Heritability Research Articles

Impact of genetic and genomic factors on host traits in striped catfish infected with Edwardsiella ictaluri

Infectious diseases pose a significant threat to sustainable agricultural production. While conventional quantitative genetic theory has successfully enhanced the resistance of animal individuals or populations, it fails to consider epidemiological factors. As a result, it may not adequately capture the maximum genetic gains in selected populations. This study aims to address this limitation by employing a genetic-epidemiological model that enables the estimation of genetic parameters for three host traits: susceptibility, infectivity, and recovery (or removal/mortality). We conducted our analysis on a population of striped catfish (Pangasianodon hypophthalmus) exposed to the Edwardsiella ictaluri pathogen, which causes bacillary necrosis of pangasius (BNP) disease, through challenge test experiments using injection and cohabitation methods. A total of 560 individuals (490 offspring and 70 parents) were evaluated for disease resistance, measured as the time (in days) from the challenge test to death. Our analysis using the genetic-epidemiological model revealed significant heritability in the epidemiological host traits. The genetic variances for infectivity were found to be greater than those for susceptibility and mortality. Additionally, genetic correlations of susceptibility with infectivity and mortality were moderate and negative, while those between infectivity and mortality were positive. Significant SNPs obtained from our genome-wide scan exhibited small additive genetic and non-significant (or incomplete) dominant effects, suggesting polygenic nature of epidemiological host traits. Genomic prediction accuracies for the transition time between susceptibility and infectivity, as well between infectivity and mortality were moderate to high (0.16 – 0.73). These findings suggest promising prospects for improving epidemiological host traits in genetic programs to enhance the overall resilience of the striped catfish population. The selection index approach yielded a predicted genetic gain ranging from 5.5 – 10.3% per generation for the epidemiological host traits. The accuracy of the selection index was moderate (0.585). Our study provides fundamental genetic parameters for modelling alternative selection strategies aimed at increasing disease resilience to infectious diseases in striped catfish and other aquaculture species.

Genetic parameter estimates and selection gain for multiple traits in white Guinea yam (Dioscorea rotundata) in Ghana

Quantifying selection gains enables a more targeted assessment of breeding program effectiveness, highlighting opportunities for strategic improvement and optimized genetic advancement in white Guinea Yam. This study assessed genetic parameters and gain for key traits in a white Guinea yam (D. rotundata) breeding population. A total of 81 genotypes were evaluated for two seasons using a 9 × 9 lattice design with three replicates. Data was collected on yam mosaic virus disease severity, tuber yield and tuber dry content for genetic analysis. Broad sense heritability was generally high (> 60) for most of the traits. At the same time, the corresponding genetic advance as a percentage of the mean was exceptionally high (30.28–93.96%) for tuber yield, tuber flesh oxidation, average tuber weight and number of tubers per plant, suggesting additive genetic effects. A multi-trait selection index of the 5% highest performing genotypes revealed positive genetic gain for plant vigour, tuber length, and width, tuber weight per plant, average tuber weight and fresh tuber yield. The genetic gain was, however, negative for tuber dry matter content compared to the check varieties, necessitating a modification of the current breeding scheme such that post-harvest food quality is not sacrificed for tuber yield. Ranking of the breeding lines based on the multi-trait selection index identified four lines (TDr1700004_014, TDr1700004_113, TDr1700001_112 and TDr1700002_090) with high genetic merits for all the economic traits. These lines can be used as potential trait progenitors and evaluated further for possible release as new varieties. Our results decipher the genetic control and provide an overview of the performance of the breeding program for key traits in white Guinea yam.

