Heritability Research Articles

Genetic parameters for egg quality traits in Pekin ducks

Pekin duck (Anas platyrhynchos domesticus) is the most widely consumed duck protein with nearly 35 million animals produced annually in the United States and exported worldwide. Pekin ducks are primarily utilized in meat production, so very little information is available about their heritability estimates and genetic correlations for traits related to egg quality. Genetically improving duck populations together with the implementation of more efficient nutritional and management strategies is paramount for the long-term sustainability of the US duck industry. There is a potential opportunity to increase meat duck productivity by improving hatching egg quality. The main objectives of this study were to estimate heritability and genetic correlations for various egg quality traits in a commercial population of Pekin ducks. Egg quality traits for 612 Pekin duck females were measured through 3 time points over 2 generations (GEN) [30, 32, and 35 wk of age (WOA)]. GEN 2 had an additional sampling occurring at 40 WOA. Genetic correlations and heritability estimates were calculated for all the traits using the BLUPF90 software, the Restricted Maximum Likelihood (REML) method, and a pedigree containing 9,418 individuals. All egg quality traits evaluated are moderately to highly heritable ranging from 0.20 for Haugh Unit (HU) and Vitelline Membrane Strength (VMS) to 0.71 for shell ratio (SR). Heritability estimates were calculated for each age of collection and in general heritability increased up to 35 WOA. Genetic correlations between egg quality traits showed a wide range of positive and negative relationships with correlation strengths ranging of -0.80 [yolk ratio (YR) and albumin ratio (AR)] to 0.99 [egg volume (EV) and egg weight (EW)]. The results of this study highlight the potential to improve hatching egg quality within Pekin ducks using a multi-trait selection scheme through direct genetic selection.

Experimental unbalance: reflections on genetic parameters and corn selection gain

Genetic progress depends on the components of variance and genetic parameters. In this context, the objective of this work was to identify the maximum allowed percentage of experimental imbalance in the estimation of variance components, genetic parameters and selection gain in intervarietal corn hybrids. The experimental design used was randomized blocks, with 60 corn hybrids with three replications. Random subsets of data were created in order to express unbalance scenarios of the phenotypic matrix, we obtained 9 scenarios (0, 10, 20, 30, 40, 50, 60, 70 and 80% unbalance).Thus, the genetic variance of the paternal genitor, the genetic variance of the maternal genitor, additive variance, individual phenotypic variance, narrow-sense heritability of intervarietal additive effects for the paternal genitor were estimated, narrow-sense heritability of intervarietal additive effects for the maternal genitor, narrow-sense heritability, broad-sense heritability, genotypic variation coefficient between progenies and variation coefficient residual. Narrow sense heritability reveals high magnitude for the characters cob mass and hundred grain mass. Maternal effect is expressed through ear insertion height, ear grain mass, cob mass and diameter, number of rows, ear mass and length, and grain yield. The imbalance inflates the variance components and genetic parameters for the highlighted characters. It supports 10% imbalance in the data matrix without compromising the reliability of the estimates. Pronounceable selection gains are obtained for grain yield based on pressures of 1 and 5%. An unbalance of 10% is supported in the selection gain for cob mass, ear length and hundred grain mass.

Genetic assessment of litter size, body weight, carcass traits and gene expression profiles in exotic and indigenous rabbit breeds: a study on New Zealand White, Californian, and Gabali rabbits in Egypt

