Low Heritability Research Articles

Variability of Agronomic Traits of Wheat (Triticum aestivum L.) Lines in Two Agroecosystems in Indonesia

Wheat is an important agricultural commodity in Indonesia, yet the country remains heavily reliant on imports to meet domestic demand. The diverse agroclimatic conditions in the highlands and lowlands pose significant challenges for national wheat production. This study aimed to evaluate the performance of wheat lines in two distinct altitude environments: Cipanas (1120 m above sea level) and Cisarua (600 m above sea level). An augmented randomized complete block design (RCBD) assessed 50 F6 wheat lines derived from the HP1744/”Selayar” cross. The results revealed significant variability in agronomic traits attributable to altitude differences. However, genotype-by-environment (GxE) interactions were found to be non-significant for all evaluated characters. Broad-sense heritability was classified as medium for the grain-filling period in Cipanas and seed weight of the main panicle in Cisarua, while all other traits exhibited low heritability. Based on the stress sensitivity index (SSI), 14 lines (28%) were identified as tolerant to higher temperatures in the medium-altitude environment, particularly in terms of seed weight of the main panicle. These findings are of utmost importance as they underscore the need to consider genetic and environmental factors in developing wheat cultivars suitable for Indonesia’s diverse agro-climatic conditions.

Estimation of genetic parameters for reproductive traits in Korean dairy cattle.

In Korea, dairy cattle breeding programs have historically prioritized productive, conformation traits, leading to positive improvements, yet reproductive traits have lagged in development. This study was conducted to develop the breeding program of key reproductive traits in the Korean dairy cattle population. Utilizing data from 7,596 farms and over seven million observations, we conducted quality control to rectify manual entry errors and selected traits in line with international genetic evaluation standards. Traits analyzed included heifer conception rate (HCR), interval from calving to first insemination (CF), cow conception rate (CCR), interval from first to last insemination (FL), and days open (DO). Genetic parameters were estimated using a single trait animal model for HCR and a multiple lactation animal model for CF, CCR, FL, and DO, considering contemporary group of herd-insemination year, insemination month, and monthly age (MA) as fixed effects. Results showed low heritability estimates, ranging from 0.007 to 0.035 across different traits and lactations. Theoretical reliability appears to be low on average due to the influence of heritability, but it showed sufficiently high reliability in some sires (over 0.8). In terms of genetic and phenotypic trends, capacity for reproductive traits declined for a long time until around 2014. In recent individuals, improved trend can be found. This study addressed the critical need for enhancing reproductive efficiency to complement the existing breeding goals, thereby supporting sustained economic viability in the dairy industry. The results underscore the need for improved data quality and methodological adjustments for reproduction records to enhance the genetic evaluation of dairy cattle in Korea.

Comparative Study of Single-Trait and Multi-Trait Genomic Prediction Models.

Conventional genomic selection models trait individually, neglecting complex trait interactions. Multi-trait models address this by considering genetic correlations, thus improving breeding value accuracy. Despite their theoretical benefits, quantifying these models' breeding advantages across genetic backgrounds is essential. This study evaluates the benefits of multi-trait models under varying population sizes and three levels of genetic correlations (low, medium, high) using simulations based on 50 K chip data from 5000 individuals. In equal heritability scenarios, the multi-trait GBLUP model consistently outperforms single-trait models, with breeding advantages increasing with heritability. For example, with a reference population of 4500, improvements range from 0.3% to 4.1%. Notably, trait combinations with low heritability are insensitive to changes in genetic correlation, with gains remaining ≤ 0.1% across different genetic correlations under low heritability conditions. In differing heritability scenarios, the multi-trait model's benefits vary, particularly enhancing low-heritability traits when paired with high-heritability ones. Additionally, modeling time increases as genetic correlation decreases. The results of this study indicate that multi-trait models improve breeding accuracy but require more modeling time and place higher demands on algorithms and software. We recommend breeding strategies tailored to different phenotypes and genetic backgrounds to balance efficiency and accuracy.

Exploring Transgressive Segregation for Enhanced Yield in F2 Segregants of Sesame (Sesamum indicum L.)