Detailed genetic analyses highlight genetic variation and genomic regions for lead tolerance in spring wheat

IntroductionUnderstanding the dynamics of Pb tolerance across different growth stages is essential for breeding wheat varieties with comprehensive tolerance to Pb contamination throughout their life cycle. Lead (Pb) in soil affects wheat plants at all growth stages. However, the seedling stage is considered a sensitive growth stage for the tolerance of most abiotic stresses. Genetic variation in lead tolerance is poorly understood, and genetic control has still not been investigated.MaterialsIn this study, 103 highly diverse wheat genotypes were investigated under normal and lead stress conditions at the seedling stage. Different seedling growth traits were scored under each treatment. GWAS was performed via two different sets of markers: 21,750 (25K Infinium iSelect array) and 37,790 SNPs (genotyping-by-sequencing) to identify SNP markers associated with the studied seedling traits.ResultsHigh genetic variation was found among all the genotypes for all the traits. High broad-sense heritability estimates ranging from 0.25-0.93 were observed. A highly significant correlation was found among all the traits scored under normal and lead stress conditions. Low or no significant phenotypic correlations were found for lead tolerance between the seedling and adult growth stages. A set of eight genotypes were classified as lead-tolerant genotypes. The GWAS revealed a set of 222 significant markers associated with lead tolerance. Markers with pleiotropic effects were detected under Pb stress and between lead and normal conditions. Interestingly, five significant markers were found to be associated with lead tolerance at the seedling and adult growth stages.DiscussionThe results of this study provide new and novel insights into genetic control and genetic variation in lead tolerance at the early growth stage. All the genes and genotypes reported in this study will be very useful for further investigations of lead tolerance in wheat at different growth stages.

Genetic resonance: dissecting the heritability and genetic correlations of human hearing acuity.

This study presents a frequency-specific, pedigree-based assessment of hearing acuity heritability. We analysed 34 Utah Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees comprising 464 individuals, using whole-genome sequencing (WGS) and audiometric evaluations. Our analysis reveals a general decline in narrow-sense heritability as frequency increases. When calculated using the Sequential Oligogenic Linkage Analysis Routines (SOLAR) software package, narrow-sense heritability estimates drop from 51% at 250 Hz to 30% at 8000 Hz. Genetic correlations (Rho(G)), the degree to which genetic variation in one trait correlates with another, are higher for hearing acuity at similar frequencies. For example, Rho(G) between 250 and 500 Hz is 0.80, and Rho(G) between 6000 and 8000 Hz is 0.91. In contrast, frequencies distant from each other exhibit decreased Rho(G) with a genetic correlation of only 0.21 for hearing acuity at frequencies 250 and 8000 Hz. This assessment of the genetics underlying hearing acuity in a family-based design provides new details of genetic factors influencing hearing acuity in a frequency-specific approach.

QTL mapping of Fusarium ear rot resistance using genotyping by target sequencing (GBTS) in maize.

Fusarium ear rot (FER) is a global disease caused by the fungal pathogen Fusarium verticillioides. Maize FER resistance is a quantitative trait controlled by polygenes. In this study, a doubled haploid (DH) population involving 159 lines, developed from the inbred lines B73 (susceptible) and CXS161 (highly resistant), was inoculated with Fusarium verticillioides across 4-year-location environment combinations in China during 2021 and 2022. The lines were genotyped using target sequencing with a 10K SNP array. The results showed that the estimated broad-sense heritability (H2) in each environment ranged from 0.659 to 0.871, with an overall H2 of 0.805. The average genetic length between adjacent markers in the genetic map constructed using multiple single-nucleotide polymorphisms (mSNP) was smaller than that constructed using SNP, whereas the maximal genetic length was almost the same. Using a genetic map constructed with a SNP, two quantitative trait loci (QTL) were identified on chromosomes 2 and 5, which explained 7.65% and 9.58% of the phenotypic variation, respectively. Using the genetic map constructed by mSNP, four QTL were identified, explaining 6.04-12.60% of the phenotypic variation. Moreover, two kompetitive allele-specific PCR (KASP) markers were developed using single-marker analysis methods, with one KASP marker validated across a backcross population that can be effectively used to identify FER resistance. In conclusion, using mSNP for genetic map construction does not confer advantages when the population size is limited and the marker density is high. However, the mSNP-constructed map identified more minor-effectQTL despite possessing a lower likelihood of the odds (LOD) values.

