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Telomere length and telomere shortening predict survival in many organisms. This raises the question of the contribution of genetic and environmental effects to variation in these traits, which is still poorly known, particularly for telomere shortening. We used experimental (cross-fostering) and statistical (quantitative genetic “animal models”) means to disentangle and estimate genetic and environmental contributions to telomere length variation in pedigreed free-living jackdaws (Corvus monedula). Telomere length was measured twice in nestlings, at ages 4 (n = 715) and 29 days (n = 474), using telomere restriction fragment (TRF) analysis, adapted to exclude interstitial telomeric sequences. Telomere length shortened significantly over the nestling period (10.4 ± 0.3 bp day–1) and was highly phenotypically (rP = 0.95 ± 0.01) and genetically (rG > 0.99 ± 0.01) correlated within individuals. Additive genetic effects explained a major part of telomere length variation among individuals, with its heritability estimated at h2 = 0.74 on average. We note that TRF-based studies reported higher heritabilities than qPCR-based studies, and we discuss possible explanations. Parent–offspring regressions yielded similar heritability estimates for mothers and fathers when accounting for changes in paternal telomere length over life. Year effects explained a small but significant part of telomere length variation. Heritable variation for telomere shortening was low (h2 = 0.09 ± 0.11). The difference in heritability between telomere length (high) and telomere shortening (low) agrees with evolutionary theory, in that telomere shortening has stronger fitness consequences in this population. Despite the high heritability of telomere length, its evolvability, which scales the additive genetic variance by mean telomere length, was on average 0.48%. Hence, evolutionary change of telomere length due to selection is likely to be slow.

Lamb survival is a critical aspect in the sheep industry as it increases the chances of economic gain in the flock. The objective of the current study was to assess the incidence of lamb mortality in Harnali sheep and to estimate maternal and additive genetic effects of lamb survival using the data of 2057 lambs born to 134 sires and 623 dams for the period of 20 years (2001-2020). The genetic evaluation was carried out using threshold animal models comprising direct and maternal effects using THRGIBBS1F90 and POSTGIBBSF90 programs. Cumulative mortality (95% CI (confidence interval)) for the S1 (lambs which died up to weaning age), S2 (lambs which died from birth to 6 months of age) and S3 (lambs which died from birth to 12 months of birth) groups was 8.41 (7.21-9.61), 14.10 (12.59-15.60) and 17.70 (16.05-19.34) %, respectively. The logistic regression analysis revealed significant (p

Significant variability is available in the F2 population of brinjal. Top crosses of brinjal Biliudda badane × mullu badane produced from F1 generation were in augmented design at ZARS Shimogga in Kharif 2017. They have several characteristics of plant breeding significance with sufficient scope for added improvement to growing conditions. The F2 study showed significant variation for nine quantitative traits. Close estimates between GCV and PCV values indicated lesser influence of environmental factors on the expression of traits under study. In this investigation, the proportion of genetic contribution of high GCV, PCV coupled with high broad sense heritability and genetic advance to the overall phenotypic expression of the studied traits like number of fruits per plant, number primary branches, number of flowers per plant was high, indicating predominant control of additive genes, and these traits could be improved upon by selection without progeny testing. High magnitude of heritability for most of the characters suggested the progress of improvement in yield and its components. Differences in mean values of parents for various characters indicated involvement of diverse parents in the crosses studied. The F2 plants exceeded either of the parents for most of the characters, which seems to be due to transgressive segregation.

Improving litter size at birth (TNB) and the number of piglets born alive (NBA) are the main breeding goals related to litter traits, which are economically important. A better understanding of genetic architecture underlying TNB and NBA traits could increase pig production efficiency. However, most previous studies on these traits focus on additive genetic effects, while epistatic interactions underlying TNB and NBA traits has not yet been well investigated, which are essential to understand how traits-related genes interact. Herein, we conducted genome scans of epistatic interactions underlying TNB and NBA traits in a total of 150 Chinese indigenous pigs (75 Jinhua and 75 Shengxian Spotted pigs) with high throughput genomic data. Based on SNPs with high interaction values and connectivity scores, we identified eight promising candidate genes (AKT2, TSC1, MTOR, PIK3R5, TIAM1, FGF14, RALB and ROR2) potentially associated with litter traits in pigs. Moreover, the underlying pathways, e.g., calcium ion transport, pointed out their roles in litter size-related traits. Our findings provide new insight into genetic architecture of litter traits in pigs and will benefit economic profits in pig production.

Context Beef cattle breeds in Australia can broadly be broken up into two subspecies, namely, Bos indicus and Bos taurus. Due to the time since divergence between the subspecies, it is likely that mutations affecting quantitative traits have developed independently in each. Aims We hypothesise that this will affect the prediction accuracy of genomic selection of admixed and composite populations that include both ancestral subspecies. Our study investigates methods to quantify population stratification in a multibreed population of tropically adapted heifers, with the aim of improving prediction accuracy of genomic selection for reproductive maturity score. Methods We used genotypes and reproductive maturity phenotypes from 3695 tropically adapted heifers from three purebred populations, namely, Brahman, Santa Gertrudis and Droughtmaster. Two of these breeds, Santa Gertrudis and Droughtmaster, are stabilised composites of varying B. indicus × B. taurus ancestry, and the third breed, Brahman, has predominately B. indicus ancestry. Genotypes were imputed to three marker-panel densities and population stratification was accounted for in genomic relationship matrices by using breed-specific allele frequencies when calculating the genomic relationships among animals. Prediction accuracy and bias were determined using a five-fold cross validation of randomly selected multibreed cohorts. Key Results Our results showed that the use of breed-adjusted genomic relationship matrices did not improve either prediction accuracy or bias for a lowly heritable trait such as reproductive maturity score. However, using breed-adjusted genomic relationship matrices allowed the capture of a higher proportion of additive genetic effects when estimating variance components. Conclusions These findings suggest that, despite seeing no improvement in prediction accuracy, it may still be beneficial to use breed-adjusted genomic relationship matrices in multibreed populations to improve the estimation of variance components. Implications As such, genomic evaluations using breed-adjusted genomic relationship matrices may be beneficial in multibreed populations.

Common beans are an important nutritious food crop to many people in developing countries. Inadequate soil-P is one of the major constraints to high bean seed yield productivity. Information about genetic effects that control inheritance of root traits in common bean grown under low soil-P conditions is scarce, and that is a challenge for genetic enhancement. This study was therefore implemented to determine inheritance and gene action of root traits in common bean for tolerance to low soil-P. The six generations were evaluated in a completely randomised design with two replicates under low soil-P in a pot experiment. Generation mean analysis revealed that both allelic and non-allelic genetic interactions controlled inheritance of root traits studied. Cumulative main gene effect was higher than epistasis effects. Additive genetic effects were more predominant than dominance effects. Additive and additive × dominance epistatic gene effects were more important in controlling inheritance of root traits under low soil-P. Broad-sense heritability for hypocotyl root number was the highest (93.98 %) while the narrow-sense heritability was moderate (51.13 %). To develop improved genotypes tolerant to low soil-P, recombination crossing should be followed by screening and selection in later generations for high seed yield, root and other preferred traits. Key words: Common bean, inheritance, genotype, gene effect, heritability, low soil-P.