The experiment involved F2 generation of three superior crosses of sesame: Thilak X Ayali 1, Thilathara X Ayali 2 and Thilak X Ayali 5, grown in a Compact Family Block Design. A total of 200 plants were grown with a spacing of 30 x 25 cm, and observations were recorded on yield related characters. Significant variation was found among most traits, except for capsule length, capsule width, number of seeds per capsule and the number of primary branches. The cross Thilathara X Ayali 2 exhibited a high frequency of transgressive segregants for multiple traits, particularly for seed yield per plant, making it highly promising for further breeding efforts. Plant height had the highest mean and range, showing considerable potential for selection. CV analysis revealed high variability for traits like the number of capsules per plant and seed yield per plant. In contrast, low variability and high stability was observed for traits like capsule length, number of seeds per capsule and days to maturity. Higher PCV and GCV were recorded for traits like days to first flowering, number of capsules per plant, and seed yield per plant, showing substantial genetic and environmental influences. Moderate PCV and GCV were found for plant height and days to maturity, while traits like capsule length, number of seeds per capsule, and capsule width had the lowest PCV and GCV, indicating limited genetic variation. Days to first flowering and days to maturity showed high heritability combined with high genetic advance, suggesting the preponderance of additive gene action and are ideal for simple selection. Traits like capsule length, capsule width, and number of seeds per capsule showed low heritability and genetic advance, making them less ideal for selection. The cross, Thilathara X Ayali 2 should be prioritized in future generations to recover desirable segregants, especially for economically important traits like seed yield.

Short communication: Do veterinary diagnoses coming from electronic recording system of veterinary treatments have the potential to be used for breeding in small populations? The case of the dual-purpose Alpine Grey cattle breed

In cattle breeding, emphasis has historically been placed on productive traits, so-called primary traits, while health and fitness traits have been overlooked due to their low heritability and partly negative genetic correlations with productivity. In addition, the recording of phenotypes caused problems due to a lack of high-quality information and / or high costs of recording. This oversight has additionally led to increased incidences of fertility issues and health problems in cattle populations, resulting in economic losses and consumer concerns regarding animal welfare and food safety. This study investigates the potential use of veterinary diagnoses, collected via the Italian electronic recording system of veterinary treatments, for breeding decisions in the local dual-purpose Alpine Grey cattle breed for which the consideration of functional traits in breeding has also become imperative over the last years. The dataset comprised 97 821 records spanning from 2021 to 2023, representing 8 273 individuals and 18 110 lactations of the Alpine Grey breed. Each record documented the administration of treatments for mammary, respiratory, and urogenital pathologies. After data editing and model development, heritability estimates were obtained for each pathology using univariate linear animal models and gibbs sampling algorithms. Results indicate that mammary pathologies affected the highest number of cows (11%), followed by respiratory (4%) and urogenital (5%) pathologies. Heritability estimates ranged from 0.01 to 0.04 across all traits, confirming generally low heritability values. Respiratory pathologies exhibited the highest heritability (0.04; sd 0.04), followed by mammary (0.03; sd 0.01) and urogenital (0.01; sd 0.01) pathologies. This study, although preliminary, provides valuable insights into the health status of local dual-purpose Alpine Grey cattle and highlights the potential of considering veterinary diagnoses for improving animal health and welfare in dairy cattle breeding. However, the low heritability of these traits, which is consistent with literature data, clearly shows the current limitations of using them for breeding. Further, the diagnostic key of the Italian electronic recording system of veterinary treatments should be specified for the use of health data for breeding purposes, as it is formulated in too general manner in its current form. Nevertheless, their significance for animal welfare and economic sustainability underlines the need for their consideration in dairy cattle breeding. Therefore, further research with larger sample sizes and consideration of additional indicators, such as somatic cell counts, is recommended to enhance the accuracy of genetic evaluations and improve breeding strategies for sustainable cattle production.

