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This study aimed to estimate variance components (VCs) for growth and reproductive traits in Nellore cattle using two relationship matrices (pedigree relationship A matrix and pedigree plus genomic relationship H matrix), and records collected before and after genomic selection (GS) implementation. The study also evaluated how genomic breeding values (GEBV) are affected by variance components and discarding old records. The analysed traits were weight at 120 days (W120), weight and scrotal circumference at 450 days (W450 and SC450, respectively). Three datasets were used to estimate VCs, including all phenotypic information (All) or records for animals born before or after GS implementation (Before or After datasets, respectively). Both relationship matrices were considered for VC estimation, the A matrix was used in all three datasets and VC from each combination were named as A_Before, A_After, and A_All). The H was used in two datasets: H_All and H_After. Different VCs were used for GEBV prediction through ssGBLUP. This step used two possible Datasets, using all available phenotypic data (Dataset 1) or just records collected since GS implementation (Dataset 2). Validation was conducted using accuracy, bias and dispersion according to the LR method and prediction accuracy from corrected phenotypes. The heritability of all traits increased from A_Before to A_After, while estimates for A_All were intermediary. In the previous order, the estimates were 0.16, 0.17, and 0.15 for W120; 0.31, 0.39, and 0.35 for W450; 0.35, 0.47, and 0.41 for SC. For W450 and SC, using the H matrix reduced the heritability (0.33 and 0.32 for W450; 0.41 and 0.38 for SC for H_After and H_All, respectively). For W120, Dataset1 and VCs from A_After showed the highest accuracy for direct and maternal GEBV (0.953 and 0.868). For W450, Dataset 1 and VC from H_After allowed the highest accuracy (0.854) but use Dataset 2 and same VC source yield similar value (0.846). For SC, Dataset 2 with VC from H_After showed the highest accuracy (0.925). To use Dataset 2 does not cause important changes in bias or dispersion with respect to Dataset 1. The VC and genetic parameters changed for W120, W450, and SC450, using records before or after the GS implementation. For W450 and SC450, genetic variance and heritability estimates increased with the use of GS. For W120, genomic predictions were more accurate using A for VC estimation. Accuracy gains were observed for W450 and SC450 using H in VC estimation and/or discarding records before GS. It is possible to discard phenotypic records before GS implementation without generating bias or dispersion in the GEBV of young candidates. [ABSTRACT FROM AUTHOR]

Background: The Arg64 allele of the rs4994 (Trp64Arg) variant in the β3-adrenergic receptor (ADRB3) gene is involved in the control of energy balance by altering lipolysis and thermogenesis in adipocytes, ultimately contributing to the development of obesity. The objective of our study was to investigate the association between the rs4994 variant of the ADRB3 gene and obesity in Hanoi preschool-age children, adjusting for their eating behaviors. Methods: A cross-sectional study was performed involving 708 children with normal weight and 304 children with obesity aged 3–5 years from 36 kindergartens in Hanoi, Vietnam. Cheek mucosa cell samples were used for DNA extraction, and genotyping at the ADRB3-rs4994 locus was performed using the polymerase chain reaction–restriction fragment length polymorphism method (PCR–RFLP). Eating behaviors were assessed using the Children's Eating Behaviour Questionnaire (CEBQ). Binary logistic regression analysis was employed to examine the association between the rs4994 variant and obesity, adjusting for confounding factors such as age, sex, residence, birth weight, and eating behaviors. Results: The frequency of the C allele in the group with obesity was 16.4%, which was higher than in the control group (11.7%, P = 0.003). Children with the CC genotype exhibited significantly greater weight and weight-for-age Z-score compared to those with the TT and TC genotypes (P = 0.004 and 0.03, respectively). Following univariate and multivariate analyses adjusted for age, sex, residence, birth weight, and eating behaviors, a significant association between the rs4994 variant and obesity was observed (P < 0.05). Conclusions: This study indicated that the ADRB3-rs4994 variant can be considered as an independent risk factor for obesity in Vietnamese preschool children. [ABSTRACT FROM AUTHOR]

Abstract Background The Arg64 allele of the rs4994 (Trp64Arg) variant in the β3-adrenergic receptor (ADRB3) gene is involved in the control of energy balance by altering lipolysis and thermogenesis in adipocytes, ultimately contributing to the development of obesity. The objective of our study was to investigate the association between the rs4994 variant of the ADRB3 gene and obesity in Hanoi preschool-age children, adjusting for their eating behaviors. Methods A cross-sectional study was performed involving 708 children with normal weight and 304 children with obesity aged 3–5 years from 36 kindergartens in Hanoi, Vietnam. Cheek mucosa cell samples were used for DNA extraction, and genotyping at the ADRB3-rs4994 locus was performed using the polymerase chain reaction–restriction fragment length polymorphism method (PCR–RFLP). Eating behaviors were assessed using the Children’s Eating Behaviour Questionnaire (CEBQ). Binary logistic regression analysis was employed to examine the association between the rs4994 variant and obesity, adjusting for confounding factors such as age, sex, residence, birth weight, and eating behaviors. Results The frequency of the C allele in the group with obesity was 16.4%, which was higher than in the control group (11.7%, P = 0.003). Children with the CC genotype exhibited significantly greater weight and weight-for-age Z-score compared to those with the TT and TC genotypes (P = 0.004 and 0.03, respectively). Following univariate and multivariate analyses adjusted for age, sex, residence, birth weight, and eating behaviors, a significant association between the rs4994 variant and obesity was observed (P

Background: Sesame is an ancient oilseed crop of India popular for its drought resistance and stable healthy oil which is easy to extract. Information regarding the genetic association of plant traits with grain yield is of great importance to breeders in selecting suitable genotypes. Hence, the present study is based on simple measures of variability and genetic variance to identify suitable genotypes for further improvement. Methods: The experiment was carried out at Student's Farm, Department of Agriculture, Loyola Academy, Secunderabad during Kharif 2021. Sixty genotypes of the Sesamum crop were studied for 13 quantitative and qualitative traits. Result: Analysis of variance revealed that the genotypes were significant (P 0.05 and P 0.01) for all of the traits studied. A positive significant correlation at the genotypic level was observed for the character 1000 seed weight (0.222) with grain yield. A positive correlation between desirable traits is encouraging to the plant breeder as it helps in the simultaneous improvement of both traits. Positive direct effects were highest for the character 1000 seed weight (0.866) followed by the number of capsules per axil (0.660) on grain yield. This study would help to select the genotypes that have a strong association among traits. [ABSTRACT FROM AUTHOR]