Florida Native sheep is among the sheep breeds best adapted to humid and hot climatic conditions such as those of Florida, USA, and have shown a superior ability to regulate nematode burdens. This is one of the oldest sheep breeds in North America and is an endangered species. To ensure genetic diversity and long-term survival of the breed, protection of the current genetic stock is critical and conservation efforts are required to promote its breeding and production. The objective of the present study was to investigate the importance of additive and non-additive genetic effects on resistance to natural Haemonchus contortus infections in Florida Native sheep using a whole genome scan. A total of 200 sheep were evaluated in the present study. Phenotypic records included faecal egg count (FEC, eggs/gram), FAMACHA® score, packed cell volume (PCV, %), body condition score and average daily gain (ADG, kg). Sheep were genotyped using the GGP Ovine 50K SNP chip and 45.2 k single nucleotide polymorphism (SNP) markers spanning the entire genome were available for quality control procedures. Mixed models were used to analyse the response variables and included the identity by state matrix to control for population structure. Bonferroni correction was used to control for multiple testing and a second arbitrary threshold (0.1 × 10−3) was used. Fifteen SNPs with additive and non-additive genetic effects and located in Ovis aries chromosome OAR1, 2, 3, 6, 8, 10, 11, 12, 13 and 21 were associated with FEC, FAMACHA® score, PCV and ADG. These SNPs could be potential genetic markers for resistance to natural H. contortus exposure in Florida Native sheep.

Although recently a large-sample GWASs identified significant loci in the background of depression, the heterogeneity of the depressive phenotype and the lack of accurate phenotyping hinders applicability of findings. We carried out a pilot GWAS with in-depth phenotyping of affective temperaments, considered as subclinical manifestations and high-risk states for affective disorders, in a general population sample of European origin. Affective temperaments were measured by TEMPS-A. SNP-level association was assessed by linear regression models, assuming an additive genetic effect, using PLINK1.9. Gender, age, the first ten principal components (PCs) and the other four temperaments were included in the regression models as covariates. SNP-level relevances (p-values) were aggregated to gene level using the PEGASUS method1. In SNP-based tests, a Bonferroni-corrected significance threshold of p ≤ 5.0 × 10−8 and a suggestive significance threshold of p ≤ 1.0 × 10−5, whereas in gene-based tests a Bonferroni-corrected significance of 2.0 × 10−6 and a suggestive significance of p ≤ 4.0 × 10−4 was established. To explore known functional effects of the most significant SNPs, FUMA v1.3.5 was used. We identified 1 significant and 21 suggestively significant SNPs in ADGRB3, expressed in the brain, for anxious temperament. Several other brain-relevant SNPs and genes emerged at suggestive significance for the other temperaments. Functional analyses reflecting effect on gene expression and participation in chromatin interactions also pointed to several genes expressed in the brain with potentially relevant phenotypes regulated by our top SNPs. Our findings need to be tested in larger GWA studies and candidate gene analyses in well-phenotyped samples in relation to affective disorders and related phenotypes.

The development of new genotypes and their availability to the agricultural market is decisive for the success of the Brazilian soybean production chain. This study aimed to estimate the components of variance and genetic parameters of aspects of agronomic importance and to predict the selection of transgressive soybean populations and families based on the agronomic ideotype. The segregating families were conducted in an enlarged block design, composed of 285 F3 segregating families corresponding to the unusual treatments, and together with seven commercial cultivars assigned as common treatments, arranged in four replications. The characters of agronomic interest were measured the first pod insertion height, plant height, number of pods on the main stem, number of pods on the branches, pods containing only one seed, pods containing two seeds, pods containing three seeds, pods containing four seeds and seed mass. Were estimated additive genetic variance, genetic variance of the F3 segregating families, genetic variance of F2 segregating population, residual variance, phenotypic variance, narrow sense heritability, coefficient of determination for the effects of the F3 segregating family, coefficient of determination for the effects of the progeny, genetic variation coefficient, residual variation coefficient and predicted genetic ranking for the best F2 segregating populations and F3 segregating families. The pronounced additive genetic gains in the progeny showed higher values for the characters measured: first pod insertion height with 1.84%, for the family and population, the additivity presented the highest values for the number of pods with four grains. The selection of the progenies through the agronomic ideotype based on the greatest genetic gains of the morphological characters weighted by the largest seed mass will thus lead these populations to joint selection for the other yield components.

Reproductive traits in breeding herds can be improved through crossbreeding, which results in breed differences, heterosis and breed complementarity. The aim of this study was to estimate group additive genetic and dominance effects for three reproductive traits; probability of artificial insemination (AIP); calving success (CS); and days to calving (DC) for Hereford (H), Angus (A), Nellore (N) and Salers (S) breeds under grazing conditions. Data were obtained from an experiment carried out during 1992-2002 by the Faculty of Agronomy, Universidad de la Republica (UdelaR), Uruguay and Caja Notarial de Seguridad Social. The data set contained reproductive information of 1,164 females from 11 different genetic groups (GG) consisting of crosses between H, N, S and A. AIP, CS and DC were examined in first-calf heifers, while CS and DC were examined in second-calf and 3- to 7-year-old cows. Least square means for each GG and group additive genetic and dominance effects were estimated for each trait. F1 crossbreed females performed better for artificial insemination probability than purebred females. Crossbred A/H heifers had the highest AIPs and CS rates, while crossbred N/H 3- to 7-year-old cows recorded the highest averages for CS and DC. Estimates of group additive genetic effects did not differ amongst A, S, N and H; however, dominance increased the AIP and CS of the heifers.

Key message Genetic modification of spike architecture is essential for improving wheat yield. Newly identified loci for the ‘Miracle wheat’ phenotype on chromosomes 1AS and 2BS have significant effects on spike traits. Abstract The wheat (Triticum ssp.) inflorescence, also known as a spike, forms an unbranched inflorescence in which the inflorescence meristem generates axillary spikelet meristems (SMs) destined to become sessile spikelets. Previously, we identified the putatively causative mutation in the branched headt (bht) gene (TtBH-A1) of tetraploid wheat (T. turgidum convar. compositum (L.f.) Filat.) responsible for the loss of SM identity, converting the non-branching spike to a branched wheat spike. In the current study, we performed whole-genome quantitative trait loci (QTL) analysis using 146 recombinant inbred lines (RILs) derived from a cross between spike-branching wheat (‘Miracle wheat’) and an elite durum wheat cultivar showing broad phenotypic variation for spike architecture. Besides the previously found gene at the bht-A1 locus on the short arm of chromosome 2A, we also mapped two new modifier QTL for spike-branching on the short arm of chromosome 1A, termed bht-A2, and 2BS. Using biparental mapping population and GWAS in 302 diverse accessions, the 2BS locus was highly associated with coding sequence variation found at the homoeo-allele of TtBH-B1 (bht-B1). Thus, RILs that combined both bht-A1 and bht-B1 alleles showed additive genetic effects leading to increased penetrance and expressivity of the supernumerary spikelet and/or mini-spike formation.