Human beauty illustrates the economic impact of heritable physical traits

Intergenerational transmission of inequality is a central question in the social sciences. We use one trait, beauty, to infer how much parents' physical characteristics transmit inequality across generations. Analyses of a large-scale longitudinal dataset in the United States, and a much smaller dataset of Chinese parents and children, show that increases in parents' looks are associated with increases in their child's looks. A large dataset of U.S. siblings shows a positive correlation of their beauty. The appropriate weighted average from the three samples shows that a one SD increase in ratings of both parents' looks is associated with a 0.25 SD increase in their child's. Coupling these estimates with those from large literatures measuring the impact of beauty on earnings and the intergenerational elasticity of income suggests that a one SD difference in parents' looks is correlated with a 0.074 SD difference in their adult child's earnings, about U.S. $2,170 annually.

Performance Comparison of Genomic Best Linear Unbiased Prediction and Four Machine Learning Models for Estimating Genomic Breeding Values in Working Dogs

This study investigates the efficacy of various genomic prediction models—Genomic Best Linear Unbiased Prediction (GBLUP), Random Forest (RF), Support Vector Machine (SVM), Extreme Gradient Boosting (XGB), and Multilayer Perceptron (MLP)—in predicting genomic breeding values (gEBVs). The phenotypic data include three binary health traits (anodontia, distichiasis, oral papillomatosis) and one behavioral trait (distraction) in a population of guide dogs. These traits impact the potential for success in guide dogs and are therefore routinely characterized but were chosen based on differences in heritability and case counts specifically to assess gEBV model performance. Utilizing a dataset from The Seeing Eye organization, which includes German Shepherds (n = 482), Golden Retrievers (n = 239), Labrador Retrievers (n = 1188), and Labrador and Golden Retriever crosses (n = 111), we assessed model performance within and across different breeds, trait heritability, case counts, and SNP marker densities. Our results indicate that no significant differences were found in model performance across varying heritabilities, case counts, or SNP densities, with all models performing similarly. Given its lack of need for parameter optimization, GBLUP was the most efficient model. Distichiasis showed the highest overall predictive performance, likely due to its higher heritability, while anodontia and distraction exhibited moderate accuracy, and oral papillomatosis had the lowest accuracy, correlating with its low heritability. These findings underscore that lower density SNP datasets can effectively construct gEBVs, suggesting that high-cost, high-density genotyping may not always be necessary. Additionally, the similar performance of all models indicates that simpler models like GBLUP, which requires less fine tuning, may be sufficient for genomic prediction in canine breeding programs. The research highlights the importance of standardized phenotypic assessments and carefully constructed reference populations to optimize the utility of genomic selection in canine breeding programs.

Relationships Between Genetic Parameters in the Component Traits of a Ratio Trait and the Distribution and Heritability of Such Ratio Trait.

The relationships between the distribution and heritability of a ratio trait and the genetic parameters of its component traits were clarified using a Monte Carlo computer simulation. The component traits of a ratio trait were assumed to be normally distributed. The genetic parameters of the ratio trait were estimated using parent-offspring regression. As the genetic and environmental correlations ( and ) of the component traits increased, the variance, skewness, and kurtosis of the ratio trait decreased. The amount of decrease had a greater effect on than on . The estimated heritability of the ratio trait decreased as increased and as decreased. The estimated heritability of a ratio trait can be higher than the heritability of any of its component traits.