Sexual conflict plays a key role in the dynamics of adaptive evolution in sexually reproducing populations, and theory suggests an important role for variance in resource acquisition in generating or masking sexual conflict over fitness and life history traits. Here, I used a quantitative genetic genotype × environment experiment in Drosophila melanogaster to test the theoretical prediction that variance in resource acquisition mediates variation in sex-specific component fitness. Holding larval conditions constant, I found that adult nutritional environments characterized by high protein content resulted in reduced survival of both sexes and lower male reproductive success compared to an environment of lower protein content. Despite reduced mean fitness of both sexes in high protein environments, I found a sex*treatment interaction for the relationship between resource acquisition and fitness; estimates of the adaptive landscape indicate males were furthest from their optimum resource acquisition level in high protein environments, and females were furthest in low protein environments. Expression of genetic variance in resource acquisition and survival was highest for each sex in the environment it was best adapted to, although the treatment effects on expression of genetic variance eroded in the path from resource acquisition to total fitness. Cross-sex genetic correlations were strongly positive for resource acquisition, survival, and total fitness and negative for mating success, although estimation error was high for all. These results demonstrate that environmental effects on resource acquisition can have predictable consequences for the expression of sex-specific genetic variance but also that these effects of resource acquisition can erode through life history. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity helps animals to buffer the effects of increasing thermal and nutritional stress created by climate change. Plastic responses to single and combined stressors can vary among genetically diverged populations. However, less is known about how plasticity in response to combined stress varies among individuals within a population or whether such variation changes across life-history traits. This is important because individual variation within populations shapes population-level responses to environmental change. Here, we used isogenic lines of Drosophila melanogaster to assess the plasticity of egg-to-adult viability and sex-specific body size for combinations of 2 temperatures (25 °C or 28 °C) and 3 diets (standard diet, low caloric diet, or low protein:carbohydrate ratio diet). Our results reveal substantial within-population genetic variation in plasticity for egg-to-adult viability and wing size in response to combined thermal-nutritional stress. This genetic variation in plasticity was a result of cross-environment genetic correlations that were often < 1 for both traits, as well as changes in the expression of genetic variation across environments for egg-to-adult viability. Cross-sex genetic correlations for body size were weaker when the sexes were reared in different conditions, suggesting that the genetic basis of traits may change with the environment. Furthermore, our results suggest that plasticity in egg-to-adult viability is genetically independent from plasticity in body size. Importantly, plasticity in response to diet and temperature individually differed from plastic shifts in response to diet and temperature in combination. By quantifying plasticity and the expression of genetic variance in response to combined stress across traits, our study reveals the complexity of animal responses to environmental change, and the need for a more nuanced understanding of the potential for populations to adapt to ongoing climate change. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the effects of the general combining ability (GCA) and the specific combining ability (SCA) on the agronomic variables of piquin pepper (Capsicum annuum var. Glabriusculum) genotypes. Methodology: A total of 36 F1 and nine parental crosses were used as plant material. The genotypes were distributed in a completely randomized block design with three replications. Ten agronomic variables were evaluated. Results: Differences (P≤ 0.01) were found in all the evaluated variables, both in the genotypes and in GCA and SCA. Additive gene action influenced heritability, where following variables stood out: days to harvest (DTH), chlorophyll (CHL), plant height (PH), average fruit weight (AFW), fruit equatorial diameter (FED), and fruit polar diameter (FPD). One the one hand, genotypes G6 and G7 recorded the highest positive yield values for GCA, with 143.96 and 66.97 kg ha-1, respectively. On the other hand, 58% of the SCA crosses obtained favorable yield results. Meanwhile, the highest positive values were obtained by the G6xG7, G8xG9, G5xG9, G3xG4, G4xG8, and G1xG8 crosses, which recorded 427.1, 190.5, 167.4, 146.8, 129.7, and 125.7 kg ha-1, respectively. Conclusions: According to the effects of GCA and SCA on the agronomic variables of piquin pepper, the genotypes G6 and G7 can be used to develop varieties, while the G6xG7, G8xG9, and G5xG9 crosses are recommended for hybrid formation within breeding programs. [ABSTRACT FROM AUTHOR]

BackgroundHost genetics can shape microbiome composition, but to what extent it does, remains unclear. Like any other complex trait, this important question can be addressed by estimating the heritability (h2) of the microbiome-the proportion of variance in the abundance in each taxon that is attributable to host genetic variation. However, unlike most complex traits, microbiome heritability is typically based on relative abundance data, where taxon-specific abundances are expressed as the proportion of the total microbial abundance in a sample.ResultsWe derived an analytical approximation for the heritability that one obtains when using such relative, and not absolute, abundances, based on an underlying quantitative genetic model for absolute abundances. Based on this, we uncovered three problems that can arise when using relative abundances to estimate microbiome heritability: (1) the interdependency between taxa can lead to imprecise heritability estimates. This problem is most apparent for dominant taxa. (2) Large sample size leads to high false discovery rates. With enough statistical power, the result is a strong overestimation of the number of heritable taxa in a community. (3) Microbial co-abundances lead to biased heritability estimates.ConclusionsWe discuss several potential solutions for advancing the field, focusing on technical and statistical developments, and conclude that caution must be taken when interpreting heritability estimates and comparing values across studies. Video Abstract.

The dataset primarily focused on selecting genotypes of sweet oranges based on their phenotypic performances. The dataset resulted significant variations in the best linear unbiased predictions (BLUPs) of 20 out of 21 traits, including leaves, flowers, fruits, and seeds. A strong positive correlation (r= 0.73 to 0.95) was observed among the majority of morphological traits. The sweet orange genotypes demonstrated considerable genetic variance, surpassing 65% for almost all traits, with a selection accuracy exceeding 92%. Using the multi-trait genotype-ideotype distance index (MGIDI), CS Jain-001 emerged as the top-ranked genotype, followed by BAU Malta-3 and CS Jain-002 in order of desirability. The broad sense heritability of selected traits was above 75.60%, and the selection gain reached a maximum of 12.60. These identified genotypes show promise as potential parent donors in breeding programs, leveraging their strengths and weaknesses to develop promising varieties in Bangladesh.