Several strains of pearl oysters (Pinctada fucata) are distributed in the coastal areas of South China. To explore strategies for genetic improvement, additive genetic, heterotic, and strain reciprocal effects on growth traits were estimated by performing a full 3 × 3 diallel cross of three pearl oyster strains that are local to Beihai, Guangxi Province; Xuwen, Guangdong Province; and Sanya, Hainan Province. The simultaneous production of progeny for all crosses was achieved using mass spawning in Lingshui, Hainan Province. For body weight, the Beihai strain showed the highest additive genetic effect (+ 5.7%) and the Sanya strain showed the lowest (− 4.3%), with similar additive genetic effect patterns for shell length, shell height, and shell width. The averaged heterotic outcomes were significant (P < 0.01) for all growth traits, varying from + 6.1% for shell length to + 19.1% for body weight. Reciprocal cross effects were determined for growth traits, with a relatively high correlation for all traits between strain additive performance and total performance (r2 = 0.72 to 0.85). These findings reveal the potential to exploit strain additive variation to improve P. fucata culture stock using direct selection methods for increased productivity of pearl oyster cultivation in China.

Key message Non-additive genetic effects seem to play a substantial role in the expression of complex traits in sugarcane. Including non-additive effects in genomic prediction models significantly improves the prediction accuracy of clonal performance. Abstract In the recent decade, genetic progress has been slow in sugarcane. One reason might be that non-additive genetic effects contribute substantially to complex traits. Dense marker information provides the opportunity to exploit non-additive effects in genomic prediction. In this study, a series of genomic best linear unbiased prediction (GBLUP) models that account for additive and non-additive effects were assessed to improve the accuracy of clonal prediction. The reproducible kernel Hilbert space model, which captures non-additive genetic effects, was also tested. The models were compared using 3,006 genotyped elite clones measured for cane per hectare (TCH), commercial cane sugar (CCS), and Fibre content. Three forward prediction scenarios were considered to investigate the robustness of genomic prediction. By using a pseudo-diploid parameterization, we found significant non-additive effects that accounted for almost two-thirds of the total genetic variance for TCH. Average heterozygosity also had a major impact on TCH, indicating that directional dominance may be an important source of phenotypic variation for this trait. The extended-GBLUP model improved the prediction accuracies by at least 17% for TCH, but no improvement was observed for CCS and Fibre. Our results imply that non-additive genetic variance is important for complex traits in sugarcane, although further work is required to better understand the variance component partitioning in a highly polyploid context. Genomics-based breeding will likely benefit from exploiting non-additive genetic effects, especially in designing crossing schemes. These findings can help to improve clonal prediction, enabling a more accurate identification of variety candidates for the sugarcane industry.

Pepper plants can be used as ornamental ones due to the contrasting traits of plants, flowers, and especially fruits. This variability can be exploited in genetic improvement programs aiming at identifying superior genotypes and obtaining hybrids. This work aimed to select parental and hybrid individuals through diallel analysis for fruit traits in Capsicum annuum. Seven pepper genotypes were crossed, and eleven fruit-related quantitative traits were evaluated. The data were subjected to diallel analysis using Griffing’s Method 1 (fixed model). There was a predominance of additive genetic effects on the fruit traits of ornamental pepper plants. Genotypes UFPB77.3 and UFPB390 are indicated as parents for the improvement of ornamental pepper plants, for fruit traits. Hybrids UFPB77.3 x UFPB099, UFPB390 x UFPB77.3, UFPB390 x UFPB001, UFPB390 x UFPB099, UFPB134 x UFPB77.3, and UFPB134 x UFPB390 present a potential for the production of hybrids and generation of segregating populations of ornamental peppers.

9 Pág. Departamento de ​Mejora Genética Animal (INIA), Uniformity of body weight is a trait of great economic importance in the production of white shrimp (Litopenaeus vannamei). A necessary condition to improve this trait through selective breeding is the existence of genetic variability for the environmental variance of body weight. Although several studies have reported such variability in other aquaculture species, to our knowledge, no estimates are available for shrimp. Our aim in this study was to estimate the genetic variance for weight uniformity in a farmed population of shrimp to determine the potential of including this trait in the selection program. We also estimated the genetic correlation of weight uniformity between two environments (selection nucleus and commercial population)., This work was funded by the Ministerio de Ciencia, Innovación y Universidades, Spain (Grant CGL2016-75904-C2-2-P), fondos FEDER and the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (FPI-SGIT2016-02).

A complete diallel analysis was carried out to determine combining ability of Shandar, NIA-Mehran, NIA-19/A, KS-282 and Shua-92 rice varieties in F1 during 2017. The objective of the study was to identify potential recombinants for future rice breeding program. The research was conducted at Nuclear Institute of Agriculture, Tandojam. Genotypic mean squares were significant (P ?0.01) for all of the traits i.e.; days to heading, days to maturity, plant height, number of tillers plant-1, panicle length, grains panicle-1 and grain yield plant-1 indicating genetic variation. Importance of both additive and non-additive gene action was found with preponderance of additive genetic effects in expression of traits studied. Showing negative GCA effects, NIA-Mehran, NIA-19/A and Shua-92 proved better parent varieties for developing early maturity. While, NIA-Mehran, KS-282 and Shua-92 for developing short stature genotypes. While, Shandar remained the best combiner for yield and yield associated traits with higher positive GCA effects. Cross combination of Shandar × KS-282 was the best with higher negative effects for days to heading and maturity and higher positive effects for grain yield plant-1. NIA-Mehran × Shua-92 gave the highest negative SCA effects indicating best combination for short stature. In case of number of tillers plant-1 and grains panicle-1, the cross NIA-19/A × KS-282 was the better combination with the highest positive SCA effects. Shandar × NIA-Mehran manifested the highest value for panicle length. Findings of reciprocal SCA revealed that the reciprocal cross combination of Shua-92 × Shandar was fruitful illustrating negative effects for days to heading and maturity. While, KS-282 × NIA-Mehran was the best reciprocal combination for yield and yield associated traits. It is concluded that rice varieties Shandar and NIA-Mehran could be used to improve yield contributing traits in rice, while, NIA-Mehran and KS-282 may be used to improve early maturity and short stature in rice crop.

Introduction Electronic cigarettes are now the most commonly used form of tobacco product among youth in the United States. Current evidence suggests that although e-cigarettes are perceived as less harmful and preferred over combustible cigarettes by adolescents, adolescents who try e-cigarettes are at greater risk of transitioning to combustible cigarettes. The genetic and environmental contributions to liability for e-cigarette use have not yet been examined using a behavioral genetic design. Methods Behavioral genetic models of lifetime and current e-cigarette use and friends who use e-cigarettes were examined among female monozygotic and dizygotic twins. Results A total of 41 female twin pairs (65.9% monozygotic twins; age = 19.7, SD = 1.6) with complete data on the study variables were included in the present analyses. The majority of the sample (68.1%) had at least some friends who use e-cigarettes. Additive genetic effects on e-cigarette use were not present, but the shared environment explained 98.7% of the variance in lifetime e-cigarette use, 96.6% in current e-cigarette use, and 94.9% in affiliation with friends who use e-cigarettes. Conclusion This first study on the behavioral genetics of e-cigarette use among adolescents and young adults suggest that environmental factors shared by twins within a family seem to play a predominant role in the initial stages of e-cigarette use, a finding that is consistent with what has been found for tobacco. The findings emphasize the importance of continuing population-based tobacco control interventions to reduce the burden of e-cigarette use among adolescents. Implications The shared environment significantly influences the initiation and regular use of electronic cigarettes and affiliation with friends who use electronic cigarettes among adolescent and young adult females. These findings underscore the importance of formulating preventive interventions that mitigate the social effects of familial influences on e-cigarette use through social skills training, education on harms of e-cigarettes for young people, or altering social norms regarding initiation of novel tobacco products.