Integrated GWAS and transcriptome analysis reveals key genes associated with muscle fibre and fat traits in Gushi chicken

ABSTRACT 1. In the following experiment meat quality traits of a Gushi-Anka F2 resource population were measured, and their heritability estimated. Intramuscular fat (IMF) had medium heritability (0.35) but leg muscle fibre density (LMD), leg muscle fibre diameter (LMF), breast muscle fibre density (BMD), fresh fat content (FFA), and absolute dry fat content (AFC) had low heritability (0–0.2). The IMF presented the most important genetic additive effect among the poultry meat quality-related traits studied. 2. The phenotypic data of meat quality traits in the Gushi-Anka F2 resource population were combined with genotyping by sequencing (GBS) data to obtain genotype data. Six meat quality traits in 734 birds were analysed by GWAS. Based on these variants, 83 significant (–log10(p) > 4.42) single nucleotide polymorphisms and four quantitative trait loci (QTL) regions corresponding to 175 genes were identified. Further linkage disequilibrium (LD) analysis was conducted on chromosome 13 (Chr13) and chromosome 27 (Chr27) QTL regions. 3. Based on the transcriptome data and GWAS results, 12 shared genes - ITGB3, DNAJC27, ETV4, C7orf50, FKBP1B, G3BP1, IGF2BP1, KCNH6, LOC416263, SCARA5, SMIM5 and TBL1XR1 were identified as candidate genes influencing muscle fibre and fat traits.

INTERRELATION OF YIELD AND ITS COMPONENTS IN COTTON (Gossypium hirsutum L.) GENOTYPES

Cotton is regarded as a profitable crop that gives people fiber and shelter. Research focuses on how yield, its components, and related attributes work together to enhance cotton. During the Kharif season of 2022, the present study was completed, implementing a randomized complete block design with ten genotypes and three replications. The study took place at the Nuclear Institute of Agriculture (NIA), located in Tandojam. This work aimed to examine the correlation and regression between upland cotton genotypes and heritability estimates for traits associated with yield. The outcomes showed that all of the parameters in the mean square of the ANOVA were significant. In contrast to the remaining genotypes, genotype FH-142 displayed the most favorable performance; it had the tallest plants, more sympodial branches, more bolls per plant, an improved seed index, and the longest staple length. The genotype CRIS-342 came in second, exhibiting good plant height, sympodial branches, a good number of bolls per plant, a ginning outturn, and the highest boll weight among the other genotypes. The findings of the correlation and regression indicated that the number of bolls per plant-1 had a highly significant and positive relationship with monopodial branches plant-1 (r = 0.73*) and (b = 2.45) and that the number of bolls per plant had a strong relationship with seed cotton yield plant-1 (r = 0.83**) and (b = 3.29). Staple length and seed cotton yield plant-1 had a negative correlation (-0.77*) with regression (b = -4.58). The highest heritability estimates in the broad sense are for monopodial branch plants (84.61), ginning outturn% (97.03), bolls plant-1 (93.96), plant height (90.70), staple length (79.31), and seed index (71.42). However, the boll's weight showed a low heritability (23.71). Further breeding programs can utilize genotype FH-142 to increase the number of sympodial branches, increase the number of boll plants, and improve the staple length. Genotype CRIS-342 can be utilized for medium-stature plant height, boll weight, and better ginning outturn. However, genotype NIA-BT-40 can be utilized for short-strategy plants with the highest ginning output.

Influence of different environmental challenges on the expression of reproductive traits in Holstein cattle in Southern Brazil.

The aim of this study was to assess the impact of genotype-environment interaction (GEI) on the manifestation of traits such as age at first calving (AFC), age at first service (AFS), and calving interval (CI) through the application of the reaction norm model in Holstein cattle raised in Paraná state, Brazil. Utilizing data from the milk testing service of the Paraná Association of Holstein Cattle Breeders (APCBRH), this study analyzed records from 179,492 animals undergoing their first, second, and third lactations from the years 2012 to 2022. These animals were part of 513 herds spread across 72 municipalities in Paraná. The environmental gradient was established by normalizing contemporary group solutions, derived from the animal model, with the 305-day-corrected milk yield serving as the dependent variable. Subsequently, reaction norms were determined utilizing a Random Regression Model. Spearman's correlation was then applied to compare the estimates of breeding values across different environmental gradients for the studied traits. The highest EG (+ 4) indicates the least challenging environments, where animals experience better environmental conditions. Conversely, lower EG (-4) values represent the most challenging environments, where animals endure worse conditions. The only trait that exhibited a moderate heritability magnitude was AFC (0.23) in the least challenging environmental condition. The other traits were classified as having low heritability magnitudes regardless of the evaluated environmental gradient. While minimal evidence was found for the influence of GEI on CI, a clear GEI effect was observed for AFC and AFS across all environmental gradients examined. A reversal in genotype ranking occurred under extreme environmental conditions. The findings suggest that the best-performing genotype under one environmental gradient may not necessarily excel under another.