Introduction Cucumber (Cucumis sativus L.) is an annual plant in the Cucurbitaceae family, which has 90 genera and 750 species. Iran, with an under-cultivation area of 89,632 hectares and a production rate of 1,804,184 tons of cucumbers, yield of 201,289 tons per hectare, and it is the third largest cucumber producing country in the world in terms of production. Use of fruits of these vegetable is different depending on the country and the consumer's taste and demand, and it is cultivated for fresh consumption as well as processing (pickled vegetables or cucumbers). The utilization of local genotypes or unmodified native reserves for production has led to very low yield of cucumbers in some countries of the world. The general objectives of cucumber breeding are resistance to diseases and pests, fruit quality and yield increase. Considering the history of cultivation of this product in Iran and due to the large under-cultivation areas of cucumber in the country, little breeding research has been done on this product and the country's required seeds are supplied annually through imports. Therefore, practical and applied research on the breeding of cucumber plant seems necessary. The present study was conducted to evaluate 27 cucumber plant lines using factor analysis and cluster analysis as a tool to identify superior genotypes and more effective traits. Materials and Methods This study was carried out in the research greenhouse of Department of Horticultural Sciences, Faculty of Agricultural Sciences, University of Guilan, with a longitude of 49 degrees and 36 minutes east and latitude 37 degrees and 16 minutes north with a height of 7 meters from the level of the open sea in February 2021. Overall, 35 cucumber inbred lines, available in the Germplasm Bank, University of Guilan, were selected and on completely randomized design, in three separate rows, and with three replications. A code was assigned to each of the lines in order to facilitate the naming of lines and easier evaluation. In the winter of 2019, the desired genotypes were first planted in the seedling tray and kept there until the second true leaves were observed. Then they were transferred to the greenhouse in the form of a completely randomized design with 27 lines of inbred cucumbers, in three separate rows with 3 replications and 3 observations. The length of the plant breeding period continued until the economic fruiting of the plant. During the growing season, various traits were checked and recorded according to the national guidelines for tests of differentiation, uniformity and stability in cucumber prepared by the Research Institute of Registration and Certification of Seeds and Seedlings. These traits are the Fruit diameter (mm), Fruit length (mm), Fruit number, Weight of single fruit (g), Total fruit weight (g), Number of female flowers in 15 nodes, Number of female flowers per node, Width of the end of the terminal leaf(cm), Length of the end of the terminal leaf(cm), Number of lateral branches in 15 nodes, Length of 15 internodes (cm). Results and Discussion Genetic diversity in plant genotypes is essential for a successful breeding program. Understanding the degree of variability in plant species is of importance because it provides the basis for selection. The results of variance analysis show that there is a highly significant variation between the studied lines at the level of 1%. The significant difference observed between genotypes for all traits indicates the existence of inherent genetic variation among genotypes. The evaluation results show that the average fruit weight trait varied from 1371.7 grams (L57) to 157.71 grams (L35) among the examined lines. Furthermore, genotype L57 (117.56 grams) had the highest statistical position in terms of single fruit weight. The results of the mean comparison table showed that L34 line had the highest fruit length values (161.84 mm) and L49 line had the highest fruit diameter values (39.83 mm). Moreover, L55 and L34 lines had the lowest values of fruit length (92.46 mm) and diameter (24.61 mm), respectively. The leaf area variable varied from 426.52 cm2 (L57) to 204.24 cm2 (L31) among the studied lines. The results of chlorophyll index traits investigation and total soluble solids showed that L51 line had the highest values in both traits. The results of statistical analyses pertaining to genotypic and phenotypic variance, as well as general heritability, revealed that the trait with the highest heritability, at 99.44%, was fruit weight. With the exception of five traits-length of 15 primary internodes, leaf surface, length and width of the terminal leaf, and single fruit weight-whose heritability values were 87.35%, 73.83%, 63.59%, 61.27%, and 26.23%, respectively, the heritability exceeded 90% for the remaining traits. These findings indicate that most of the traits examined exhibited high heritability, suggesting they were less influenced by environmental factors. Factor analysis, an essential multivariate technique, was employed to explore trait relationships and assess the genetic diversity among genotypes. The results of factor analysis for 27 evaluated cucumber genotypes show that eight factors were identified. They were 23.52, 12.63, 11.81, 9.95, 8.6, 7.34, 6.27, 4.21 percent. in total explained 88% of the total diversity of traits in the studied population. In total, they justified 88% diversity of total traits in the studied population. The results of the cluster analysis placed the studied genotypes in four different groups based on the mean of traits. To ensure the cut-point in the dendrogram and to determine the actual number of groups, the discrimination function analysis method was used. The results of discrimination function analysis showed that the success of cluster analysis in grouping genotypes was 100%. Since the genotypes in each of the clusters have a greater genetic affinity with the genotypes in the same cluster and, conversely, a greater genetic distance with the genotypes in different clusters, hybridization can be done among the genotypes in different clusters according to the value of traits average for each cluster for more productivity of phenomena such as heterosis and transgressive segregation. On this basis, it seems that it is possible to produce hybrids that are superior to their parents in terms of various traits by hybridization between the genotypes in the first and second clusters with the genotypes in the third and fourth clusters. Conclusion According to the results obtained from this study, L57 and L54 genotypes had higher values than the rest of the genotypes in terms of fruit number and total fruit weight. Also, according to the results of cluster analysis, L57 line had higher total mean values in traits of total fruit weight, single fruit weight, diameter of the tail of the fruit, fruit, kernel diameter, fresh and dry weight of leaves and leaf area. In this study, the genotypes of the second and third groups in the fruit number trait, and the genotypes of the first and third groups in the fruit weight trait, due to having the maximum difference, were found suitable for use in crosses in order to create more diversity. In general, the results of this research showed that there was a suitable diversity among the studied lines in terms of all measured traits. In addition to the fact that the results obtained from this research can be used in future breeding programs, the results of multivariate statistical methods also show solutions for the scientific crossing of genotypes in future research. So that the genotypes placed in different groups in cluster analysis (Group 1: L57, Group 2: L54, L52, L47, L32, L49, and L27, Group 3: L43 and L35, Group 4: L59, L53, L51, L34, L26, L55, L25, L39, L31, L30, L33, L28, L29, L36, L24, L44, L22, and L20) and had superior characteristics in terms of different components, can be crossed together to create recombinant genotypes.

This study aimed to address the genetic and environmental features that affect the calf's sex in dairy farms, which favors female birth for extra milk production and efficient replacements. A total of 4913 calves' records from 1047 Friesian cows collected at Sakha dairy farm between 1975 and 2020 were analyzed to estimate genetic parameters and various environmental effects on calf gender, including year and season of mating, first calving year, gestation length, parity, service period, and number of services per conception. Variance components, heritabilities, and repeatability values were estimated using the THRGIBBS1F90 program based on Gibbs sampling. The results showed highly significant effects of the season (P < 0.001) and year of mating, gestation length (P < 0.01), and the others (P < 0.05) on calf gender. For female birth, direct (h2 a), sire (h2 s), and dam (h2 m) heritability and repeatability estimates are 0.13- 0.16, around 0.12, 0.09, and 0.15-0.18, respectively. Short gestational length, few services per conception, plus first and fifth parties were the main predictors of female births. Moderate estimates of female birth and sire heritability demonstrate that genetic manipulation can change additive genetic variability. With only 0.15-0.18% confidence, the moderate repeatability estimates of female birth indicated that previous calf sex can influence calf gender in subsequent pregnancies. By manipulating some management techniques in addition to genetic parameters in dairy cows before mating, it is possible to change the gender proportion of fresh births to a preferred value. [ABSTRACT FROM AUTHOR]

Wood density is an intricate trait that encapsulates water transport, growth, and productivity. It is probably the most used parameter to deduce wood quality. In this study, the wood density of 81 European provenances of Norway spruce tested in three provenance trials from the Romanian Carpathians was analysed and compared at 49 years after planting. We also analysed the correlations between wood density and the provenances' geographic coordinates, as well as other traits, such as diameter at breast height, total height, and survival rate. For the genetic variance analysis of the wood density in each provenance trial and across sites, linear mixed models were used. Significant differences between the Norway spruce provenances regarding wood density were found only in the Dorna Candrenilor trial, where the mean wood density per provenance had values ranging from 0.311 ± 0.030 g/cm³ to 0.356 ± 0.019 g/cm³. No significant correlations between wood density and the provenances' geographic coordinates were found. Negative correlations were found between wood density and the other traits analysed. Provenances with good performances in provenance trials could be used in assisted migration. [ABSTRACT FROM AUTHOR]