Assessment of Genetic Divergence in Rice (Oryza sativa L.) Germplasm Using D2 Analysis

The present investigation was conducted with 41 genotypes of Rice during Kharif 2023 under Randomized Block Design (RBD) with three replications. Data were recorded for thirteen quantitative characters to obtain estimates of variability, heritability, genetic advance and genetic divergence. Significant differences were observed among the genotypes for all the characters studied. This study concluded, the highest grain yield was observed in VASUMATHI 38.9 followed by DHAN-69 34.33 based on mean performance at Prayagraj region. A higher magnitude of PCV as well as GCV coefficient of variation was noted for the number of total tillers per plant (22.05) and (21.20). Whereas the lowest PCV and GCV coefficient of variation was recorded for Days to maturity (7.40 and 6.80). High estimates of heritability (above 60%) in broad sense were recorded for all the thirteen characters under study, which ranged from 92.45% number of total tillers per plant to 61.55 harvest index. along with high genetic advance for number of spikelets per panicle (54.38), plant height (cm) (27.95), days to 50% flowering (22.93), and days to maturity (17.72). Biological yield (g) (15.33), harvest index (%) (11.06) and flag leaf length (cm) (10.05) D2 analysis distributed the 41 genotypes into six clusters. The largest cluster was cluster I with 36 genotypes followed by cluster II, III, IV, V, VI with 1 genotype each. Highest contribution in manifestation of genetic divergence was exhibited by grain yield per plant (22.82) followed by biological yield (21.28) and test weight (12.56). Lowest intercluster distance was between cluster I and cluster IV which was (60.58). The intercluster distance was maximum between cluster IV and VI (247.17). Therefore, genotypes present in these clusters should be used for the future hybridization program. Highlights: Germplasms were grouped into 6 clusters. Cluster IV and VI were the most divergent clusters

Atp1a2 and Kcnj9 Are Candidate Genes Underlying Sensitivity to Oxycodone-Induced Locomotor Activation and Withdrawal-Induced Anxiety-Like Behaviors in C57BL/6 Substrains.

Opioid use disorder is heritable, yet its genetic etiology is largely unknown. C57BL/6J and C57BL/6NJ mouse substrains exhibit phenotypic diversity in the context of limited genetic diversity which together can facilitate genetic discovery. Here, we found C57BL/6NJ mice were less sensitive to oxycodone (OXY)-induced locomotor activation versus C57BL/6J mice in a conditioned place preference paradigm. Narrow-sense heritability of OXY-induced locomotor activity traits ranged from 0.22 to 0.31, implicating suitability for genetic analysis. Quantitative trait locus (QTL) mapping in an F2 cross identified a chromosome 1 QTL explaining 7%-12% of the variance in OXY locomotion and anxiety-like withdrawal in the elevated plus maze. A second QTL for EPM withdrawal behavior on chromosome 5 near Gabra2 (alpha-2 subunit of GABA-A receptor) explained 9% of the variance. To narrow the chromosome 1 locus, we generated recombinant lines spanning 163-181 Mb, captured the QTL for OXY locomotor traits and withdrawal, and fine-mapped a 2.45-Mb region (170.16-172.61 Mb). Transcriptome analysis identified five, localized striatal cis-eQTL transcripts and two were confirmed at the protein level (KCNJ9, ATP1A2). Kcnj9 codes for a potassium channel (GIRK3) that is a major effector of mu opioid receptor signaling. Atp1a2 codes for a subunit of a Na+/K+ ATPase enzyme that regulates neuronal excitability and shows functional adaptations following chronic opioid administration. To summarize, we identified two candidate genes underlying the physiological and behavioral properties of opioids, with direct preclinical relevance to investigators employing these widely used substrains and clinical relevance to human genetic studies of opioid use disorder.

Estimation of genetic parameters of body conformation and racing performance traits in Yili horses.