Rabbits are essential for commercial meat production due to their efficient growth and productivity, breeds like New Zealand White (NZW), Californian (CAL), and Gabali (GAB) rabbits offer unique genetic traits in litter, growth, and carcass traits. This study aimed to evaluate heritability (h2), genetic and phenotypic correlations (rg and rp) for litter size, body weight and carcass traits across California (CAL), New Zealand white (NZW) and Gabali (GA) rabbits. Along with exploring gene expression profiles of TBC1D1, NPY, AGRP, POMC, Leptin, GH, GHR, IGF-1, CAA, GPR, ACC, CPT1, FAS, and CART in the brain, liver, and meat tissues of different rabbit breeds. The breed genotype had a significant impact on litter size (LS), litter weight (LW), body weight at 12 weeks (BW12), and daily weight gain (DWG) traits. NZW rabbits displayed superior performance in terms of litter size and litter weight, while CAL rabbits recorded the highest values for BW12 and DWG. Heritability estimates (h2) were generally low for litter size (ranging from 0.05 to 0.12) and medium for body weight (ranging from 0.16 to 0.31). Both genetic (rg) and phenotypic (rp) correlations for litter size were positive and moderate (ranging from 0.08 to 0.48), while correlations for body weight ranged from 0.21 to 0.58. Additionally, CAL rabbits exhibited higher carcass traits compared to NZW and GA rabbits. In terms of breed-specific gene expression patterns, New Zealand White (NZW) rabbits displayed the highest expression levels of key genes related to energy metabolism (TBC1D1), appetite regulation (NPY, AGRP, POMC), nutrient transport (CAA), and G protein-coupled receptors (GPR) in both brain and liver tissues. Californian (CAL) rabbits exhibited superior gene expression of the ACC gene in brain tissue and GH, GHR, and IGF-1 genes in brain and meat tissues. Gabali (GAB) rabbits demonstrated the highest expression levels of TBC1D1, NPY, AGRP, GPR, and ACC genes in meat tissues. These breed-specific gene expression differences, combined with genetic evaluation efforts, have the potential to enhance reproductive and productive performance in rabbits, offering valuable insights for rabbit breeding programs and genetic selection.

The world as I see it: genetic and environmental influences on primal world beliefs in a large Swedish twin sample

ABSTRACT Beliefs about the general character of the world – called primals – have received much attention in recent years. Primals (e.g. believing that the world is safe) are associated with psychological and social outcomes, such as personality traits, character strengths and life satisfaction. We performed the first study of genetic and environmental influences on primals, and explored phenotypic associations between primals and the big five personality traits, in a large (~9000) population-wide Swedish twin sample. Correlations between primals and personality traits were low to moderate. Broad-sense heritability estimates of primals ranged between 21% and 49%, suggesting that genetic factors contribute significantly to people’s beliefs about the general character of the world. In contrast, we found little support for shared environmental effects (e.g. rearing environment). Conclusively, we demonstrate that primals and personality are related, yet distinct, constructs and that individual differences in primals depend on both genetic and non-shared environmental factors.

Association mapping of important agronomic traits in Mucuna pruriens (L.) DC.

BackgroundThe tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model.ResultsThe results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon’s information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10− 3 for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83.ConclusionFifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume.

Exploring Genetic Variability and Morpho-Agronomic Trait Associations Among Ethiopian Flax (Linum Usitatissimum L.) Accessions for Enhanced Fiber and Seed Yield

ABSTRACT Flax is a versatile crop grown for its fiber and seed oil. Despite extensive conservation efforts in Ethiopia, the genetic potential of flax accessions conserved in the gene bank remains largely underexplored for fiber and seed yield. Here, we aimed to assess the genetic variability and association of morpho-agronomic traits and identify potential accessions for fiber and seed yield among 150 flax accessions. The study was conducted at Holeta Agricultural Research Center during 2022/23 growing season using an augmented design. Data were collected on flowering and maturity dates, plant and technical height, basal and secondary branch, boll and seed numbers, 1000-seed weight, and yield. Results revealed significant variation both between blocks and within treatments, with flowering time, maturity, plant height, boll number, seed weight, and yield contributing for the highest variability (58.7%). Cluster analysis revealed nine distinct genetic groups, each exhibiting specific trait patterns. Seed yield had strong associations with maturity, plant height, and boll number. High broad-sense heritability for days to flowering, plant height, and yield traits suggests selection could be effective based on phenotypic expressions. The study highlights the potential of Ethiopian flax genetic diversity for enhancing fiber and seed yield, suggesting effective selection based on key traits.

Accelerated mustard [Brassica juncea (L.) Czern &amp; Coss] improvement for salt tolerance: Photosynthetic traits and selection indices