Many quantitative genetic models assume that all genetic variation is additive because of a lack of data with sufficient structure and quality to determine the relative contribution of additive and non-additive variation. Here the fractions of additive (fa) and non-additive (fd) genetic variation were estimated in Sitka spruce for height, bud burst and pilodyn penetration depth. Approximately 1500 offspring were produced in each of three sib families and clonally replicated across three geographically diverse sites. Genotypes from 1525 offspring from all three families were obtained by RADseq, followed by imputation using 1630 loci segregating in all families and mapped using the newly developed linkage map of Sitka spruce. The analyses employed a new approach for estimating fa and fd, which combined all available genotypic and phenotypic data with spatial modelling for each trait and site. The consensus estimate for fa increased with age for height from 0.58 at 2 years to 0.75 at 11 years, with only small overlap in 95% support intervals (I95). The estimated fa for bud burst was 0.83 (I95=[0.78, 0.90]) and 0.84 (I95=[0.77, 0.92]) for pilodyn depth. Overall, there was no evidence of family heterogeneity for height or bud burst, or site heterogeneity for pilodyn depth, and no evidence of inbreeding depression associated with genomic homozygosity, expected if dominance variance was the major component of non-additive variance. The results offer no support for the development of sublines for crossing within the species. The models give new opportunities to assess more accurately the scale of non-additive variation. [ABSTRACT FROM AUTHOR]

Doubled haploid (DH) plants have been widely used for breeding and biological research in crops. Populus spp. have been used as model woody plant species for biological research. However, the induction of DH poplar plants is onerous, and limited biological or breeding work has been carried out on DH individuals or populations. In this study, we provide an effective protocol for poplar haploid induction based on an anther culture method. A total of 96 whole DH plant lines were obtained using an F1 hybrid of Populus simonii × P. nigra as a donor tree. The phenotypes of the DH population showed exceptionally high variance when compared to those of half-sib progeny of the donor tree. Each DH line displayed distinct features compared to those of the other DH lines or the donor tree. Additionally, some excellent homozygous lines have the potential to be model plants in genetic and breeding studies. [ABSTRACT FROM AUTHOR]

Abstract Background Host genetics can shape microbiome composition, but to what extent it does, remains unclear. Like any other complex trait, this important question can be addressed by estimating the heritability (h 2 ) of the microbiome—the proportion of variance in the abundance in each taxon that is attributable to host genetic variation. However, unlike most complex traits, microbiome heritability is typically based on relative abundance data, where taxon-specific abundances are expressed as the proportion of the total microbial abundance in a sample. Results We derived an analytical approximation for the heritability that one obtains when using such relative, and not absolute, abundances, based on an underlying quantitative genetic model for absolute abundances. Based on this, we uncovered three problems that can arise when using relative abundances to estimate microbiome heritability: (1) the interdependency between taxa can lead to imprecise heritability estimates. This problem is most apparent for dominant taxa. (2) Large sample size leads to high false discovery rates. With enough statistical power, the result is a strong overestimation of the number of heritable taxa in a community. (3) Microbial co-abundances lead to biased heritability estimates. Conclusions We discuss several potential solutions for advancing the field, focusing on technical and statistical developments, and conclude that caution must be taken when interpreting heritability estimates and comparing values across studies. Video Abstract

Evolutionary adaptation through genetic change requires genetic variation and is a key mechanism enabling species to persist in changing environments. Although a substantial body of work has focused on understanding how and why additive genetic variance (VA) differs among traits within species, we still know little about how they vary among species. Here we make a first attempt at testing for interspecific variation in two complementary measures of VA and the role of phylogeny in shaping this variation. To this end, we performed a phylogenetic comparative analysis using 1822 narrow‐sense heritability (h2) for 68 species of birds and mammals and 378 coefficients of additive genetic variance (CVA) estimates for 23 species. Controlling for within‐species variation attributable to estimation method and trait type, we found some interspecific variation in h2 (~15%) but not CVA. Although suggestive of interspecific variation in the importance of non‐(additive) genetic sources of variance, sample sizes were insufficient to test this hypothesis directly. Additionally, although power was low, no phylogenetic signal was detected for either measure. Hence, while this suggests interspecific variation in VA is probably small, our understanding of interspecific variation in the adaptive potential of wild vertebrate populations is currently hampered by data limitations, a scarcity of CVA estimates and a measure of their uncertainty in particular. [ABSTRACT FROM AUTHOR]

Monoamine transporters (MATs) are responsible for the reuptake of dopamine, serotonin, and norepinephrine, modulating concentrations of these essential brain neurotransmitters and thus regulating behavior, mood, and cognitive functions. Studying the role of various genes in complex physiological processes is a promising area of neurobiology and sport physiology. Here, we summarize mounting evidence linking specific genetic variants of MAT genes to various aspects of sport performance. For example, the 10-repeat allele of the dopamine transporter gene (DAT), the L-allele of the serotonin transporter gene (SERT), and the single nucleotide polymorphism rs1805065 of the norepinephrine transporter gene (NET) appear to correlate with a higher athletic performance due to stress resistance, as well as the maintenance of motivation and cognitive behavioral competencies, i.e. qualities required to achieve sporting success. Thus, physiological performance in various sports may be partially genetically determined and controlled by the variability in the MAT genes. [ABSTRACT FROM AUTHOR]

The viability of using inbred progenies, i.e., S1 or S2, in recurrent selection programs for perennial plants was evaluated in comparison with full sibs using the expression of gain from selection. Populations with different genetic properties, were considered in obtaining the estimates, with the population genetic variance always equal to 1 used as reference, as well as different experimental strategies. The estimates of genetic covariances between average additive effects of the alleles and the dominance effects of homozygotes, which occur when S1 or S2 is used, although negative for the lower values of the average allele frequencies, were always smaller than the additive genetic variance. Per unit of time, the total gain from selection with S1 was greater than with S2 and full sibs. However, it is argued that the best strategy is a cycle with S1, followed by a cloned progeny test with full sibs. [ABSTRACT FROM AUTHOR]

Genetic selection has been applied for many generations in animal, plant, and experimental populations. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allelic architecture are different for the recently introduced technique of genomic selection compared to traditional selection methods and whether they depend on the genetic architectures of traits. Here, we investigate the allele frequency changes of old and new causal loci under 50 generations of phenotypic, pedigree, and genomic selection, for a trait controlled by either additive, additive and dominance, or additive, dominance, and epistatic effects. Genomic selection resulted in slightly larger and faster changes in allele frequencies of causal loci than pedigree selection. For each locus, allele frequency change per generation was not only influenced by its statistical additive effect but also to a large extent by the linkage phase with other loci and its allele frequency. Selection fixed a large number of loci, and 5 times more unfavorable alleles became fixed with genomic and pedigree selection than with phenotypic selection. For pedigree selection, this was mainly a result of increased genetic drift, while genetic hitchhiking had a larger effect on genomic selection. When epistasis was present, the average allele frequency change was smaller (~15% lower), and a lower number of loci became fixed for all selection methods. We conclude that for long-term genetic improvement using genomic selection, it is important to consider hitchhiking and to limit the loss of favorable alleles. [ABSTRACT FROM AUTHOR]