The Yili horse is a riding-type breed that has been continuously bred independently in China. The genetics of body conformation and racing performance traits need to be comprehensively considered in making breeding decisions. This study is the first to estimate the genetic parameters of 13 body conformation and racing performance traits in Yili horses using a linear model. In total, 9937 body conformation and 2576 race records of 9100 Yili horses obtained from 1993 to 2022 were reviewed. The results showed that heritability estimates of body measurement traits were medium to high, ranging from 0.334 (cannon bone perimeter, CP) to 0.720 (withers height, WH), whereas heritability of the linear scale traits were low to medium, ranging from 0.080 (body length score, BLS) to 0.245 (overall score, OS). The heritability of racing performance traits was low to medium, ranging from 0.054 (racing time, RT) to 0.347 (average speed, AS), but there was a high level of repeatability, ranging from 0.341 (ranking score, RS) to 0.604 (AS). Notably, high genetic correlations were estimated among body measurement (0.588 on average) and racing performance traits (0.924 on average). Overall, body measurement traits and racing performance traits were highly influenced by genetics, had high potential for selection. These findings confirm the possibility of carrying out an evaluation program of Yili horses. We are also continuing to track and evaluate the performance of Yili horses and provide research ideas and methodologies for genetic evaluation of other local horse breeds.

A multi-trait approach identified 7 novel genes for back pain.

Back pain (BP) is a complex heritable trait with an estimated heritability of 40% to 60%. Less than half of this can be explained by known genetic variants identified in genome-wide association studies. We applied a powerful multi-trait and gene-based approach to association analysis of BP to identify novel genes associated with BP. Using phenotypes and imputed genotypes from the UK Biobank 500k dataset, we generated a multi-trait phenotype by combining 3 BP-related phenotypes: chronic BP, dorsalgia, and intervertebral disk disorders. We performed gene-based association analysis for 3 BP-related phenotypes and multi-trait phenotype. Conditional analysis was applied to account for the effects of genetic variants outside the gene. Finally, we replicated significantly associated genes using the FinnGen database. We identified 32 genes associated with BP and replicated 16 of them. Thirteen genes were detected using the multi-trait phenotype. Seven of the detected genes, MIPOL1, PTPRC, RHOA, MAML3, JADE2, MLLT10, and RERG, were not previously reported. Several new genes are known to be associated with traits genetically correlated with BP or to be involved in pathways associated with BP. Using new powerful methods of association analysis, we identified 7 novel genes associated with BP. Our results provide new insights into the genetics of back pain.

Use of termination events and mortality data recorded during the lactation as a proxy to predict the genetics of resilience and health of dairy cattle.

Increasing production and environmental challenges in dairy cattle means that selecting for resilience is becoming more important. This study explored whether data on cows that exit before completing their lactation and those that die during lactation can be used to predict resilience. To identify predictors of resilience, exiting the herd by 60, 120, 180, and 240 d were defined as traits. Additional traits were defined, by including all the cows that died during the entire lactation to the cows that exited at different times up to 240 d of lactation. For all traits, cows that exited the herd or died were coded as 1, otherwise as 0 at the end of the lactation. We used performance and exit data of Holstein (H) and Jersey (J) cows that calved between 1998 and 2023. The data were analyzed using a multi-trait sire model to estimate heritability and correlations with milk yield (MY), somatic cell count (SCC), calving interval (CIN), and selected type traits. The results showed that the proportion of cows that exited by 60 d was 2%, increasing by about 2% every 2 mo until exit by 240 d. The trend over the years in the proportion of exits, taking Exit 180d and Exit 180 + death as an example, showed an undesirable increase from 5.6% in 2000 to 9.4% in 2022. Heritability of all exit traits was low, increasing from below 1% for exit by 60 to 2.8% for exit by 240 d + all deaths over the lactation. The genetic correlation of early exit (i.e., 60 or 120 d) with first test-day MY was positive (unfavorable) and higher at the beginning (0.4), decreasing over time to be favorable in J (-0.2) and near zero in H (0.1) by the end of the lactation. On the other hand, the genetic correlation of exit with first test-day SCC became stronger (favorable) at the end of the lactation (0.3 to 0.4). Exit at any time during the lactation had the strongest genetic correlation with CIN (i.e., fertility). The genetic correlation of exit traits with body condition score (BCS) and angularity showed that the likelihood of cow exit, especially up to 180 d, was higher for thin and more angular cows. The genetic correlation estimates imply that cows with high potential for MY, poor fertility, poor BCS, and high scores for angularity are more likely to exit early due to metabolic stress. The change in genetic correlation between exit and MY early from unfavorable to favorable in J is due to more culling for milk and less for fertility and udder health is leading to an undesirable genetic trend for exit by 180 d as well as exit by 180 d + all death. However, the increasing phenotypic trend of exit rates in both breeds suggests a need for close monitoring. The selective use of exit data can help to develop genetic evaluations for resilience and health traits and validate and complement data collected to improve health and welfare during the transition period.