Inheritance Analysis for Quantitative Traits in F2 Populations of Mustard Genotypes Grown Under Heat Stress Environments

Genetic variability is the basic requirement for improving crops which further leads to progress in crop breeding. This study was carried out to determine the inheritance pattern of various agronomically important traits in F2 populations of mustard genotypes. The objective of this study was to determine the genetic variability for agro-morphological traits under control conditions (CC) and heat stress environments (HS) and provide the future strategies to improve this important oilseed crop. The experiment was conducted at the Botanical Garden, Sindh Agriculture University, Tandojam. During 2022-23, a total of 27 genotypes including nine parental mustard genotypes and eighteen F2 progenies were grown under control and heat stress conditions. The experiment was laid out in a randomized complete block design with three replications. The analysis of variance for the genotypes, treatments, and F2 progenies revealed significant differences (P≤0.05) in most of the studied characters, highlighting the importance of genetic variations in the evaluated breeding materials of mustard for stress breeding. When estimating heritability for different characters, including seed yield plant-1, it was found that F2 crosses showed varying levels of heritability for different characteristics, ranging from low to moderate and high. This implies that careful selection may be conducted for traits that have low heritability, especially for seed yield.; however, those characters which showed high heritability would be selected at early generation stage to improve the characters.

Estimation of Genetic Parameters for Milk Production Rate and Its Stability in Holstein Population.

Milk production rate (MPR) refers to the rate of milk secretion per hour (kg/h), calculated from the harvested milk yield and milking interval, and it is considered an appropriate measure to evaluate the production potential of cows. The objective of this study was to estimate the phenotypic and genetic parameters of milk production rate traits. In this study, the milking records of 4760 Holstein cows were collected, and four milk yield traits and six milk production rate traits were defined. The MIXED procedure was used to detect the impacts of non-genetic effects on milk yield and milk production rate traits, including parity, measured season and lactation stage. Variance and covariance components for milk yield and milk production rate traits were estimated using a univariate linear repeatability model. Parity, measurement season and lactation stage had significant effects (p < 0.01) on milk yield, milk production rate and its stability. Milk yield and milk production traits had high heritability, and ranged from 0.25 to 0.39. The stability of milk production rate had low heritability (0.04~0.05). Milk production rate is beneficial for the devolving novel trait in dairy breeding and provides new insights for herd management and genetic selection of production performance of dairy cattle.

Molecular markers and their importance for pig production and breeding: an overview

The DNA polymorphisms are changes in the sequence of nucleotide bases that result in genetic differences among two or more individuals. These polymorphisms have been used as molecular markers and contribute to studies in swine related to genetic diversity, pedigree analysis, selection, and discovery of genomic regions controlling economically important traits. Among the molecular markers, Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) have been most studied in pigs mainly due to their greater abundance in the genome, ease of detection and possibility of automation. The knowledge and application of information from molecular marker shave contribute to a more efficient and competitive pig production. Furthermore, in pig breeding programs, the molecular markers are especially important to allow higher efficiency in selection for traits with low heritability, difficult or expensive to measure, sex-limited, and that express later in the animal’s life, resulting in a higher prediction accuracy for these traits. Considering the relevance of DNA molecular markers for the development of pig production and the advances in research in this area, we aimed to present an overview of the main research results related to the discovery, contribution and implementation of molecular markers in pig breeding and production. This review contextualizes and summarizes important results and recent findings in order to update the reader and stimulate future research based on the identification and relevance of molecular markers applied to pig production.

Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines.

In plant breeding programs, rapid production of novel varieties is highly desirable. Genomic selection allows the selection of superior individuals based on genomic estimated breeding values. However, it is worth noting that superior individuals may not always be superior parents. The choice of the crossing pair significantly influences the genotypic value of the resulting progeny. This study has introduced a new crossing strategy, termed cross potential selection, designed to expedite the production of novel varieties of inbred crops. Cross potential selection integrates fast recurrent selection and usefulness criterion to generate novel varieties. It considers the segregation of each crossing pair and computes the expected genotypic values of the top-performing individuals, assuming that the progeny distribution of genotypic values follows a normal distribution. It does not consider genetic diversity and focuses only on producing a novel variety as soon as possible. We simulated a 30-year breeding program in 2 scenarios, low heritability (h2=0.3) and high heritability (h2=0.6), to compare cross potential selection with 2 other selection strategies. Cross potential selection consistently demonstrated the highest genetic gains among the 3 strategies in early cycles. In the 3rd year of the breeding program with a high heritability (h2=0.6), cross potential selection exhibited the highest genetic gains, 138 times that of 300 independent breeding simulations. Regarding long-term improvement, the other selection strategies outperformed cross potential selection. Nevertheless, compared with the other 2 strategies, cross potential selection achieved significant short-term genetic improvements. Cross potential selection is a suitable breeding strategy for the rapid production of varieties within limited time and cost.