Butterfly pea (Clitoria ternatea L.) is a leguminous plant with several potential health benefits. The scientific name is derived from its origin on Ternate Island, North Maluku. Therefore, this study aimed to analyze the genetic variability in butterfly pea using Intergenic Simple Sequence Repeat (ISSR) markers in North Maluku. Field surveys, collection trips, and habitat studies of butterfly pea plants were conducted on Ternate, Tidore, Halmahera, and Morotai Islands. Genetic diversity was analyzed based on molecular data from the ISSR method. The molecular analysis results obtained using PCR-ISSR on 18 accessions showed a low degree of similarity. Among these, 15 accessions from Ternate, Tidore, Morotai, and Halmahera were in group A, while 3 from Ternate, Tidore, and Halmahera were in group B. All accessions exhibited a genetic similarity level of 0.709, indicating significant diversity. The arrangement among accessions on the dendrogram was similar to the phylogenetic tree, showing separation and spread at 0.608–0.924 based on the Jaccard coefficient. The results suggested that C. ternatea probably originated from Ternate, and subsequently spread to Tidore, Halmahera, and Morotai due to its use as a herbal medicine and ornamental plant. This information could be used as the basis for butterfly pea conservation and cultivation activities in Indonesia, specifically in Ternate Island, North Maluku. [ABSTRACT FROM AUTHOR]

Abstract Evolutionary adaptation through genetic change requires genetic variation and is a key mechanism enabling species to persist in changing environments. Although a substantial body of work has focused on understanding how and why additive genetic variance (VA) differs among traits within species, we still know little about how they vary among species. Here we make a first attempt at testing for interspecific variation in two complementary measures of VA and the role of phylogeny in shaping this variation. To this end, we performed a phylogenetic comparative analysis using 1822 narrow‐sense heritability (h2) for 68 species of birds and mammals and 378 coefficients of additive genetic variance (CVA) estimates for 23 species. Controlling for within‐species variation attributable to estimation method and trait type, we found some interspecific variation in h2 (~15%) but not CVA. Although suggestive of interspecific variation in the importance of non‐(additive) genetic sources of variance, sample sizes were insufficient to test this hypothesis directly. Additionally, although power was low, no phylogenetic signal was detected for either measure. Hence, while this suggests interspecific variation in VA is probably small, our understanding of interspecific variation in the adaptive potential of wild vertebrate populations is currently hampered by data limitations, a scarcity of CVA estimates and a measure of their uncertainty in particular.

Simple Summary: Human epidermal growth factor receptor 2 (HER2) participates in breast cancer pathogenesis and progression. However, the role of HER2 in canine mammary tumors is not completely understood, and data from different immunohistochemical studies are conflicting. A remarkable genetic variation of the canine HER2 gene has been recognized, including several single nucleotide polymorphisms (SNPs), which may account for the contradictory results. This study aims to assess the relationship between SNPs rs24537329 and rs24537331 in canine HER2 gene and clinicopathological features, clinical progression, and outcome of canine mammary tumors (CMT). Our results demonstrated that SNP rs24537331 was associated with decreased tumoral necrosis and with longer disease-specific overall survival; however, no significant associations were found between SNP rs24537329 and the tumors' clinicopathological characteristics or survival. Our data suggest that SNP rs24537331 may have a protective effect in CMT, allowing the identification of a subgroup of animals prone to develop less aggressive forms of the disease. This investigation emphasizes the importance of the animal's genetic background assessment as a valuable tool to be used by clinicians and oncologists in CMT management. The role of HER2 in canine mammary tumors is not completely elucidated, and the contradictory results published so far may be, in part, explained by the genetic variability recognized in the canine HER2 gene. Single nucleotide polymorphism (SNPs) in HER2 were recently associated with less aggressive canine mammary tumor histotypes. This study assesses the relationship between SNPs rs24537329 and rs24537331 in canine HER2 gene and clinicopathological characteristics and outcome of mammary tumors in a group of 206 female dogs. Allelic variants were observed in 69.8% and 52.7% of the dogs for SNP rs24537329 and rs24537331, respectively. Our results demonstrated that SNP rs24537331 was associated with decreased tumoral necrosis (HR: 3.09; p = 0.012) and with longer disease-specific overall survival (HR: 2.59; p = 0.013). However, no statistically significant associations were found between SNP rs24537329 and the tumors' clinicopathological characteristics or survival. Our data suggest that SNP rs24537331 may have a protective effect in canine mammary tumors, allowing the identification of a subgroup of animals prone to develop less aggressive forms of the disease. This study emphasizes the importance of the genetic tests associated with clinical images and histological examinations when assessing CMT outcomes. [ABSTRACT FROM AUTHOR]

Objectives: Genome-wide association studies have revealed over 200 genetic susceptibility loci for prostate cancer (PCa). By combining them, polygenic risk scores (PRS) can be generated to predict risk of PCa. We summarize the published evidence and conduct meta-analyses of PRS as a predictor of PCa risk in Caucasian men. Patients and methods: Data were extracted from 59 studies, with 16 studies including 17 separate analyses used in the main meta-analysis with a total of 20,786 cases and 69,106 controls identified through a systematic search of ten databases. Random effects meta-analysis was used to obtain pooled estimates of area under the receiver-operating characteristic curve (AUC). Metaregression was used to assess the impact of number of single-nucleotide polymorphisms (SNPs) incorporated in PRS on AUC. Heterogeneity is expressed as I 2 scores. Publication bias was evaluated using funnel plots and Egger tests. Results: The ability of PRS to identify men with PCa was modest (pooled AUC 0.63, 95% CI 0.62-0.64) with moderate consistency (I 2 64%). Combining PRS with clinical variables increased the pooled AUC to 0.74 (0.68-0.81). Meta-regression showed only negligible increase in AUC for adding incremental SNPs. Despite moderate heterogeneity, publication bias was not evident. Conclusion: Typically, PRS accuracy is comparable to PSA or family history with a pooled AUC value 0.63 indicating mediocre performance for PRS alone. [ABSTRACT FROM AUTHOR]

The success of breeding programs depends on the available genetic variability and the adequate selection of parents to produce seeds that generate added value to the developed cultivars that solve limiting problems of the crops. The determination of genetic gain is a powerful tool to advance the selection of outstanding progenitors that are subsequently used to obtain improved cultivars for traits of interest. With the main objective of calculating the genetic gain in different cycles, this research evaluated the yield, vegetative parameters, and oil production components in two oil palm populations identified as C0-Monterrey and C1-Vizcaina. The analysis was carried out using the analysis of variance. Genetic variation and heritability coefficients for all the evaluated traits were also calculated to obtain the components of phenotypic, genotypic, and environmental variation. Genetic gains (Δg) were more representative in the yield traits of fresh fruit bunches, with 19%, for the number of bunches per plant, with a Δg of 18.7%, and for the oil to bunch with a Δg of 6%. Low environmental influences were observed in the phenotypic variation for the different traits evaluated. Finally, high heritability values were observed for genetic traits such as height increase, with 93%, and average bunch weight, with 85%. The development of new progenies using elite dura-type female parents derived from these evaluated populations, with excellent yields of fresh fruit, bunch components, and slow growth, will be the future of oil palm cultivation. In the meantime, progeny trials must focus on improving the ability to select outstanding parents for the best DxP progenies. [ABSTRACT FROM AUTHOR]