AbstractPhotosynthetic traits can sense and signal abiotic stress at early growth stages of mustard [Brassica juncea (L.) Czern &amp; Coss]. The integration stress responses with multiple selection indices can select the fittest/tolerant genotypes. With this goal, a set of 210 diverse mustard genotypes were phenotyped under control and salt‐stress (electrical conductivity = 12 dS m−1). Significant dynamic response of the plant to salt stress with reduction for all morpho‐physiological traits and genotype × treatment interaction was observed under salinity. A higher accumulation of Na+ was recorded in the roots, followed by shoots. A close correspondence between phenotypic coefficient of variation and genotypic coefficient of variation under control and salt stress conditions results in high heritability (h2) in broad sense. A significant negative association between shoot and root Na+ content and rate of photosynthesis also indicated that Na+ was significantly restricted in the root. This was not found to be efficient because considerable Na+ buildup was observed in the shoot. Multiple trait‐based indices, such as membership function value of salinity tolerance, classical Smith–Hazel index, factor analysis ideotype–best linear unbiased prediction index, and multi‐trait genotype‐ideotype distance index, deduced CS 2009‐159, CS 2009‐420, CS 2009‐124, and Swarn Jyoti (RH‐9801) are promising for identifying salt‐tolerant genotypes that can serve as donors for the development of salt‐tolerant cultivars.

Modeling embryo survival: Genetic and environmental influences on eye-up rate in a north American Atlantic salmon selective breeding program

Selective breeding programs improve target traits but can also unintentionally change genetically correlated traits in the selected strain. The U.S. Department of Agriculture–Agricultural Research Service National Cold Water Marine Aquaculture Center (NCWMAC) in Franklin, Maine maintains a North American Atlantic salmon selective breeding program focused on improving commercially important traits (e.g., carcass weight). However, the program has experienced a significant decline in the percent of eyed embryos over its 14 years of operation, leading to concerns that reproductive performance was being unintentionally changed by selection for the target traits. The aims of this study were to 1) model eye up success as a potentially heritable trait utilizing the recorded pedigree and 2) assess the relationship between eye-up rate and environmental conditions experienced by the broodstock. Over 14 years of data encompassing 1537 full-sib families produced by 1537 dams and 885 sires was analyzed. Counts of eyed embryos and carcass weight were analyzed with a linear multi-trait trait model that included maternal genetic effects and a spawn year effect to determine the strength of genetic and environmental influences on the eyed embryo rate. To investigate the environmental influences in more detail, we assessed the correlation between water quality parameters in the broodstock rearing system observed over the same 14-year time period and the estimated spawn year effects. There was small heritability of the direct genetic effect (0.059 ± 0.009) and the maternal genetic effect (0.039 ± 0.013). Comparatively, the proportion of phenotypic variance explained by the maternal environmental effect was moderate (0.165 ± 0.012). The genetic correlations between carcass weight and eye up rate were very small and had a large amount of uncertainty. The correlation between the direct genetic effects on eye-up and carcass weight was −0.0528 ± 0.1469 while the correlation between the maternal genetic effect on eye-up and the direct genetic effect on carcass weight was 0.2030 ± 0.1791. The correlation between maternal common environmental effects on the two traits was also low at 0.0676 ± −0.0804. The effect of spawn year was statistically significant (p < 0.01), and the values were negatively correlated with mean un-ionized ammonia (mg/L, −0.56, p = 0.04,), nitrate concentrations (mg/L r = −0.65, p = 0.01) and temperature (°C, r = −0.61, p = 0.02) experienced by the broodstock prior to spawning. Overall, the results suggest that the decrease in eyed embryos over time was not caused by inadvertent selection but instead due to increases in water temperature and/or nitrogenous waste concentrations in the broodstock rearing system. Further investigation of the mechanisms behind these apparent environmentally induced declines and potential mitigation measures to prevent decreases in eye-up rates are needed.

Genetic effects on the skin methylome in healthy older twins

Whole-skin DNA methylation variation has been implicated in several diseases, including melanoma, but its genetic basis has not yet been fully characterized. Using bulk skin tissue samples from 414 healthy female UK twins, we performed twin-based heritability and methylation quantitative trait loci (meQTL) analyses for >400,000 DNA methylation sites. We find that the human skin DNA methylome is on average less heritable than previously estimated in blood and other tissues (mean heritability: 10.02%). meQTL analysis identified local genetic effects influencing DNA methylation at 18.8% (76,442) of tested CpG sites, as well as 1,775 CpG sites associated with at least one distal genetic variant. As a functional follow-up, we performed skin expression QTL (eQTL) analyses in a partially overlapping sample of 604 female twins. Colocalization analysis identified over 3,500 shared genetic effects affecting thousands of CpG sites (10,067) and genes (4,475). Mediation analysis of putative colocalized gene-CpG pairs identified 114 genes with evidence for eQTL effects being mediated by DNA methylation in skin, including in genes implicating skin disease such as ALOX12 and CSPG4. We further explored the relevance of skin meQTLs to skin disease and found that skin meQTLs and CpGs under genetic influence were enriched for multiple skin-related genome-wide and epigenome-wide association signals, including for melanoma and psoriasis. Our findings give insights into the regulatory landscape of epigenomic variation in skin.