Mate choice for genetic benefits remains controversial, largely because few studies have estimated the relative contributions of additive and non-additive sources of genetic variation to offspring fitness. Moreover, there remains a deficit of these estimates for species where female-mate preferences have been quantified in the wild, especially species characterized by monandry or monogamy. Here, we use artificial fertilization techniques combined with a cross-classified breeding design to simultaneously test for "good genes" and "compatible genes" benefits of mate choice in the monandrous red backed toadlet (Pseudophryne coriacea). In addition, we used a genomic approach to estimate effects of parental-genetic relatedness (assessed using 27, 768 single nucleotide polymorphisms) on offspring fitness. Our results revealed no significant additive genetic effects (sire effects), but highly significant non-additive genetic effects (sire × dam interaction effects), on fertilization success, survival during embryonic development, and hatching success. We also found significant associations between parental genetic similarity and offspring survival (whereby survival was higher when parents were more related), and significant positive relationships between fertilization success and embryo survival through to hatching. These results indicate that offspring viability is significantly influenced by the genetic compatibility of parental genotypes, that more related parents are more genetically compatible, and that gametes with greater compatibility at fertilization produce more viable offspring. More broadly, our findings provide new quantitative genetic evidence that genetic incompatibility underpins female mate preferences. Continued quantitative genetic assessment of the relative importance of good genes versus compatible genes is needed to ascertain the general importance of genetic benefits as a driver of female mate choice.

Estimates of genetic parameters for economic traits are important to enable the breeder estimate the breeding value of individuals available for selection. Thus, this study was carried out to estimate genetic parameters namely heritability and genetic correlations among egg production traits in two strain crosses using bivariate animal model in Bayesian (MCMC) method. The egg production data were obtained from four generations which comprised the base population of two commercial egg strains and the local chicken, the inbred population derived from the base population, the F crossbred population obtained 1 from the crossing of the local and exotic inbred chickens and the backcross population obtained from the backcrossing of the crossbred to their parents. A total number of 1,138 daughters of 62 sires and 620 dams were used for the study. The autocorrelations among samples in the MCMC chain were less than 0.1 for all lag values indicating that all samples of the posterior distribution were independent. The estimated heritability for age at first egg, body weight at first egg, hen day egg number, weight of first egg, egg weight at thirty weekand egg weight at forty week were 0.62, 0.48, 0.47, 0.53, 0.54 and 0.56 for strain 1 crosses and 0.43, 0.48, 0.49, 0.52, 0.52 and 0.53 for strain 2 crosses. The corresponding highest posterior density interval ranged from 0.22 to 0.91 for strain 1 crosses and 0.07 to 0.83 for strain 2 crosses. The genetic correlations among egg production traits ranged from 0.06 to1.97 in strain 1 and 0.06 to 2.59 in strain 2 crosses. The estimates were within the range reported in literature for egg production traits in chicken and imply that appreciable amount of additive genes exist in the strain crosses which could be used for the selection of superior birds. The magnitude of genetic correlations implies that selection of one trait could lead to correlated response to the other traits.Keywords: Autocorrelations, egg production, genetic correlations, heritability, strain crosses.

The investigation was carried out in focusing the genetic variability for different traits of wheat influenced by heat tolerance mechanism to find out relationships among phenological, physiological and yield contributing traits. Spring wheat cultivar of 25 genotypes were selected and cultivated under late sowing condition at the Regional Wheat Research Institute, Shympur, Rajshahi, Bangladesh from December, 2016 to April, 2017. Significant variability among the genotypes exposed for different traits related to heat tolerance. Results showed that the genotypes G24, G10, G01, G13, G16, G25 and G14 ranked as better category considering maximum number of traits in mean performance indicating their tolerance to heat stress under late sowing condition. Phenotypic variances (σg2) of all traits were greater than those of genotypic variances (σg2). The same trends were also found in their co-efficient of variances. The phenotypic co-efficient of variances (PCV) of all traits were greater compare to those of genotypic co-efficient of variances (GCV) and their values were closer to each other. The heading days (HD), canopy temperature at vegetative stage (CTvg), canopy temperature at grain filling stage (CTgf), biomass, plant height (PH), spike/m2 (SPM), spikelet/spike (SPS), grain/ spike (GPS), thousand grain weight (TGW) and yield exhibited higher heritability (hb2) estimated under irrigated late sowing (ILS) condition. Under the same ILS condition SPAD, SPM, SPS, GPS, TGW and yield showed moderate to high genetic advance (GA) obtained through computing their mean percentage (%) and the rest traits HD, maturity days (MD), CTvg, CTgf, biomass, PH and harvest index (HI) exposed smaller genetic advance (% mean). The co-efficient of variation (CV%) of all attributes in all genotypes were significantly lower (1.36 - 6.96). Both heritability and genetic advance were found lower for MD, SPAD and HI indicated their non additive genetic effects for which these traits might not be recommended for selection. However, spike/m2, spikelet/spike, grain/spike, thousand grain weight and yield belonged to higher heritability and high to moderate genetic advance in mean percentage (%) along with wide genetic variation and lower environmental influence in heat stress situation indicated the most likely heritability due to the effects of additive genes that might be suggested as effective process of selection for these traits in heat stress condition.

Grain yield is a complex phenomenon, which results from the interaction of various contributing causes highly influenced by environmental variation. Phenotypic selection cannot directly improve the characters in heterozygous crops like moth bean unless dissected by genetic analysis. A study undertaken to determine the extent of genetic variability for seed yield and ten other quantitative characters in 40 genotypes of moth bean. The analysis of variance revealed significant differences among genotypes for all the characters. High genotypic coefficient and phenotypic coefficient of variation recorded for number of branch per plant, seed yield per plant, harvest index and leaf area indicated potential variability available for these traits and small difference between them suggesting positive selection in desired direction for improvement of this character. The high heritability along with high genetic advance in day to flowering, number of pod per plant, seed yield per plant, harvest index, number of branch per plant, test weight and leaf area per plant suggested that genotypic variation for the characters probably attributed to high additive genetic effect and selection would be wrathful based on phenotypic performance.