PSVI-6 Genomic determinants of the rumen microbiome and metabolome in Angus steers

Abstract The rumen microbiome provides approximately 70% of energy required for the ruminant host through fermentation byproducts. Due to microbial impacts on host health and productivity, several studies have associated microbiome and metabolome variation with important sustainability phenotypes, such as feed efficiency and methane emissions. Recent studies have indicated the microbial communities present in rumen fluid are under low-to-moderate host genetic control. However, microorganisms present on the rumen wall have been underrepresented in research, negating their unique role in host-microbiome interactions. Current studies investigating heritability of the rumen planktonic microorganisms are plagued by small sample sizes, high management and breed heterogeneity, and low resolution for classifying microbial communities. To determine the heritability of the rumen fluid and epithelium-associated microbiome and metabolome, Angus steers (n = 350) were enrolled in a 70-d feed efficiency trial, where real-time dry matter intake was measured. Body weights were collected throughout the trial to calculate average daily gain and residual feed intake. Mid-trial, a novel surgery method was used to swab the rumen wall to capture epithelium-associated microorganisms. On d 70, 50 mL of rumen fluid was obtained from steers using orogastric tubing for collection of planktonic microbial communities. Metagenomic DNA extracted from both rumen fluid and epimural samples was used for reduced representation sequencing to predict microbial features such as diversity, composition, and putative function. Genomic DNA isolated from whole blood was used to perform low-pass whole genome sequencing for use in downstream heritability estimates and variant association analyses. Many core microbial abundances are under low-to-moderate host genetic control (h2 &amp;gt; 0.15; P &amp;lt; 0.05); however, many microorganisms had low heritability estimates (h2 &amp;lt; 0.10). Preliminary genome-wide associations studies are vastly underpowered to detect host genetic variants associated with microbial features, but data generated using the total number of animals will better refine these polymorphisms. Several key heritable metabolites were identified in amino acid metabolism pathways in rumen fluid (P &amp;lt; 0.05). The rumen microbiome appears to act as a complex polygenic trait and incorporating microbial features into prediction models may improve feed efficiency estimations. Understanding host genetic control of the rumen microbiome and metabolome may empower downstream applications to enhance genomic and phenotypic predictions for feed efficiency and other sustainability traits in beef cattle.

PSLBI-26 Purebred-crossbred genetic parameters for sow pelvic organ prolapse

Abstract The incidence rate of sow pelvic organ prolapses (vaginal, uterine, or rectal) has increased in recent years. Using a relatively large dataset, this study aimed to estimate the genetic parameters for sow pelvic organ prolapse in purebred and crossbred sow herds. Data were collected from 2018 to 2023 in 32 purebred and 8 crossbred farms, including records from 75,162 purebred sows of a single maternal line and 18,988 two-way crossbred commercial sows. Pelvic organ prolapse was categorized as either normal or prolapsed at the individual sow level, with average incidence rates of 1.81% and 3.93% for purebred and crossbred, respectively. Prolapses in purebred and crossbred were considered two different traits in the model. The bivariate model included fixed effects of parity group and region, and random effects of contemporary group, additive genetic and residual. The contemporary group was defined as the farm, mating year, and month at the first parity. Genetic parameters were estimated using BLUPF90+ with the AIREML option. Heritability estimates were 0.09 for purebreds and 0.11 for crossbreds, with a genetic correlation of 0.83. Results suggested that selection strategies aimed at reducing prolapse incidence in purebred herds will also benefit crossbred sow herds. Due to the low heritability, reducing the incidence of prolapse will have to rely on genetic improvement and enhanced animal management strategies.