Multivariate Analysis Techniques and Tolerance Indices for Detecting Bread Wheat Genotypes of Drought Tolerance

Drought stress is one of the biggest hardships in wheat cultivation because of the strong negative relationship between water deficit and crop yields owing to a lower grain weight, a shorter grain-filling period, a slower grain-filling rate, and reduced grain quality. Genotype–environment interaction (GEN:ENV) generates hardships in selecting wheat genotypes and ideotypes due to biased genetic estimates. Diverse strategies have been proposed to respond to the urgent need for concurrent improvements in yield performance and stability. This study’s purpose was to appraise genetic variation and GEN:ENV effects on yield and yield components to discover drought-stress-tolerant genotypes and ideotypes. This study evaluated 20 genotypes in three consecutive seasons under non-stressful and drought-stress conditions in a total of six ENVs. The broad-sense heritability ranged from 0.54 to 0.82 based on expected mean squares and ranged from 0.60 to 0.90 based on plot mean, but in the other three ways, it was usually greater than 0.90. The high values of (σgen:env2) revealed the effect that broad-sense heritability has on the expression of traits. G01, G03, G06, G07, G08, G10, G12, G13, G16, G17, and G18 were stable genotypes for grain yield (GY), according to additive main effects and a multiplicative interaction biplot for the six ENVs. Based on scores in the weighted average of absolute scores biplot (WAASB), G02, G04, G05, G08, G10, and G18 were selected as stable and high-performance for GY, and they were all selected as the best genotype groups using the WAASB-GY superiority index. From the results obtained from principal component analysis and hierarchical clustering and from the tolerance discrimination indices, G02, G04, G05, G18, and G19 are genotypes that produce a suitable yield under non-stressful and drought-stress conditions. In essence, combining approaches that take into consideration stability and high performance can contribute significantly to enhancing the reliability of recommendations for novel wheat genotypes.

Forensic height estimation using polygenic score in Korean population.

Height is known to be a classically heritable trait controlled by complex polygenic factors. Numerous height-associated genetic variants across the genome have been identified so far. It is also a representative of externally visible characteristics (EVC) for predicting appearance in forensic science. When biological evidence at a crime scene is deficient in identifying an individual, the examination of forensic DNA phenotyping using some genetic variants could be considered. In this study, we aimed to predict 'height', a representative forensic phenotype, by using a small number of genetic variants when short tandem repeat (STR) analysis is hard with insufficient biological samples. Our results not only replicated previous genetic signals but also indicated an upward trend in polygenic score (PGS) with increasing height in the validation and replication stages for both genders. These results demonstrate that the established SNP sets in this study could be used for height estimation in the Korean population. Specifically, since the PGS model constructed in this study targets only a small number of SNPs, it contributes to enabling forensic DNA phenotyping even at crime scenes with a minimal amount of biological evidence. To the best of our knowledge, this was the first study to evaluate a PGS model for height estimation in the Korean population using GWAS signals. Our study offers insight into the polygenic effect of height in East Asians, incorporating genetic variants from non-Asian populations.

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.

Identifying dryland-resilient chickpea genotypes for autumn sowing, with a focus on multi-trait stability parameters and biochemical enzyme activity