The human hippocampus can be subdivided into subfields with unique functional properties and differential vulnerability to disease or neuropsychiatric conditions. Identifying genes that confer susceptibility to such processes is an important goal in developing treatments. Recent advances in automatic subfield segmentation from magnetic resonance images make it possible to use these measures as phenotypes in large-scale genome-wide association studies. Such analyses are likely to rely largely on standard resolution (~1 mm isotropic) T1 -weighted images acquired on 3.0T scanners. Determining whether the genetic architecture of subfields can be detected from such images is therefore an important step. We used Freesurfer v6.0 to segment hippocampal subfields in two large twin studies, the Vietnam Era Twin Study of Aging and the Human Connectome Project. We estimated heritability of subfields and the genetic overlap with total hippocampal volume. Heritability was similar across samples, but little genetic variance remained after accounting for genetic influences on total hippocampal volume. Importantly, we examined genetic relationships between subfields to determine whether subfields can be grouped based on a smaller number of underlying, genetically independent factors. We identified three genetic factors in both samples, but the high degree of cross loadings precluded formation of genetically distinct groupings of subfields. These results confirm the reliability of Freesurfer v6.0 generated subfields across samples for phenotypic analyses. However, the current results suggest that it will be difficult for large-scale genetic analyses to identify subfield-specific genes that are distinct from both total hippocampal volume and other subfields using segmentations generated from standard resolution T1 -weighted images.

Doubled-haploid lines (DHs) are normally produced from F1 plants in maize (Zea mays L.). Several studies have found a low frequency of recombinants in doubled haploids produced from F1 plants that could limit the selection response. Hence, an attempt was made to produce doubled haploids from the F2 generation to verify whether one more round of meiotic recombination could lead to increased genetic variability and assess the response to selection. The F1 and F2 plants of two cross-combinations, VL1043 × CM212 and VL121096 × CM202, were subjected to doubled-haploid production and evaluated in terms of their reaction to Fusarium stalk rot and yield traits along with F2 individuals of the same two crosses. There was significant variation in the number of DHs produced when F1 and F2 plants were subjected to DH production in the cross VL121096 × CM202. Furthermore, substantial genetic variability was observed among the DHs produced from the F1 generation (DHF1s), F2 generation (DHF2s), and F2s for Fusarium stalk rot (FSR) resistance. The genetic variance was more extensive in DHF2 compared to DHF1 plants in the cross VL1043 × CM212. Extreme candidate plants (highly resistant, resistant, and highly susceptible) were found in the F2 generation with a more standardized range than in the DHs. In the DH populations, the close correspondence between the phenotypic coefficient of variability (PCV) and the genotypic coefficient of variability (GCV) indicated less influence from the environment compared to the F2 plants. The heritability estimates in the DHs were greater than in the F2 plants of the VL1043 × CM212 cross, while in the VL121096 × CM202 cross, the heritability was almost the same between the DHs and F2 plants due to the relatively small population size of the DHs. The positively skewed leptokurtic distribution of the DH populations indicated the role of fewer genes, with the majority of them exhibiting complementary epistasis with decreasing effects in response to FSR. The mean estimated yield and genotypic variance in the top crosses produced from randomly chosen DHF1 and DHF2 plants of the cross VL1043 × CM212 were similar in magnitude. [ABSTRACT FROM AUTHOR]

[Display omitted] • The first study to explain the underlying mechanism of heterosis from the perspective of 3D genome in plants. • Superior heterosis hybrids tend to contain more transcriptionally active chromatin. • 3D chromatin compartments correlate with genetic variance among parents. • More accessible chromatin accelerates highly expressed ELD (expression level dominance) genes in superior heterosis hybrids. • Hormone- and cell-cycle-related genes are more up-regulated with changes of 3D genome thereby promoting leaf size. Heterosis is the major event driving plant development and promoting crop breeding, but the molecular bases for this phenomenon remain elusive. We aim to explore the effect of three-dimensional (3D) chromatin architecture on the underlying mechanism of heterosis. Here, we constructed the North Carolina II (NC-II) population to select superior and inferior heterosis sets by comparing mid-parent heterosis (MPH) in Brassica napus. To decipher the impact of 3D chromatin architecture on the underlying mechanism of heterosis, we combined genetics, transcriptomics and 3D genomics approaches. We suggest that F1 hybrids with superior heterosis tend to contain more transcriptionally active A compartments compared with F1 hybrids with inferior heterosis, and approximately 19–21% compartment significantly altered in the F1 hybrids relative to the parental lines. Further analyses show that chromatin compartments correlate with genetic variance among parents, which may form the basis for differentially active chromatin compartments. Having more A compartments in F1 hybrids confers a more accessible chromatin circumstance, which promotes a higher proportion of highly expressed ELD (expression level dominance) genes in superior heterosis F1 hybrids (46–64%) compared with inferior heterosis F1 hybrids (22–31%). Moreover, genes related to hormones which affect plant growth, are more up-regulated with changes of 3D genome architecture, and we validate that increased hormone content contributes to cell proliferation and expansion by influencing the key genes of cell cycle thereby promoting leaf size. Dynamic 3D chromatin architecture correlates with genetic variance among parents and contributes to heterosis in Brassica napus. [ABSTRACT FROM AUTHOR]

Abstract A capacity for rapid adaptation should enhance the persistence of populations subject to temporal and spatial heterogeneity in natural selection, but examples from nature remain scarce. Plectritis congesta (Caprifoliaceae) is a winter annual that exhibits local adaptation to browsing by ungulates and hypothesized to show context‐dependent trade‐offs in traits affecting success in competition versus resistance or tolerance to browsing. We grew P. congesta from 44 insular populations historically exposed or naïve to ungulates in common gardens to (1) quantify genetic, plastic and competitive effects on phenotype; (2) estimate a capacity for rapid adaptation (evolvability); and (3) test whether traits favoured by selection with ungulates present were selected against in their absence. Plants from browsed populations bolted and flowered later, had smaller inflorescences, were less fecund and half as tall as plants from naïve populations on average, replicating patterns in nature. Estimated evolvabilities (3–36%) and narrow‐sense heritabilities (h2; 0.13–0.32) imply that differences in trait values as large as reported here can arise in 2–18 generations in an average population. Phenotypic plasticity was substantial, varied by browsing history and fruit phenotype and increased with competition. Fecundity increased with plasticity in flowering height given competition (0.47 ± 0.02 florets/cm, β ± se), but 23–77% faster in naïve plants bearing winged fruits (0.53 ± 0.04) than exposed‐wingless plants (0.43 ± 0.03) or exposed‐winged and naïve‐wingless plants (0.30 ± 0.03, each case). Our results support the hypothesis that context‐dependent variation in natural selection in P. congesta populations has conferred a substantial capacity for adaptation in response to selection in traits affecting success in competition versus resistance or tolerance to browsing in the absence versus presence of ungulates, respectively. Theory suggests that conserving adaptive capacity in P. congesta will require land managers to maintain spatial heterogeneity in natural selection, prevent local extinctions and maintain gene flow.