313 Many farmers want a prediction of future performance, not necessarily breeding potential

Abstract High heritability is a characteristic of many performance traits in cattle translating to a relatively strong correlation between an (accurate) estimated breeding value for an animal and its (future) production potential. However, the broad sense heritability (i.e., numerator in the formula includes both additive and non-additive genetic variance) is often larger than the narrow sense heritability (i.e., numerator includes only the additive genetic variance) especially for low heritability traits like reproductive performance. Moreover, the repeatability of a trait can be greater again, the difference between the heritability and repeatability is the inclusion of a permanent environmental variance in the numerator. Accurate and pertinent omic-based animal-level features can contribute to an increase in narrow sense heritability owing to a possible reduction in the residual variance; such data can also provide insights into both non-additive genetic variance and the permanent environmental variance. Even at the level of the contemporary group, omic-level data from the likes of bulk blood/saliva/milk sample, can improve how systematic environmental effects are modeled in the mixed model equations thus also reducing the residual variance. The greater heritability will contribute to a strengthening of the correlation between future phenotypic performance potential and estimated additive genetic merit. Importantly, omic measures for individual animals can help predict the permanent environmental effect of that animal capturing the yet untapped contributor to phenotypic variance. Irrespective, predictions need to be replaced by prescriptions; end users are inundated with data yet crave actionable information. Animal breeders have a lush (pardon the pun!) history of distilling estimates of genetic merit for a plethora of traits into a single value per animal (i.e., breeding indexes); this is the first step in transitioning from predictions to prescriptions. Given the familiarity of end users with breeding indexes, the potential exists to develop production indexes to rank commercial animals on future expected performance taking cognizance of genetic and non-genetic effects. Such production indexes align well with the associated breeding index but where the estimates of genetic merit for the traits in question are replaced by estimates of production merit; these estimated production values are the sum of the additive genetic, non-additive genetic and permanent environmental effects. The weighting factors in the production indexes are more short-term using current costs and prices as opposed to breeding indexes which are longer term. In comparison with the breeding indexes, the production indexes can include ancillary information like gender, age, and month of calving/birth. Like breeding indexes, they are updated in real time. Examples of the application of genome-enabled production indexes are guides for valuing animals for purchase or culling.

Genetic variation in phenology of wild Arabidopsis thaliana plants.

Phenology and the timing of development are often under selection, but at the same time influence selection on other traits by controlling how traits are expressed across seasons. Plants often exhibit high natural genetic variation in phenology when grown in controlled environments, and many genetic and molecular mechanisms underlying phenology have been dissected. There remains considerable diversity of germination and flowering time within populations in the wild and the contribution of genetics to phenological variation of wild plants is largely unknown. We obtained collection dates of naturally inbred Arabidopsis thaliana accessions from nature and compared them to experimental data on the descendant inbred lines that we synthesized from two new and 155 published controlled experiments. We tested whether the genetic variation in flowering and germination timing from experiments predicted the phenology of the same inbred lines in nature. We found that genetic variation in phenology from controlled experiments significantly, but weakly, predicts day of collection from the wild, even when measuring collection date with accumulated photothermal units. We found that experimental flowering time breeding values were correlated to wild flowering time at location of origin estimated from herbarium collections. However, local variation in collection dates within a region was not explained by genetic variation in experiments, suggesting high plasticity across small-scale environmental gradients. This apparent low heritability in natural populations may suggest strong selection or many generations are required for phenological adaptation and the emergence of genetic clines in phenology.

Association between psychiatric disorders and irritable bowel syndrome: A bidirectional Mendelian randomization study