Single-Step GWAS Multi-Trait Threshold Linear Model for Growth Rate and Heteroblasty in Eucalyptus globulus

Eucalyptus globulus Labill. is one of the most important species in the paper industry. Teratosphaeria nubilosa has affected plantations worldwide, infecting young foliage. Genome-wide association studies (GWASs) are essential to identify genomic segments associated with susceptibility to this disease. The inclusion of genomic strategies in breeding programs is key to the sustainability of the species. The aim of this study was to identify genomic regions associated with growth and heteroblasty (change from juvenile to adult foliage: ADFO) in a tree breeding population of E. globulus. Tree growth was measured as total height (TH) and diameter at breast height (DBH). All traits were evaluated at 14 and 21 months. A multi-trait threshold linear model was developed following the single-step genomic selection methodology. Genetic correlations (rg) and narrow-sense heritability (h2) for all traits were estimated. Windows of 0.2 Mb were used. Only the windows with an estimated variance greater than 1% were considered. The rg ranged from 0.51 to 0.97. The h2 was high for ADFO (0.83–0.84) and lower for HT (0.37) and DBH (0.53). In growth traits, no QTLs were found that explained more than 1% of the variance. However, two genomic regions related to ADFO were identified on chromosomes 3 and 11.

Performance of weighted genomic BLUP and Bayesian methods for Hanwoo carcass traits.

To improve the quality and yield of the Korean beef industry, selection criteria often focus on estimated breeding values for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS). This study estimated genetic parameters and assessed the accuracy of genomic estimated breeding values (GEBVs) using SNP weighting methods. We compared the accuracy of these methods with the genomic best linear unbiased prediction (GBLUP) and various Bayesian approaches (BayesA, BayesB, BayesC, and BayesCPi) for the specified traits. The study used single-trait animal models, including GBLUP, weighted GBLUP (WGBLUP), and the Bayesian methods to predict genomic breeding values in a population of Hanwoo steers. A total of 19154 phenotypes were collected with all animals genotyped using the Illumina Bovine 50K SNP chip. The average heritability for the carcass traits was 0.33 (GBLUP) and 0.35 (Bayesian), with Bayesian methods yielding heritability estimates that were on average 0.02 points (6.1%) higher than GBLUP. The accuracy of genomic predictions ranged from 0.7-0.83 (GBLUP), 0.83-0.87 (WGBLUP), and 0.81-0.87 across the Bayesian methods. WGBLUP accuracies for the carcass traits were, on average 8.97% higher than the GBLUP accuracies and 1.80% higher than the Bayesian alphabets. The Bayesian alphabet's accuracy is also, on average 6.00% higher than the GBLUP accuracy. According to these findings, the weighting GBLUP approach provides higher prediction accuracy for Hanwoo carcass traits than the Bayesian alphabet. Therefore, WGBLUP can be used for genomic selection in the Hanwoo evaluation program.