Multi-criteria and participatory assessment of upland rice varieties in contrasted farm environments in Madagascar Description of the subject. For the ecological zone of the mid-western highlands of Madagascar, six upland rice varieties were selected by a research program. Objectives. The aim was to determine their potential for extension in this area. Method. The six varieties were co-assessed for two years across a network of 20 reference farms. Results. The multilocation trials showed a diverse range of environments indicated by the average grain yield in rice, ranging between 1.04 and 4.50 t·ha-1. FOFIFA 182 was significantly superior (2.90 t·ha-1) and SCRID 195 largely inferior (1.65 t·ha-1). In addition, there was a group of four undistinguished varieties (around 2.40 t·ha-1). The study of the genetic-environment interaction made it possible to differentiate a variety that produced a lower yield under low-fertility conditions (SCRID 90) and a less stable one, SCRID 91. SCRID 195, the lowest yielding variety, was also the most infected by Striga asiatica, a hemiparasitic plant. The farmers' assessment at the end of the 2-year period was added to the results of the research study on rice yield and Striga constraints, which were their two main criteria for variety performance. The farmers’ assessment also reported on six other secondary criteria: threshing, earliness, drought resistance, grain quality, taste and grain weight. Conclusions. This research-farmer co-assessment made it possible to define the best-performing varieties in terms of yield and Striga control, namely NERICA 4 (already in extension) and FOFIFA 182 (proposed for extension). It also identified new varieties of interest, based on other criteria selected by the farmers and highlighted the need for future studies focused on a cropping system approach related to upland rice performance.

Heritability and association between agronomic traits with sesamin and sesamolin are very important. The aims of this study were to estimate broad-sense heritability and to investigate association of agronomic traits with sesamin and sesamolin in sesame. Seven parental lines and twenty-one hybrid genotypes were evaluated in RCBD with three replications. Agronomic traits were recorded. Sesamin and sesamolin were determined using HPLC. Parent and hybrid populations had large genetic coefficient of variation for both sesamin and sesamolin. Broad-sense heritability of sesamin and sesamolin was high for both parent and hybrid populations. Therefore, selection for those traits based on phenotype in the early generation should be effective. Plant height had significant negative correlation and the largest negative direct effect on both target traits in parental population. Day to harvest was the most influential trait on the target traits in hybrids. These results may facilitate sesame breeding programs to improve lignan content in sesame.

Wild plant species provide excellent examples of qualitative traits that evolve in response to environmental challenges (e.g., flower color, heavy metal tolerance, cyanogenesis, and male sterility). In addition to such discrete characters, a dazzling array of continuously distributed, quantitative traits are expressed at every phase of the life cycle. These traits are known or suspected to have evolved by natural selection because they are heritable, differ among populations or closely related taxa occupying distinct habitats, and have individual phenotypes associated with survival and reproductive success. This special issue [American Journal of Botany 109(11)] focuses on the tools and approaches for detecting or inferring the ecological and genetic factors contributing to changes in genetically based variation of quantitative traits within or among populations, or causing their divergence among taxa. The assembled articles use one or more of three primary approaches to detect the process or outcome of natural selection on morphological, life history, reproductive, chemical, and physiological quantitative traits: the analysis of phenotypic or artificially imposed selection to detect direct and indirect selection on traits whose function is well‐understood; common garden experiments, including reciprocal transplants and "resurrection" experiments; and quantitative genetic analyses designed to detect and to estimate the environmental and genetic sources of phenotypic variation or to forecast short‐term evolutionary change. Together, these articles examine and reveal the adaptive capacity of quantitative traits and the genetically based constraints that may limit their directional evolutionary change, thereby informing and testing inferences, hypotheses, and predictions concerning the evolutionary trajectories of wild plant species. [ABSTRACT FROM AUTHOR]

Plant breeding is focused on the genotype and population levels while targeting effects at higher levels of biodiversity, from crop covers to agroecosystems. Making predictions across nested levels of biodiversity is therefore a major challenge for the development of intercropping practices. New prediction tools and concepts are required to design breeding strategies with desirable outcomes at the crop community level. We reviewed theoretical advances in the field of evolutionary ecology to identify potentially operational ways of predicting the effects of artificial selection on communitylevel performances. We identified three main types of approaches differing in the way they model interspecific indirect genetic effects (IIGEs) at the community level: (1) The community heritability approach estimates the variance for IIGE induced by a focal species at the community level; (2) the joint phenotype approach quantifies genetic constraints between direct genetic effects and IIGE for a set of interacting species; (3) the communitytrait genetic gradient approach decomposes the IIGE for a focal species across a multivariate set of its functional traits. We discuss the potential operational capacities of these approaches and stress that each is a special case of a general multitrait and multispecies selection index. Choosing one therefore involves assumptions and goals regarding the breeding target and strategy. Obtaining reliable quantitative, community-level predictions at the genetic level is constrained by the size and complexity of the experimental designs usually required. Breeding strategies should instead be compared using theoretically informed qualitative predictions. The need to estimate genetic covariances between traits measured both within and among species (for IIGE) is another obstacle, as the two are not determined by the exact same biological processes. We suggest future research directions and strategies to overcome these limits. Our synthesis offers an integrative theoretical framework for breeders interested in the genetic improvement of crop communities but also for scientists interested in the genetic bases of plant community functioning. [ABSTRACT FROM AUTHOR]

This study investigated the main factors influencing the genetic variance and the variance of breeding values (EBV). The first is the variance of genetic values in the base population, and the latter is the variance of genetic values in the population under evaluation. These variances are important as improper variances can lead to systematic bias. The inverse of the genetic relationship matrix (K-1) and the phenotypic variance are the main factors influencing the genetic variance and heritability (h2). These factors and h2 are also the main factors influencing the variance of EBVs. Pedigree- and genomic-based relationship matrices (A and G as K) and phenotypes on 599 wheat lines were used. Also, data were simulated, and a hybrid (genomic-pedigree) relationship matrix (H as K) and phenotypes were used. First, matrix K underwent a transformation (K* = wK + a11' + ßI), and the responses in the mean and variation of diag(K-1) and offdiag(K-1) elements, and genetic variance in the form of h2 were recorded. Then, the original K was inverted, and matrix K-1 underwent the same transformations as K, and the responses in the h2 estimate and the variance of EBVs in the forms of correlation and regression coefficients with the EBVs estimated based on the original K-1 were recorded. In response to weighting K by w, the estimated genetic variance changed by 1/w. We found that µ(diag(K)) - µ(offdiag(K)) influences the genetic variance. As such, a did not change the genetic variance, and increasing ß increased the estimated genetic variance. Weighting K-1 by w was equivalent to weighting K by 1/w. Using the weighted K-1 together with its corresponding h2, EBVs remained unchanged, which shows the importance of using variance components that are compatible with the K-1. Increasing ßI added to K-1 increased the estimated genetic variance, and the effect of a11' was minor. We found that larger variation of diag(K-1) and higher concentration of offdiag(K-1) around the mean (0) are responsible for lower h2 estimate and variance of EBVs. [ABSTRACT FROM AUTHOR]