The estimates of general combining ability effects suggested that among females GDM-4 and among males IC-399819 and EC-766060 were the best general combiners for seed yield and few other characters. The estimates of specific combining ability revealed that the hybrids GM-2 x EC-766437 followed by GM-2 x RH-406 and GDM-4 x EC-766378 exhibited positive sca effects in desirable direction for seed yield per plant. The hybrid GDM-4 x EC-766043 followed by GDM-4 x RH-749 and GDM-4 x EC-766495 exhibited significant negative sca effects for days to 50 per cent flowering and GM-3 x EC-766437 for days to maturity. While the hybrid GDM-4 x EC-766043 depicted significant sca effects in desired direction for oil and protein content. In general, involvement of both additive and non-additive gene effects, observed for most of the characters suggested that it would be desirable to follow cyclic method of breeding such as reciprocal recurrent selection, which would be most effective to stabilize additive genes to improve population mean and also to generate as well as to retain variability for several cycles of selection.

Ongoing adaptive evolution, and resulting “evolutionary rescue” of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants have low additive genetic values for local fitness. Local migration-selection balance and micro-evolutionary stasis could then result. However, key quantitative genetic effects of natural immigration, comprising the degrees to which gene flow increases the total local additive genetic variance yet counteracts local adaptive evolutionary change, have not been explicitly quantified in wild populations. Key implications of gene flow for population and evolutionary dynamics consequently remain unclear. Our quantitative genetic analyses of long-term data from free-living song sparrows (Melospiza melodia) show that mean breeding value for local juvenile survival to adulthood, a major component of fitness, increased across cohorts more than expected solely due to drift. Such micro-evolutionary change should be expected given nonzero additive genetic variance and consistent directional selection. However, this evolutionary increase was counteracted by negative additive genetic effects of recent immigrants, which increased total additive genetic variance but prevented a net directional evolutionary increase in total additive genetic value. These analyses imply an approximate quantitative genetic migration-selection balance in a major fitness component, and hence demonstrate a key mechanism by which substantial additive genetic variation can be maintained yet decoupled from local adaptive evolutionary change.

In a companion paper Balbona et al. (Behav Genet, in press), we introduced a series of causal models that use polygenic scores from transmitted and nontransmitted alleles, the offspring trait, and parental traits to estimate the variation due to the environmental influences the parental trait has on the offspring trait (vertical transmission) as well as additive genetic effects. These models also estimate and account for the gene-gene and gene-environment covariation that arises from assortative mating and vertical transmission respectively. In the current study, we simulated polygenic scores and phenotypes of parents and offspring under genetic and vertical transmission scenarios, assuming two types of assortative mating. We instantiated the models from our companion paper in the OpenMx software, and compared the true values of parameters to maximum likelihood estimates from models fitted on the simulated data to quantify the bias and precision of estimates. We show that parameter estimates from these models are unbiased when assumptions are met, but as expected, they are biased to the degree that assumptions are unmet. Standard errors of the estimated variances due to vertical transmission and to genetic effects decrease with increasing sample sizes and with increasing $$r^2$$ r 2 values of the polygenic score. Even when the polygenic score explains a modest amount of trait variation ($$r^2=.05$$ r 2 = . 05 ), standard errors of these standardized estimates are reasonable ($$< .05$$ < . 05 ) for $$n=16K$$ n = 16 K trios, and can even be reasonable for smaller sample sizes (e.g., down to 4K) when the polygenic score is more predictive. These causal models offer a novel approach for understanding how parents influence their offspring, but their use requires polygenic scores on relevant traits that are modestly predictive (e.g., $$r^2>.025)$$ r 2 > . 025 ) as well as datasets with genomic and phenotypic information on parents and offspring. The utility of polygenic scores for elucidating parental influences should thus serve as additional motivation for large genomic biobanks to perform GWAS’s on traits that may be relevant to parenting and to oversample close relatives, particularly parents and offspring.

In sorghum [Sorghum bicolor (L.) Moench], hybrid cultivars for the biofuel industry are desired. Along with selection based on testcross performance, evaluation of the breeding population per se is also important for the success of hybrid breeding. In addition to additive genetic effects, non-additive (i.e., dominance and epistatic) effects are expected to contribute to the performance of early generations. Unfortunately, studies on early generations in sorghum breeding programs are limited. In this study, we analyzed a breeding population for bioenergy sorghum, which was previously developed based on testcross performance, to compare genomic selection models both trained on and evaluated for the per se performance of the 3rd generation S0 individuals. Of over 200 ancestral inbred accessions in the base population, only 13 founders contributed to the 3rd generation as progenitors. Compared to the founders, the performances of the population per se were improved for target traits. The total genetic variance within the S0 generation progenies themselves for all traits was mainly additive, although non-additive variances contributed to each trait to some extent. For genomic selection, linear regression models explicitly considering all genetic components showed a higher predictive ability than other linear and non-linear models. Although the number and effect distribution of underlying loci was different among the traits, the influence of priors for marker effects was relatively small. These results indicate the importance of considering non-additive effects for dissecting the genetic architecture of early breeding generations and predicting the performance per se.

A half diallel cross between 8 inbred lines of maize was evaluated at two different planting dates for nine quantitative characters. Planting dates and crosses mean squares were significant for all studied traits. Mean squares due to crosses x planting dates were significant obtained for most studied traits. General (GCA) and specific (SCA) combing ability mean squares were significant for all traits. High ratios which largely exceeded the unity for days to 50% tassling and silking, plant height, ear height, no of rows/ ear , no of grains / row and 100 kernel weight were obtained, indicating that a large part of the total genetic variability associated with these traits indicates that of additive and additive by additive gene action. For remain cases, GCA/SCA ratios were less than unity, therefore, it could be summarized that the most percentage of the total genetic variability for these traits was due to non-additive gene action. For plant height, ear height and grain yield/ plant, the ratio of SCA x D/SCA was higher than GCA x D/GCA. This result indicates that non- additive effects were more influenced by sowing date than additive genetic effects for this trait. P1 seemed to be the best general combiner for early maturity, short plants, low ear position, grain yield/plant and some of its components in the combined analysis of both sowing dates. The parental combination P1xP3, P1xP5, P1xP7, P2xP4, P2xP5, P2xP7 , P3xP4, P3xP5, P3xP6 , P3xP4, P6xP7 and , P7xP8 for grain yield/plant exhibited significant positive effects being 13.54, 14.68, 12.79, 21.81, 21.61, 9.15, 21.64, 27.34, 7.36, 6.37 and 33.49, respectively

Knowledge on factors influencing traits during critical early growth periods is essential for predicting population persistence. Genetic effects and microhabitat stream conditions at female selected oviposition sites influence larval phenotypes. However, limited work has examined contributions of both factors across sequential ontogenetic stages for larvae of wild origin. Using a wild population of lake sturgeon (Acipenser fulvescens) from Black Lake, Michigan (USA), fertilized eggs were collected from stream substrate just prior to hatch at one-meter intervals along seven transect lines at an adult-selected spawning area. Microhabitat variables (depth, discharge, substrate size) were recorded at egg collection points. Body length, body area, and yolk-sac area were quantified for yolk-sac larvae (N = 359) at the time of hatch. Following the onset of exogenous feeding, larval growth was measured weekly for four weeks. Parentage was assigned using genetic-based analysis. Inter-individual variation in phenotypic traits quantified at hatch were attributed to stream microhabitat variables; mean depth had the largest influence. No additive genetic effects were detected at hatch. Post-emergence larval growth significantly varied within and among half-sibling groups with the greatest range in body size observed at 33 days post-hatch. Additive genetic variance and heritability increased with age. Results demonstrate that female-selected incubation habitats influenced traits at hatch for wild-origin fish, but effects do not persist to a sequential ontogenetic stage. Alternatively, growth after the onset of exogenous feeding was largely influenced by intrinsic (genetic) factors which must be considered when designing and implementing rehabilitation strategies for lake sturgeon and potentially other threatened riverine fishes.

