consumed more food. In addition, unsupervised machine learning decompositions of foraging identified specific behavior sequences, or "modules", that are affected by Arc. These findings highlight the genetic basis of cognitive biases in decision making, show links between behavior modules and cognitive bias, and provide insight into the ethological roles of Arc in naturalistic foraging.

Modification of TSH-related genetic effects by indicators of socioeconomic position.

Thyroid-stimulating hormone (TSH) is influenced by genetic and environmental factors such as socioeconomic position (SEP). However, interactions between TSH-related genetic factors and indicators of SEP have not been investigated to date. The aim of the study was to determine whether education and income as SEP indicators may interact with TSH-related genetic effect allele sum scores (GESTSH_2013 and GESTSH_2020) based on two different GWAS meta-analyses that affect TSH values in a population-based study. In 4085 participants of the Heinz Nixdorf Recall Study associations between SEP indicators, GESTSH and TSH were quantified using sex- and age-adjusted linear regression models. Interactions between SEP indicators and GESTSH were assessed by GESTSH × SEP interaction terms, single reference joint effects and calculating genetic effects stratified by SEP group. Participants within the highest education group showed the strongest genetic effect with on average 1.109-fold (95% CI: 1.067-1.155) higher TSH values per GESTSH_2013 SD, while in the lowest education group, the genetic effect was less strong (1.061-fold (95% CI: 1.022-1.103)). In linear regression models including interaction terms, some weak indication for a positive GESTSH_2013 by education interaction was observed showing an interaction effect size estimate of 1.005 (95% CI: 1.000-1.010) per year of education and GESTSH_2013 SD. No indication for interaction was observed for using income as SEP indicator. Using the GESTSH_2020, similar results were observed. Our results gave some indication that education may affect the expression of TSH-related genetic effects. Stronger genetic effects in high-education groups may be explained by environmental factors that have an impact on gene expression and are more prevalent in high SEP groups.

Genetic regulators of cytokine responses upon BCG vaccination in children from West Africa

Genetic variation is a key factor influencing cytokine production capacity, but which genetic loci regulate cytokine production before and after vaccination, particularly in African population is unknown. Here, we aimed to identify single-nucleotide polymorphisms (SNPs) controlling cytokine responses after microbial stimulation in infants of West-African ancestry, comprising of low-birth-weight neonates randomized to bacillus Calmette-Guérin (BCG) vaccine-at-birth or to the usual delayed BCG. Genome-wide cytokine cytokine quantitative trait loci (cQTL) mapping revealed 12 independent loci, of which the LINC01082-LINC00917 locus influenced more than half of the cytokine-stimulation pairs assessed. Furthermore, nine distinct cQTLs were found among infants randomized to BCG. Functional validation confirmed that several complement genes affect cytokine response after BCG vaccination. We observed a limited overlap of common cQTLs between the West-African infants and cohorts of Western European individuals. These data reveal strong population-specific genetic effects on cytokine production and may indicate new opportunities for therapeutic intervention and vaccine development in African populations.

The genomic landscape of contemporary western Remote Oceanians

The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands ∼3,000 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report new genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous, sex-biased admixture events that occurred ∼1,700-2,300 years ago, indicating a peopling history common to the whole archipelago. However, East Asian-related ancestry proportions differ markedly across islands, suggesting that the Papuan-related population turnover was geographically uneven. Furthermore, we detect Polynesian ancestry arriving ∼600-1,000 years ago to Central and South Vanuatu in both Polynesian-speaking and non-Polynesian-speaking populations. Last, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide an insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.

Are resistances to acute hyperthermia or hypoxia stress similar and consistent between early and late ages in rainbow trout using isogenic lines?