Genetic Parameters Estimation and Identification of Promising Rice Genotypes Grown in Rainfed Condition Using Mgidi Index in Rampur, Chitwan

Rice, the world’s most vital crop with over 40,000 varieties cultivated for 8 to 13 thousand years, produced around 520.65 million metric tons annually—largely in China, India, and Bangladesh—while nearly half the global population relies on it as a primary food source, facing significant challenges in rainfed areas that impede productivity. This study evaluated 24 rice genotypes, including 22 pipeline varieties from the National Rice Research Program (NRRP) in Dhanusa and two checks, Bahaguni-2 and Sabitri. The Multi-Trait Genotype-Ideotype Distance Index (MGIDI) was used as selection tool to rank genotypes based on their proximity to an ideal genotype. Broad-sense heritability (h²) estimates ranged from 0.03 for panicle length to 0.96 for days to 80% maturity, suggesting high potential for selection gains in days to 80% maturity (h² = 0.96) and plant height (h² = 0.91), while tiller number and grain yield showed low heritability (h² > 0.5). Variance analysis indicated substantial genetic control for plant height and days to 80% maturity, while panicle length and grain yield were more influenced by environmental factors. Principal component analysis revealed four factors explaining 76.5% of the trait variation, with FA1 (days to 50% flowering, days to 80% maturity) accounting for the most variation. Selection gains were assessed using MGIDI and FAI-BLUP indexes, with MGIDI achieving a 15.13% gain for targeted traits and FAI-BLUP yielding 1.25%. Selected genotypes from MGIDI included SVIN 127, SVIN 098, SVIN 643, SVIN 084, and IR 18F1085, with SVIN 127 and SVIN 098 also appearing in the FAI-BLUP index, highlighting their potential value for breeding. This research demonstrates the effectiveness of both selection indexes in identifying superior genotypes for enhanced breeding efficiency. SAARC J. Agric., 22(2): 239-255 (2024)

Potential Therapeutic drug Targets for Hypertension Identified using Proteomics and Mendelian Randomization.

Hypertension (HT) is the most prevalent risk factor for cardiovascular disease (CVD) worldwide. Despite being a highly heritable trait, the underlying mechanisms of HT remain elusive due to its complex genetic architecture. Discovering disease-associated proteins with causal genetic evidence offers a potential strategy for identifying therapeutic targets for HT. We analyzed the plasma proteome of 4,657 plasma proteins from 7,213 European American (EA) participants in the ARIC study. Genome-wide association study (GWAS) data for HT were sourced from FinnGen R10, which includes 102,864 cases and 289,117 controls. Cis-Mendelian randomization (MR) was conducted to assess the causal effect of circulating proteins on the risk of HT. A multiverse sensitivity analysis was performed to evaluate the robustness of these causal relationships. Colocalization analysis was conducted to determine whether these features share the same associated single nucleotide polymorphisms (SNPs). The causal effects of HT-associated proteins were then validated using cis-protein quantitative trait loci (Cis-pQTL) genetic instruments from the deCODE database. Among 1,788 proteins, genetically predicted levels of 18 plasma proteins were associated with HT in the discovery stage. Seven of these proteins showed strong support for colocalization. After replication, only ERAP1 and ACVRL1 were validated as therapeutic candidates for HT, demonstrating a negative correlation with the risk of HT. By combining cis-MR analysis with colocalization analysis, we identified ERAP1 and ACVRL1 as potential targets for interventions in the primary prevention of HT, with ERAP1 emerging as a particularly promising drug target after further validation.

Haplotype Analysis and Gene Pyramiding for Pre-Harvest Sprouting Resistance in White-Grain Wheat.

The Huanghuai winter wheat region, China's primary wheat-producing area, predominantly cultivates white-grained wheat. Pre-harvest sprouting (PHS) significantly impacts yield and quality, making the breeding of PHS-resistant varieties crucial for ensuring China's wheat production security. This study evaluated the PHS rate of 344 white-grained wheat varieties over two consecutive growing seasons (2022/2023 and 2023/2024). Furthermore, it analyzed the effects of allelic variations and their combinations in six genes (Tamyb10, TaDFR, TaMKK3-A, TaGASR34, Tasdr, and TaMFT) on PHS resistance. Results revealed average PHS rates of 66.1% and 64.4% for the two growing seasons, with coefficients of variation of 39.1% and 40.2%, respectively, and a narrow-sense heritability of 0.72. These findings indicate substantial genetic variation and relatively high genetic stability within the tested materials. Among the six molecular markers examined, the superior haplotype GS34-7Bb exhibited the lowest average PHS rate (41.9%) over two growing seasons, demonstrating the strongest PHS resistance. Analysis of different haplotype combinations identified two advantageous genotypes for PHS resistance in white-grained wheat: TaMKK3-Ab + GS34-7Bb + Tasdr-2Aa + TaMFT-A1b (average PHS rate: 20.8%) and TaMKK3-Ab + GS34-7Bb + Tasdr-2Ab + TaMFT-A1b (average PHS rate: 34.2%). Notably, the distribution frequency of superior haplotypes of PHS-related genes and these two advantageous haplotype combinations showed varying degrees of decline over time.