The present investigation consists of 34 finger millet genotypes used for studying genetic variability parameters, correlation and path analysis which was carried out at Field Experiment Centre, Department of Genetics and Plant Breeding during Kharif 2019 in Randomized Block Design with three replications. The data were recorded for 15 quantitative characters to study genetic variability, heritability, genetic advance, correlation and path analysis. The analysis of variance indicated significant difference among 34 genotypes for all the characters studied. Moderate GCV and PCV values were observed for harvest index and test weight. High heritability coupled with high genetic advance as percent mean observed for plant height the role of additive genes in the inheritance of these traits and hence these characters could be improved through simple phenotypic selection. Correlation studies revealed significant positive association of grain yield per plant with harvest index for both genotypic level and phenotypic level. The path coefficient analysis indicated that selection for ear head length, number of fingers per ear, biological yield, harvest index as both genotypic level and phenotypic level would directly increase seed yield. IE-3473, IE-4759 were observed as promising genotypes for important quantitative traits.

Empresas florestais necessitam maximizar lucros e minimizar o nível de risco e incerteza, sendo uma das principais estratégias plantar povoamentos de crescimento rápido e de alta produtividade. Foi com esse intuito que a Empresa Florestas do Niassa, estabeleceu um experimento com cinco procedências e 28 progênies de P. Tecunumanii Eguiluz & Perry, no norte de Moçambique. O experimento foi estabelecido em blocos ao acaso com quatro linhas de repetição. Aos dois, quatro e oito anos de idade foram medidas altura total, diâmetro altura do peito (DAP) e sobrevivência. Os resultados de sobrevivência aos oito anos de idade não apresentaram diferenças significativas, tendo ficado acima dos 90% para todas as procedências incluindo a testemunha. Houve diferenças significativas de crescimento entre procedência para os restantes parâmetros avaliados. O melhor desempenho aos oito anos foi para as procedências Villa Santa, San Rafael del Norte e Yucul. O desdobramento das procedências entre progênies com o uso do recurso de agrupamento de clusters identificou três grupos distintos: O primeiro, composto pelas 12 (41,38%) progênies de melhor desempenho, majoritariamente da Villa Santa e Yucul; o segundo intermediário e composto por sete (24,14%) das progênies, na sua maioria de Yucul e Km 33; o último foi composto por 10 (34,4%) das progênies de pior desempenho, na sua maioria de San Jeronimo e Km 33. A maior parte das 10 melhores progênies classificadas com base no efeito genético aditivo predito e ganho genético, pertencem a Villa Santa, confirmando os resultados dos clusters. Já a maioria das progênies (45%) ao nível dos 20 melhores indivíduos classificados, pertenceram a procedência Villa Santa e podem ser usadas para futuros projetos de melhoramento no ambiente do Niassa. A seleção das melhores progênies pode ser feita a partir do DAP, dado que este apresentou um coeficiente de correlação acima dos 90% com o volume.

A cross experiment was carried out in Animal Production Research Institute (APRI), in cooperation with Benha University, Egypt for three years starting from February 2013 and terminated 2016. Four pedigreed local strains of chickens Matrouh (MT), Mandarah (MN), Inshas (IN) and Silver Montazah (SM) strains were used. A total of 34 sires and 230 dams from MN strain, 32 sires and 194 dams from MT strain were chosen randomly from 250 cockers and 600 pullets to produce purebreds and crossbreds progenies in the first generation. In the second generation, the crossbred hens of MNxMT were artificially inseminated with fresh semen of Inshas strain (IN), while the crossbred hens of MTxMN were artificially inseminated with fresh semen collected from cocks of Silver Montazah strain (SM) to produce three-way crossbreds (½IN×¼MN¼MT and ½SM×¼MT¼MN). Single trait animal model was used in estimating heritability and in predicting the breeding values (PBV). Crossbreeding effects of direct additive (GI), maternal effects (GM), direct heterosis (HI) and maternal heterosis (HI) were estimated using the procedure of generalized least-squares. The overall means of all genetic groups were 154 day, 1420 g, 39.38 g, 45 egg, 1957 g, 61 egg, 2727 g, 16 day, 411 g, 18 egg, 784 g, 13.5 egg and 593 g for ASM, BWSM, WFE, EN90D, EM90D, EN120D, EM120D, PF10E, EMF10E, EN2DW, EM2DW, EN1WM and EM1WM, respectively Estimates of heritability were moderate for ASM and BWSM (0.23 and 0.69), while they were low for egg production and partial egg recording traits. The GLM showed that three-way crossbreds reported the earlier ASM, heavier BWSM and WFE, the highest EN90D, EN120D and EN2DW and the heaviest EM90D, EM120D and EM2DW. The ranges of predicted breeding values (PBV) of MT strain were slightly higher than that for MN birds. Ranges of PBV recorded by ½MT½MN were nearly similar to those ranges recorded by ½MN½MT. Cross fathered by SM cocks and mothered by (½MT½MN) had higher ranges in PBV for egg production and partial egg recording traits than those cross fathered by IN cocks and mothered by (½MN½MT). The effects of GI on all traits (p≤0.01) and in favour of MN breed. The percentages of GM were significant for sexual maturity traits and non-significant for egg production and partial egg recording traits. Percentages of HI (-3.8, 28.5, -4.6, 29.3, 28.8, 24.9, 19.7, -36.1, -3.2, 17.4, 10.6 and 8.8%) and HM (-2.6, 1.2, 0.03, 7.8, 8.2, 7.8, 8.1, -10.5, 0.2, 7.2, 0.7, 3.2 and 3.3%) were mostly highly significant for all traits for ASM, BWSM, EN90D, EM90D, EN120D, EM120D, PF10E, EMF10E, EN2DW, EM2DW, EN1WM and EM1WM, respectively. We can recommend that Mandarah strain (MN) could be used as a sire and Matrouh (MT) as a dam, depending on the estimates of the direct additive genetic effect GI for the studied traits which were in favor of MN.