ObjectivePrevious studies have suggested that irritable bowel syndrome (IBS) is strongly associated with psychiatric disorders. However, it is unclear whether this association is causal, concomitant, or accidental. Thus, we performed Mendelian randomization (MR) analysis to evaluate the causal effects of several psychiatric disorders on IBS. MethodsSummary data of genome-wide association studies (GWASs) were obtained mainly from the Psychiatric Genomics Consortium (PGC) on individuals of European ancestry and from a recent GWAS on IBS. We used three MR methods, the inverse-variance weighting (IVW), weighted median (WM), and MR-Egger regression (MR-Egger). In addition, two other indicators, namely, the MR-IVW Cochran's Q statistic and MR-Egger intercept, were used to assess heterogeneity and detect directional horizontal pleiotropy, respectively. ResultsHeritability was high for bipolar disorder (81.18 %, 95 % CI = 73.18–148.18 %), schizophrenia (33.88 %, 95 % CI = 33.57–38.19 %), and panic disorder (30.66 %, 95 % CI = 20.74–40.58 %). For other disorders, there was a low liability-scale SNP heritability for major depressive disorder (MDD) (0.67 %, 95 % CI = 0.61–0.73 %), anxiety disorder (7.63 %, 95 % CI = 1.67–13.59 %), PTSD (0.96 %, 95 % CI = 0.12–1.8 %), and IBS (2.44 %, 95 % CI = 2.13–2.75 %). We also observed that schizophrenia had a significant causal effect on IBS according to MR-IVW. Notably, the individual causal estimates of genetic instruments for MDD and schizophrenia were heterogeneous, but no pleiotropic effects were observed. ConclusionsOur analyses revealed the causal effects of MDD and schizophrenia on IBS, a matter that has been subject to debate for decades, and also showed that IBS had causal effects on MDD.

Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs.

The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570-27186456 and SSC11:7220366-14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.

Quantitative genetic analysis indicate non-heritability of major fatty acid in the muscle of Chinese mitten crab (Eriocheir sinensis)

The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species, and crab meat generally has the high percentage of long-chain polyunsaturated fatty acids (LC-PUFAs) in the total fatty acids, which contributes the unique flavor and high nutrition value for adult crab. Muscle is the largest edible tissue in crustaceans, containing a variety of fatty acids, and understanding the genetic parameters of fatty acids in the meat of E. sinensis would be useful for the aquaculture of this species. This study investigated the heritability, genetic and phenotypic correlations of major fatty acids in the muscle of E. sinensis. Progeny from 25 full-sib families were reared under a common environment until they reached market size, and 429 mature crabs were selected for analysis. The results showed that the heritabilities of most fatty acids were low ranged from 0.01 (n-3PUFA) to 0.21 (MUFA), but the high heritabilities were recorded for C20:3n3 and C20:3n6 with values of 0.99 and 0.32, respectively. Furthermore, the strongest positive genetic correlations were found between C20:5n3 and C22:6n3(0.99), n-3PUFA(0.99), and PUFA and LC- PUFAs (0.99), n-3PUFA(0.99), whereas the strongest phenotype correlation was found between C20:5n3 and n-3 PUFA (0.96); C20:3n6 showed a significant negative genetic correlation with C20:3n3(−0.86) and C18:0 (−0.98), whereas C20:3n6 showed significant negative phenotypic correlation with C20:3n3(−0.14), C20:5n3(−0.15) and C22:6n3(−0.18). In conclusion, the percentages of major fatty acids, particularly C20:5n3, C22: 5n3 and C20:4n6, in E. sinensis muscle have very low heritabilities, suggesting that these fatty acids contents/composition in the muscle are ineffective targets for the selective breeding programs of E. sinensis.

Genetic improvement approaches of indigenous cattle breeds for adaptation, conservation and sustainable utilization to changing climate in Ethiopia

This paper attempts to review the cattle genetic improvement approaches for sustainable utilization, adaptation, and conservation in the face of changing climatic conditions. Livestock production is affected by climate change, which poses a greater threat to populations that rely on them for their overall food security. Climate change negatively affects cattle production directly through its impact on animal physiology, behavior, and health and indirectly through its effect on feed and water availability, quality and quantity of pasture, forage crops, and rangeland due to increased temperature droughts. Improvement of cattle genetic resources that are efficient and well adapted to extreme temperatures, low-quality diets, and disease challenges is critical to effectively cope with climate change. Designing suitable breeding strategies will facilitate improving the performance of cattle breeds and enhance their tolerance to the dynamics of climate change. Replacement of local cattle breeds with exotic ones and unplanned crossbreeding with them without enough consideration of environmental conditions are among the major factors contributing to the loss of locally adapted breeds that possess certain adaptive traits. Maintenance of indigenous cattle’s genetic diversity, which underpins resistance to environmental stresses is a viable strategy to mitigate the possible effects of future climatic challenges. In contrast to the traditional selection, genomic selection increases the accuracy of selection with the largest genetic gain, for the low heritability traits such as adaptability and longevity. In conclusion, any breeding strategies should be relevant in terms of breed suitability, performance, and adaptability in the given production environment to sustain cattle production.