BackgroundChickpea is a key pulse crop grown in the spring in dryland regions. The cold resistance potential of chickpeas allows for the development of genotypes with varying sowing dates to take advantage of autumn and winter rainfall, particularly in dryland regions. In this study, we assessed grain yield, plant height, 100-seed weight, days to maturity, and days to flowering of 17 chickpea genotypes in five autumn-sown dryland regions from 2019 to 2021. Additionally, the response of selected chickpea genotypes to cold stress was examined at temperatures of -4 °C, 4 °C, and 22 °C by analyzing biochemical enzymes.ResultsMixed linear model of ANOVA revealed a significant genotype × environment interaction for all traits measured, indicating varying reactions of genotypes across test environments. This study reported low estimates of broad-sense heritability for days to flowering (0.34), days to maturity (0.13), and grain yield (0.08). Plant height and seed weight exhibited the highest heritability, with genotypic selection accuracies of 0.73 and 0.92, respectively. Moreover, partial least square regression highlighted the impactful role of rainfall during all months except of October, November, and February on grain yield and its interaction with environments in autumn-planted chickpeas. Among the genotypes studied, G9, G10, and G17 emerged as superior based on stability parameters and grain yield. In particular, genotype G9 stood out as a promising genotype for dryland regions, considering both MTSI and genotype by yield*trait aproaches. The cold assay indicated that − 4 °C is crucial for distinguishing between susceptible and resistant genotypes. The results showed the important role of the enzymes CAT and GPX in contributing to the cold tolerance of genotype G9 in autumn-sown chickpeas.ConclusionsSignificant G×E for agro-morphological traits of chickpea shows prerequisite for multi-trial analysis. Chickpea`s direct root system cause that monthly rainfall during plant establishment has no critical role in its yield interaction with dryland environment. Considering the importance of agro-morphological traits and their direct and indirect effects on grain yield, the utilization of multiple-trait stability approches is propose. Evaluation of chickpea germplasm reaction against cold stress is necessary for autumn-sowing. Finally, autumn sowing of genotype FLIP 10–128 C in dryland conditions can led to significant crop performance.

Deciphering the genetic basis of agronomic, yield, and nutritional traits in rice (Oryza sativa L.) using a saturated GBS-based SNP linkage map

Developing high-yielding rice varieties that possess favorable agronomic characteristics and enhanced grain Zn content is crucial in ensuring food security and addressing nutritional needs. This research employed ICIM, IM, and multi-parent population QTL mapping methods to identify important genetic regions associated with traits such as DF, PH, NT, NP, PL, YLD, TGW, GL, GW, Zn, and Fe. Two populations of recombinant inbred lines consisting of 373 lines were phenotyped for agronomic, yield and grain micronutrient traits for three seasons at IRRI, and genotyped by sequencing. Most of the traits demonstrated moderate to high broad-sense heritability. There was a positive relationship between Zn and Fe contents. The principal components and correlation results revealed a significant negative association between YLD and Zn/Fe. ICIM identified 81 QTLs, while IM detected 36 QTLs across populations. The multi-parent population analysis detected 27 QTLs with six of them consistently detected across seasons. We shortlisted eight candidate genes associated with yield QTLs, 19 genes with QTLs for agronomic traits, and 26 genes with Zn and Fe QTLs. Notable candidate genes included CL4 and d35 for YLD, dh1 for DF, OsIRX10, HDT702, sd1 for PH, OsD27 for NP, whereas WFP and OsIPI1 were associated with PL, OsRSR1 and OsMTP1 were associated to TGW. The OsNAS1, OsRZFP34, OsHMP5, OsMTP7, OsC3H33, and OsHMA1 were associated with Fe and Zn QTLs. We identified promising RILs with acceptable yield potential and high grain Zn content from each population. The major effect QTLs, genes and high Zn RILs identified in our study are useful for efficient Zn biofortification of rice.

Variability in thermal tolerance of clutches from different mothers indicates adaptation potential to climate warming in sea turtles.

The current climate warming is a challenge to biodiversity that could surpass the adaptation capacity of some species. Hence, understanding the means by which populations undergo an increase in their thermal tolerance is critical to assess how they could adapt to climate warming. Specifically, sea turtle populations could respond to increasing temperatures by (1) colonizing new nesting areas, (2) nesting during cooler times of the year, and/or (3) by increasing their thermal tolerance. Differences in thermal tolerance of clutches laid by different females would indicate that populations have the potential to adapt by natural selection. Here, we used exhaustive information on nest temperatures and hatching success of leatherback turtle (Dermochelys coriacea) clutches over 14 years to assess the occurrence of individual variability in thermal tolerance among females. We found an effect of temperature, year, and the interaction between female identity and nest temperature on hatching success, indicating that clutches laid by different females exhibited different levels of vulnerability to high temperatures. If thermal tolerance is a heritable trait, individuals with higher thermal tolerances could have greater chances of passing their genes to following generations, increasing their frequency in the population. However, the high rate of failure of clutches at temperatures above 32°C suggests that leatherback turtles are already experiencing extreme heat stress. A proper understanding of mechanisms of adaptation in populations to counteract changes in climate could greatly contribute to future conservation of endangered populations in a rapidly changing world.