Accurate performance evaluation and genetic parameters estimation are the prerequisites for any successful genetic improvement program. This study was conducted to estimate genetic parameters for growth and Kleiber ratio traits in Boer x Central Highland goats. On-station data collected from 2009 to 2018 were utilized for the study. A general linear model procedure of the Statistical Analysis System (SAS, version 9.0) was used to analyze fixed effects, and genetic parameters were estimated using the WOMBAT software fitted animal model. The log-likelihood ratio test was used for selecting the best fitted model. Based on best fitted models, the total heritability (h2t) estimate for birth weight (BWT), weaning weight (WWT), six-month weight (SMWT), nine-month weight (NMWT), and yearling weight (YWT) were 0.38, 0.12, 0.05, 0.30, and 0.28, respectively. The total heritability (h2t) estimates for weight gain from birth to weaning (ADG1), 3 to 6 months (ADG2), 6 to 9 months (ADG3), and 9 to 12 months of age (ADG4) were 0.09, 0.08, 0.16, and 0.14, respectively. The heritability estimates for Kleiber ratios in different growth phases were found to be low (0.09 to 0.18) based on the selected models. Even with this figure, including the Kleiber ratio in the selection criteria would be imperative to improve the feed efficiency of crossbred goats. The direct genetic correlation estimates among growth traits range from 0.60 ± 0.14 to 0.97 ± 0.12. Except for NMWT, ADG4, and Kleiber ratio from 9 months to yearling age, the maternal effect had a significant influence on all considered traits. However, the contribution of the maternal genetic effect was more important for early growth traits. Thus, considering both the direct additive genetic effect and the maternal genetic effect is imperative for accurate genetic evaluation and for high selection response. The moderate heritability estimates for most of the growth traits implies the possibility of selection in conjunction with crossbreeding for a better genetic response. The positive and high genetic correlation estimates among growth traits confirm the possibility of a selection of goats at an early age.

BackgroundGenetically informed studies have provided mixed findings as to what extent parental substance misuse is associated with offspring substance misuse and antisocial behavior due to shared environmental and genetic factors.MethodsWe linked data from nationwide registries for a cohort of 2 476 198 offspring born in Sweden 1958–1995 and their parents. Substance misuse was defined as International Classification of Diseases diagnoses of alcohol/drug use disorders or alcohol/drug-related criminal convictions. Quantitative genetic offspring-of-siblings analyses in offspring of monozygotic and dizygotic twin, full-sibling, and half-sibling parents were conducted.ResultsBoth maternal and paternal substance misuse were robustly associated with offspring substance misuse [maternal adjusted hazard ratio (aHR) = 1.83 (95% confidence interval (CI) 1.80–1.87); paternal aHR = 1.96 (1.94–1.98)] and criminal convictions [maternal aHR = 1.56 (1.54–1.58); paternal aHR = 1.66 (1.64–1.67)]. Additive genetic effects explained 42% (95% CI 25–56%) and 46% (36–55%) of the variance in maternal and paternal substance misuse, respectively, and between 36 and 44% of the variance in substance misuse and criminality in offspring. The associations between parental substance misuse and offspring outcomes were mostly due to additive genetic effects, which explained 54–85% of the parent-offspring covariance. However, both nuclear and extended family environmental factors also contributed to the associations, especially with offspring substance misuse.ConclusionsOur findings from a large offspring-of-siblings study indicate that shared genetic influences mostly explain the associations between parental substance misuse and both offspring substance misuse and criminality, but we also found evidence for the contribution of environmental factors shared by members of nuclear and extended families.

Striga hermonthica (Del.) Benth parasitism, low soil N, and nutritional deficiencies of normal‐endosperm maize (Zea mays L.) threaten maize yield and exacerbate nutritional problems in sub‐Sahara Africa (SSA). This study was conducted (a) to evaluate genetic variation among extra‐early maturing maize hybrids with provitamin A and quality protein characteristics, (b) to investigate gene action governing the inheritance of Striga resistance, grain yield, low N tolerance, and other measured traits under low‐N, high‐N, and Striga‐infested environments, and (c) to identify hybrids with high yield and stability across environments. One hundred and fifty hybrids developed using North Carolina Design II were evaluated with six checks under low‐N, high‐N, and Striga‐infested environments in Nigeria. Mean squares for hybrids were highly significant (P

General combining ability (GCA) and specific combining ability (SCA) have been applied in breeding maize and other crops for decades. Sugarcane breeding has seen low genetic gains, which may be att...

Variation in DNA methylation (DNAm) is associated with lifestyle factors such as smoking and body mass index (BMI) but there has been little research exploring its ability to identify individuals with major depressive disorder (MDD). Using penalised regression on genome-wide CpG methylation, we tested whether DNAm risk scores (MRS), trained on 1223 MDD cases and 1824 controls, could discriminate between cases (n = 363) and controls (n = 1417) in an independent sample, comparing their predictive accuracy to polygenic risk scores (PRS). The MRS explained 1.75% of the variance in MDD (β = 0.338, p = 1.17 × 10−7) and remained associated after adjustment for lifestyle factors (β = 0.219, p = 0.001, R2 = 0.68%). When modelled alongside PRS (β = 0.384, p = 4.69 × 10−9) the MRS remained associated with MDD (β = 0.327, p = 5.66 × 10−7). The MRS was also associated with incident cases of MDD who were well at recruitment but went on to develop MDD at a later assessment (β = 0.193, p = 0.016, R2 = 0.52%). Heritability analyses found additive genetic effects explained 22% of variance in the MRS, with a further 19% explained by pedigree-associated genetic effects and 16% by the shared couple environment. Smoking status was also strongly associated with MRS (β = 0.440, p ≤ 2 × 10−16). After removing smokers from the training set, the MRS strongly associated with BMI (β = 0.053, p = 0.021). We tested the association of MRS with 61 behavioural phenotypes and found that whilst PRS were associated with psychosocial and mental health phenotypes, MRS were more strongly associated with lifestyle and sociodemographic factors. DNAm-based risk scores of MDD significantly discriminated MDD cases from controls in an independent dataset and may represent an archive of exposures to lifestyle factors that are relevant to the prediction of MDD.

Summary Heat stress negatively impacts the reproductive performance of dairy cows. The main objective of this study was to dissect the genetic basis underlying dairy cow fertility under heat stress conditions. Our first goal was to estimate genetic components of cow conception across lactations considering heat stress. Our second goal was to reveal individual genes and functional gene‐sets that explain a cow’s ability to conceive under thermal stress. Data consisted of 74 221 insemination records on 13 704 Holstein cows. Multitrait linear repeatability test‐day models with random regressions on a function of temperature–humidity index values were used for the analyses. Heritability estimates for cow conception under heat stress were around 2–3%, whereas genetic correlations between general and thermotolerance additive genetic effects were negative and ranged between −0.35 and −0.82, indicating an unfavorable relationship between cows’ ability to conceive under thermo‐neutral vs. thermo‐stress conditions. Whole‐genome scans identified at least six genomic regions on BTA1, BTA10, BTA11, BTA17, BTA21 and BTA23 associated with conception under thermal stress. These regions harbor candidate genes such as BRWD1, EXD2, ADAM20, EPAS1, TAOK3, and NOS1, which are directly implicated in reproductive functions and cellular response to heat stress. The gene‐set enrichment analysis revealed functional terms related to fertilization, developmental biology, heat shock proteins and oxidative stress, among others. Overall, our findings contribute to a better understanding of the genetics underlying the reproductive performance of dairy cattle under heat stress conditions and point out novel genomic strategies for improving thermotolerance and fertility via marker‐assisted breeding.