Repeatability of critical thermal maximum (CTmax) in two freshwater ectotherms across contexts.

Critical thermal maximum (CTmax) is the most widely used method for quantifying acute upper thermal limits in ectotherms. CTmax protocol exposes animals to a consistent rate of environmental warming until they lose motor function. CTmax has been used to assess intraspecific variation among life stages, populations, or as a function of body size, often with the assumption that it is a durable and heritable trait at the individual level. The existence of within-individual repeatability of CTmax has been used to infer the potential for thermal adaptation via the positive correlation between the repeatability of a trait and its heritability. However, for how widely used CTmax has become, surprisingly few studies have quantified within-individual repeatability in aquatic ectotherms, and none have assessed repeatability across contexts. We examined the cross-context repeatability of CTmax in two freshwater ectotherms (one decapod crustacean and one teleost fish): rusty crayfish Faxonius rusticus (n=31) and pumpkinseed Lepomis gibbosus (n=38). Individual repeatability was measured on a weekly basis across multiple trials (n=5 pumpkinseed CTmax measurements, n=7 rusty crayfish) that varied in acclimation temperature, oxygen saturation, and salinity. CTmax was most strongly influenced by acclimation temperature. Repeatability varied based on the statistical approach and between the two species. Pumpkinseed repeatability across contexts was moderate (ca. 0.4), similar to previous reports on within-context CTmax repeatability studies in fishes. In rusty crayfish, repeatability was much lower (ca. 0.16). This suggests CTmax repeatability may be both taxon- and context-dependent, thus further investigation into repeatability is needed across species for this important and widely used trait.

GWAS Identifies SNP Markers and Candidate Genes for Off-Flavours and Protein Content in Faba Bean (Vicia faba L.).

Faba bean (Vicia faba L.) is a valuable ingredient in plant-based foods such as meat and dairy analogues. However, its typical taste and aroma are considered off-flavours in these food applications, representing a bottleneck during processing. Breeding is needed to develop varieties with minimal off-flavours and high protein content. The genetic regulation of these traits is underexplored. To dissect their genetic architecture, we performed a genome-wide association study (GWAS). A total of 245 faba bean accessions (the CGN population) were genotyped using the 90K-SPET targeted assay. These accessions were phenotyped in 2021 and 2022 in the Netherlands for protein, oil, fatty acids, lipid-derived products, phenolic acids, flavonoids, and tannins. The CGN population showed large phenotypic variation and moderate-to-high narrow-sense heritability for most traits. The growing environment significantly affected all traits, with trait-specific genotype-by-year (GxY) interactions. Condensed tannins and fatty acids were the most stable across the two years and had the highest heritability estimates (h2 > 0.6). GWAS identified a total of 148 single nucleotide polymorphisms (SNPs) loci in 2021 and 167 in 2022. Key candidate regulators included genes involved in lipid biosynthesis (ATS2, KAS, LPP), amino acid transport (CAT4) for protein storage, zero tannins locus-1 (zt-1), and regulators of the phenylpropanoid pathway, such as a shikimate kinase gene and transcription factors bHLH137-like and MYB. These results pave the way for validation studies and biotechnological applications to improve the quality of faba bean-based foods.