Genetic variation and association of yield, yield components, and carbon storage in sorghum (Sorghum bicolor [L.] Moench) genotypes

Trait heritability and the response to selection depend on genetic variation, a prerequisite to developing sorghum varieties with desirable agronomic traits and high carbon sequestration for sustainable crop production and soil health. The present study aimed to assess the extent of genetic variability and associations among agronomic and carbon storage traits in selected sorghum genotypes to identify the best candidates for production or breeding. Fifty genotypes were evaluated at Ukulinga, Bethlehem and Silverton sites in South Africa during the 2022/23 growing season. The following agronomic and carbon storage traits were collected: days to 50% heading (DTH), days to 50% maturity (DTM), plant height (PH), total plant biomass (PB), shoot biomass (SB), root biomass (RB), root-to-shoot biomass ratio (RS), grain yield (GY), harvest index (HI), shoot carbon content (SCc), root carbon content (RCc), grain carbon content (GCc), total plant carbon stock (PCs), shoot carbon stock (SCs), root carbon stock (RCs), and root-to-shoot carbon stock ratio (RCs/SCs), and grain carbon stock (GCs). Higher genotypic coefficient of variations (GCVs) were recorded for GY at 45.92%, RB (39.24%), RCs/SCs (38.45), and RCs (34.62). Higher phenotypic coefficient of variations (PCVs) were recorded for PH (68.91%), followed by GY (51.8%), RB (50.51%), RS (41.96%), RCs/SCs (44.90%), and GCs (41.90%). High broad-sense heritability and genetic advance were recorded for HI (83.76 and 24.53%), GY (78.59 and 9.98%), PB (74.14 and 13.18%) and PCs (53.63 and 37.57%), respectively, suggesting a marked genetic contribution to the traits. Grain yield exhibited positive association with HI (r = 0.76; r = 0.79), DTH (r = 0.13; r = 0.31), PH (r = 0.1; r = 0.27), PB (r = 0.01; r = 0.02), RB (r = 0.05; r = 0.06) based on genotypic and phenotypic correlations, respectively. Further, the path analysis revealed significant positive direct effects of SB (0.607) and RB (0.456) on GY. The RS exerted a positive and significant indirect effect (0.229) on grain yield through SB. The study revealed that PB, SB, RB, RS, RCs, and RCs/SCs are the principal traits when selecting sorghum genotypes with high yield and carbon storage capacity.

Soybean pod shattering resistance allele pdh1 and marker-assisted selection.

Pod shattering is a major production constraint of soybean [Glycine max (L.)]. The objectives of this study were to (i) estimate heritability for pod shattering resistance, (ii) determine the frequency of the pod shattering resistance allele pdh1 in the International Institute for Tropical Agriculture (IITA) soybean germplasm and Zambian commercial varieties, and (iii) determine the effectiveness of the DNA marker for the pod shattering resistance allele pdh1. A total of 59 genotypes were evaluated for pod shattering in field trials conducted in Malawi and Zambia and genotyped with a marker for pdh1. TGx2002-8FM and TGx2002-9FM were the most resistant among genotypes in early and medium maturity classes and can be used for genetic enhancement of pod shattering resistance in these specific maturity classes. Narrow sense heritability estimates for pod shattering ranged from 0.27 to 0.80. Of the 59 genotypes, 57 (96.6%) carried the resistance allele pdh1 while only two genotypes (3.6%) carried the susceptible allele, suggesting near-fixation of the resistance allele pdh1 in the IITA germplasm. The marker for pdh1 was highly effective in selecting resistant genotypes.

Genetic and environmental effects on morphological traits of social phenotypes in wasps.