Global warming is expected to increase the frequency and intensity of heatwaves, resulting in more common combined acute hyperthermia and hypoxia conditions in fish farms. Such poor thermal and oxygenation conditions induce problems, including growth losses, increased pathogens pressure and mortality. Selective breeding is a promising solution to improve resistance to non-optimal water quality. Indeed, genetic variability to survive in acute hyperthermia or hypoxia conditions has been proved in fish. However, the characterization of these traits is not yet detailed enough to include them in a selection program. Here, we investigated the ranking stability of genotypes for acute hyperthermia or hypoxia resistances over age and between acute hyperthermia and acute hypoxia resistances. To this end, we established rankings of six isogenic lines of rainbow trout (Oncorhynchus mykiss) for their resistance to acute hyperthermia and hypoxia stress factors at 6 and 15 months. The experimental design was robust with more than a hundred fish per line and age. There were statistically significant resistance variations among lines confirming the potential of genetic selection for these traits. Hyperthermia and hypoxia resistance rankings were found stable 1 year apart for most genotypes. Therefore, it would be possible to select for resistance to hyperthermia and hypoxia at an early stage. No overall relationship was found between acute hyperthermia and hypoxia resistance traits: some lines were resistant to both stress factors while others were resistant to one but sensitive to the other. This indicates no strong antagonistic genetic effects between acute hyperthermia and hypoxia resistance traits in rainbow trout.

Genetic Architectures Underlie Onset Age of Atopic Dermatitis

Genetic attributions for age of onset have been investigated for multiple entities (Blauwendraat et al., 2019; Kamboh et al., 2012; Power et al., 2017; Woolston et al., 2017), but evidence is still lacking in allergic diseases. Wan et al. (2017) found that FLG mutations are associated with earlier atopic dermatitis (AD) onset. Ferreira et al. (2020) performed a GWAS for allergic diseases, including AD, supporting the notion of strong genetic effects on early- and late-onset AD. These are the only studies that have investigated the genetic associations in age of onset for AD and were limited to predominantly European populations.

Genetic and social contributions to sex differences in lifespan in Drosophila serrata.

Sex differences in lifespan remain an intriguing puzzle in evolutionary biology. While explanations range from sex differences in selection to sex differences in the expression of recessive lifespan‐altering mutations (via X‐linkage), little consensus has been reached. One unresolved issue is the extent to which genetic influences on lifespan dimorphism are modulated by the environment. For example, studies have shown that sex differences in lifespan can either increase or decrease depending upon the social environment. Here, we took an experimental approach, manipulating multiple axes of the social environment across inbred long‐ and short‐lived genotypes and their reciprocal F1s in the fly Drosophila serrata. Our results reveal strong genetic effects and subtle yet significant genotype‐by‐environment interactions for male and female lifespan, specifically due to both population density and mating status. Further, our data do not support the idea that unconditional expression of deleterious X‐linked recessive alleles in heterogametic males accounts for lower male lifespan.

Identification and verification of grain shape QTLs by SNP array in rice.

Grain shape strongly influences the economic value and grain yield of rice. Thus, identifying quantitative trait loci (QTLs) for grain shape has been a longstanding goal in rice genetic research and breeding programs. Single nucleotide polymorphism (SNP) markers are ubiquitous in the rice genome and are more abundant and evenly distributed on the 12 rice chromosomes than traditional markers. An F2 population was genotyped using the RICE6K SNP array to elucidate the mechanisms governing grain shape. Thirty-five QTLs for grain shape were detected on 11 of 12 chromosomes over 2 years. The major QTL cluster qGS7 was detected in both years and displayed strong genetic effects on grain length and width, showing consistency with GL7/GW7. Some minor QTLs were also detected, and the effects of four QTLs on seed size were then validated using BC1F6 populations with residual heterozygous lines in each QTL region. Our findings provide insights into the molecular basis of grain shape as well as additional resources and approaches for producing hybrid high-yield rice varieties.

Enhancing the heat tolerance of reef-building corals to future warming.

Reef-building corals thriving in extreme thermal environments may provide genetic variation that can assist the evolution of populations to rapid climate warming. However, the feasibility and scale of genetic improvements remain untested despite ongoing population declines from recurrent thermal stress events. Here, we show that corals from the hottest reefs in the world transfer sufficient heat tolerance to a naïve population sufficient to withstand end-of-century warming projections. Heat survival increased up to 84% when naïve mothers were selectively bred with fathers from the hottest reefs because of strong heritable genetic effects. We identified genomic loci associated with tolerance variation that were enriched for heat shock proteins, oxidative stress, and immune functions. Unexpectedly, several coral families exhibited survival rates and genomic associations deviating from origin predictions, including a few naïve purebreds with exceptionally high heat tolerance. Our findings highlight previously uncharacterized enhanced and intrinsic potential of coral populations to adapt to climate warming.