The experiment was conducted in Randomized Block Design (RBD) with three replications at Potato Research Station, Sardarkrushinagar Dantiwada Agricultural University, Deesa during rabi 2017-18. The crop was harvested at 90 days after planting. The analysis of variance revealed that mean sum of squares due to genotypes were found highly significant for all the traits. This is proved that the existence of tremendous variability in the experimental material for different traits. However, from tuber yield point of view, MS/9-2196, J/7-37, K. Ganga and K. Anand were elite genotypes based on per se performance. The genotypes, K. Lauvkar, K. Sindhuri and DSP-7 exhibited low physiological weight loss, while genotypes, K. Surya, MS/12-655 and K. Ganga had low loss due to rottage on weight basis. Thus, these genotypes may be considered as good for storage ability at room temperature storage condition. The high heritability along with high genetic advance in plant height, leaf area, fresh weight of tops per plant, number of tuber per plant, tuber yield per plant, average tuber weight, physiological weight loss, loss due to rottage on weight basis, loss due to rottage on number basis and total weight loss, suggested that genotypic variation for the characters is probably attributed to high additive genetic effect and selection would be rewarding based on phenotypic performance.

Extensive studies have been conducted on the analysis of genome function, especially on the expression quantitative trait loci (eQTL). These studies offered promising results for characterization of the functional sequencing variation and understanding of the basic processes of gene regulation. Parent of origin effect (POE) is an important epigenetic phenomenon describing that the expression of certain genes depends on their allelic parent-of-origin and it is known to play important roles in human complex diseases. However, traditional eQTL mapping approaches do not allow for the detection of imprinting, or they focus on modeling the additive genetic effect thereby ignoring the estimation of the dominance genetic effect. In this study, we proposed a statistical framework to test the additive and dominance genetic effects of the candidate eQTLs along with detection of the POE with a functional model and an orthogonal model for RNA-seq data. We demonstrated the desirable power and preserved Type I errors of the methods in most scenarios, especially the orthogonal model with un-biased estimation of the genetic effects and over-dispersion of the RNA-seq data. The application to a HapMap project trio dataset validated existing imprinting genes and discovered two novel imprinting genes with potential dominance genetic effect and RB1 and IGF1R genes. This study provides new insights into the next generation statistical modeling of eQTL mapping for better understanding of the genetic architecture underlying the mechanisms of gene expression regulation.

The biennial bearing and the long productive nature of coffee makes it difficult to release coffee variety within a short time span. This study aimed at evaluating the yield performance of the Arabusta hybrids and its backcrosses developed by Coffee Research Institute of the Kenya Agricultural and Livestock Research Organization (KALRO-CRI) using the morphological traits. Nineteen coffee genotypes were evaluated at Siaya ATC and KALRO-Alupe using randomized complete block design with three replications and the morphological data for growth and yield was recorded during the year 2018. The results indicated that there was significant difference in yield among the coffee genotypes and between the sites. Yield had positive significant associations with parentage berries per node (r= 0.61), berries on the longest primary (r= 0.58) and berries per node on the longest primary(r=0.60). The genotypic coefficient of variation (GCV) values for the morphological traits varied from 6.50 to 31.01%. Broad sense heritability ranged from 0.15 to 0.61 with bean yield recording heritability of 0.31. The number of berries on the longest primary had high broad sense heritability and high genetic advance indicating the presence of additive genes that can be used in coffee improvement through selection. Key words: Environment, Genetic advance, Robusta, Response, Selection, Variation

BACKGROUND: Variation in facial shape may arise from the combinatorial or overlapping actions of paralogous genes. Given its many members, and overlapping expression and functions, the EPH receptor family is a compelling candidate source of craniofacial morphological variation. We performed a detailed morphometric analysis of an allelic series of E14.5 Ephb1-3 receptor mutants to determine the effect of each paralogous receptor gene on craniofacial morphology. RESULTS: We found that Ephb1, Ephb2, and Ephb3 genotypes significantly influenced facial shape, but Ephb1 effects were weaker than Ephb2 and Ephb3 effects. Ephb2(−/−) and Ephb3(−/−) mutations affected similar aspects of facial morphology, but Ephb3(−/−) mutants had additional facial shape effects. Craniofacial differences across the allelic series were largely consistent with predicted additive genetic effects. However, we identified a potentially important non-additive effect where Ephb1 mutants displayed different morphologies depending on the combination of other Ephb paralogs present, where Ephb1(+/−), Ephb1(−/−), and Ephb1(−/−); Ephb3(−/−) mutants exhibited a consistent deviation from their predicted facial shapes. CONCLUSIONS: This study provides a detailed assessment of the effects of Ephb receptor gene paralogs on E14.5 mouse facial morphology and demonstrates how loss of specific receptors contributes to facial dysmorphology.

AIMS Coronary artery disease (CAD) has a strong genetic predisposition. However, despite substantial discoveries made by genome-wide association studies (GWAS), a large proportion of heritability awaits identification. Non-additive genetic-effects might be responsible for part of the unaccounted genetic variance. Here we attempted a proof-of-concept study to identify non-additive genetic effects, namely epistatic interactions, associated with CAD. METHODS AND RESULTS We tested for epistatic interactions in ten CAD case-control studies and UK Biobank with focus on 8,068 SNPs at 56 loci with known associations with CAD risk. We identified a SNP pair located in cis at the LPA locus, rs1800769 and rs9458001, to be jointly associated with risk for CAD (odds ratio OR=1.37, p = 1.07 $\times$ 10-11), peripheral arterial disease (OR = 1.22, p = 2.32 $\times$ 10-4), aortic stenosis (OR = 1.47, p = 6.95 $\times$ 10-7), hepatic lipoprotein(a) (Lp(a)) transcript levels (beta = 0.39, p = 1.41 $\times$ 10-8), and Lp(a) serum levels (beta = 0.58, p = 8.7 $\times$ 10-32), while individual SNPs displayed no association. Further exploration of the LPA locus revealed a strong dependency of these associations on a rare variant, rs140570886, that was previously associated with Lp(a) levels. We confirmed increased CAD risk for heterozygous (relative OR = 1.46, p = 9.97 $\times$ 10-32) and individuals homozygous for the minor allele (relative OR = 1.77, p = 0.09) of rs140570886. Using forward model selection, we also show that epistatic interactions between rs140570886, rs9458001, and rs1800769 modulate the effects of the rs140570886 risk allele. CONCLUSIONS These results demonstrate the feasibility of a large-scale knowledge-based epistasis scan and provide rare evidence of an epistatic interaction in a complex human disease. We were directed to a variant (rs140570886) influencing risk through additive genetic as well as epistatic effects. In summary, this study provides deeper insights into the genetic architecture of a locus important for cardiovascular diseases. TRANSLATIONAL PERSPECTIVE Genetic variants identified by GWAS studies explain about a quarter of the heritability of coronary artery disease by additive genetic effects. Our study demonstrates that non-additive effects contribute to the genetic architecture of the disease as well and identifies complex interaction patterns at the LPA locus, which affect LPA expression, Lp(a) plasma levels and risk of atherosclerosis. This proof-of-concept study encourages systematic searches for epistatic interactions in further studies to shed new light on the aetiology of the disease.