Many species exhibit distinct phenotypic classes, such as sexes in dioecious species or castes in social species. The evolution of these classes is affected by the genetic architecture governing traits shared between phenotypes. However, estimates of the genetic and environmental factors contributing to phenotypic variation in distinct classes have rarely been examined. We studied the genetic architecture underlying morphological traits in phenotypic classes in the social wasp Vespula maculifrons. Our data revealed patriline effects on a few traits, indicating weak genetic influences on caste phenotypic variation. Interestingly, traits exhibited higher heritability in queens than workers. This result suggests that genetic variation has a stronger influence on trait variation in the queen caste than the worker caste, which is unexpected because queens typically experience direct selection. Moreover, estimates of heritability for traits were correlated between the castes, indicating that variability in trait size was governed by similar genetic architecture in the two castes. However, we failed to find evidence for a significant relationship between caste dimorphism and caste correlation, as would be expected if trait evolution was constrained by intralocus genetic conflict. Our analyses also uncovered variation in the allometric relationships for traits. These analyses suggested that worker traits were proportionally smaller than queen traits for most traits examined. Overall, our data provide evidence for a strong environmental and moderate genetic basis of trait variation among castes. Moreover, our results suggest that selection previously operated on caste phenotype in this species, and phenotypic variation is now governed primarily by environmental differences.

Genetic architecture and socio-environmental risk factors for major depressive disorder in Nepal.

Major depressive disorder (MDD) is the leading cause of disability globally, with moderate heritability and well-established socio-environmental risk factors. Genetic studies have been mostly restricted to European settings, with polygenic scores (PGS) demonstrating low portability across diverse global populations. This study examines genetic architecture, polygenic prediction, and socio-environmental correlates of MDD in a family-based sample of 10 032 individuals from Nepal with array genotyping data. We used genome-based restricted maximum likelihood to estimate heritability, applied S-LDXR to estimate the cross-ancestry genetic correlation between Nepalese and European samples, and modeled PGS trained on a GWAS meta-analysis of European and East Asian ancestry samples. We estimated the narrow-sense heritability of lifetime MDD in Nepal to be 0.26 (95% CI 0.18-0.34, p = 8.5 × 10-6). Our analysis was underpowered to estimate the cross-ancestry genetic correlation (rg = 0.26, 95% CI -0.29 to 0.81). MDD risk was associated with higher age (beta = 0.071, 95% CI 0.06-0.08), female sex (beta = 0.160, 95% CI 0.15-0.17), and childhood exposure to potentially traumatic events (beta = 0.050, 95% CI 0.03-0.07), while neither the depression PGS (beta = 0.004, 95% CI -0.004 to 0.01) or its interaction with childhood trauma (beta = 0.007, 95% CI -0.01 to 0.03) were strongly associated with MDD. Estimates of lifetime MDD heritability in this Nepalese sample were similar to previous European ancestry samples, but PGS trained on European data did not predict MDD in this sample. This may be due to differences in ancestry-linked causal variants, differences in depression phenotyping between the training and target data, or setting-specific environmental factors that modulate genetic effects. Additional research among under-represented global populations will ensure equitable translation of genomic findings.

Single- and multiple-trait quantitative trait locus analyses for seed oil and protein contents of soybean populations with advanced breeding line background

Soybean seed oil and protein contents are negatively correlated, posing challenges to enhance both traits simultaneously. Previous studies have identified numerous oil and protein QTLs via single-trait QTL analysis. Multiple-trait QTL methods were shown to be superior but have not been applied to seed oil and protein contents. Our study aimed to evaluate the effectiveness of single- and multiple-trait multiple interval mapping (ST-MIM and MT-MIM, respectively) for these traits using three recombinant inbred line populations from advanced breeding line crosses tested in four environments. Using original and simulated data, we found that MT-MIM did not outperform ST-MIM for our traits with high heritability (H2 > 0.84). Empirically, MT-MIM confirmed only five out of the seven QTLs detected by ST-MIM, indicating single-trait analysis was sufficient for these traits. All QTLs exerted opposite effects on oil and protein contents with varying protein-to-oil additive effect ratios (-0.4 to -4.8). We calculated the economic impact of the allelic variations via estimated processed values (EPV) using the National Oilseed Processors Association (NOPA) and High Yield + Quality (HY + Q) methods. Oil-increasing alleles had positive effects on both EPVNOPA and EPVHY+Q when the protein-to-oil ratio was low (-0.4 to -0.7). However, when the ratio was high (-4.1 to -4.8), oil-increasing alleles increased EPVNOPA and decreased EPVHY+Q, which penalizes low protein meal. In conclusion, single-trait QTL analysis is adequately effective for high heritability traits like seed oil and protein contents. Additionally, the populations’ elite pedigrees and varying protein-to-oil ratios provide potential lines for further yield assessment and direct integration into breeding programs.