The man-made cereal triticale was fully resistant to the biotrophic diseases powdery mildew, leaf rust, yellow rust, and stem rust from its introduction in Europe in the mid-1970s until about 1990. In the following years, new races that were able to infect at least some triticale genotypes developed in all four pathogen populations, and resistance breeding came into focus. Here, we analyzed 656 winter triticale cultivars from 12 countries for resistance to these biotrophic diseases and Fusarium head blight (FHB) at up to 8 location-year combinations (environments). FHB ratings were corrected for plant height and heading stage by comparing three statistical methods. Significant (p < 0.001) genetic variances were found for all resistances with moderate to high entry-mean heritabilities. All traits showed a normal distribution, with the exception of stem rust, where the ratings were skewed towards resistance. There were no substantial correlations among the five disease resistances (r = −0.04 to 0.26). However, several genotypes were detected with multi-disease resistance with a disease rating below average for all five diseases simultaneously. In future, such genotypes must be selected primarily to cope with future challenges of less pesticide use and global climate change. [ABSTRACT FROM AUTHOR]

Bacterial mutation and genetic diversity in aquaculture have led to increasing phenotypic variances, which can weaken or invalidate strategies for controlling diseases. However, few studies have monitored the degree of mutation in fish bacterial pathogens caused by environmental pressure within a short period. In this study, transcriptomic sequences from Edwardsiella piscicida, Vibrio harveyi and Streptococcus parauberis under stressed environments were used for investigating the emergence of variants. In detail, a sub‐inhibitory concentration of formalin and phenol for E. piscicida, sea water at 30°C for V. harveyi and flounder serum for S. parauberis were used as stressed environments, and significant single‐nucleotide polymorphisms (SNPs) and/or mutation sites were investigated after culture in the ordinary liquid media (control) and the stressed environment through a genome‐wide association study. As results, several SNPs or mutations during incubation were observed under different environments in E. piscicida and/or V. harveyi in the genes relevant to flagella, fimbria type 3 secretion systems, and outer and inner membranes that have been directly exposed to external environments. In particular, given that flagella and fimbriae are considered important factors in differentiating the serotypes in some bacterial pathogens, it can be speculated that different environmental pressures are the source of phenotypic or serotypic differentiation from the same origin. On the other hands, S. parauberis did not exhibit notable changes for 4 h when inoculated in the serum from olive flounder. The results presented in this study provide examples of possible molecular evolution in pathogens relevant to the aquaculture industry as a response to different environmental pressure. [ABSTRACT FROM AUTHOR]

The ability to predict the outcome of selection and mating decisions enables breeders to make strategically better selection decisions. To improve genetic progress, those individuals need to be selected whose offspring can be expected to show high genetic variance next to high breeding values. Previously published approaches enable to predict the variance of descendants of 2 future generations for up to 4 founding haplotypes, or 2 outbred individuals, based on phased genotypes, allele effects, and recombination frequencies. The purpose of this study was to develop a general approach for the analytical calculation of the genetic variance in any future generation. The core development is an equation for the prediction of the variance of double haploid lines, under the assumption of no selection and negligible drift, stemming from an arbitrary number of founder haplotypes. This double haploid variance can be decomposed into gametic Mendelian sampling variances (MSVs) of ancestors of the double haploid lines allowing usage for non-double haploid genotypes that enables application in animal breeding programs as well as in plant breeding programs. Together with the breeding values of the founders, the gametic MSV may be used in new selection criteria. We present our idea of such a criterion that describes the genetic level of selected individuals in 4 generations. Since breeding programs do select, the assumption made for predicting variances is clearly violated, which decreases the accuracy of predicted gametic MSV caused by changes in allele frequency and linkage disequilibrium. Despite violating the assumption, we found high predictive correlations of our criterion to the true genetic level that was obtained by means of simulation for the "corn" and "cattle" genome models tested in this study (0.90 and 0.97). In practice, the genotype phases, genetic map, and allele effects all need to be estimated meaning inaccuracies in their estimation will lead to inaccurate variance prediction. Investigation of variance prediction accuracy when input parameters are estimated was not part of this study., Competing Interests: Conflicts of interest TAMN and MPLC would like to acknowledge that they are listed as inventors on a patent application, no. EP23192016.6, pending at the European Patent Office, related to the technology discussed in this paper, specifically the prediction of variances of 2 or more generations ahead and the selection looking 2 or more generations ahead based on predicted variances of descendants. JtN has no conflicts of interest to declare., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

While senescence is a common occurrence in wild populations, not all traits decline with age simultaneously and some do not show any senescence. A lack of senescence in secondary sexual traits is thought to be due to their importance for reproductive success. However, if reproductive success senesces, why would secondary sexual traits apparently not senesce? Here, we explored this question in a wild population of red deer (Cervus elaphus) using antler form (number of points), a secondary sexual trait which shows little senescence, despite the occurrence of reproductive senescence. In line with expectations for traits that senesce, genetic variance in antler form increased with age and selection weakened with age. Therefore, there was no indication that a stronger selection on individuals that survived to older ages was countering the dilution of selection due to fewer individuals being alive. Furthermore, the effect of selective disappearance masking a slight decline in antler form in the oldest years was small. Interestingly, although genetic variance and positive selection of antler form were found, there was no evidence of a response to selection, supporting a genetic decoupling of antler senescence and reproductive senescence. Finally, a positive genetic covariance in antler form among age classes provides a possible explanation for the lack of senescence. These findings suggest that the antler form is under a genetic constraint that prevents it from senescing, providing an interesting evolutionary explanation for negligible senescence in a secondary sexual trait, and consequently, the existence of asynchrony in senescence among traits within populations., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

This study investigated the main factors influencing the genetic variance and the variance of breeding values (EBV). The first is the variance of genetic values in the base population, and the latter is the variance of genetic values in the population under evaluation. These variances are important as improper variances can lead to systematic bias. The inverse of the genetic relationship matrix (K−1) and the phenotypic variance are the main factors influencing the genetic variance and heritability (h2). These factors and h2 are also the main factors influencing the variance of EBVs. Pedigree- and genomic-based relationship matrices (A and G as K) and phenotypes on 599 wheat lines were used. Also, data were simulated, and a hybrid (genomic-pedigree) relationship matrix (H as K) and phenotypes were used. First, matrix K underwent a transformation (K* = wK + α11′ + βI), and the responses in the mean and variation of diag(K−1) and offdiag(K−1) elements, and genetic variance in the form of h2 were recorded. Then, the original K was inverted, and matrix K−1 underwent the same transformations as K, and the responses in the h2 estimate and the variance of EBVs in the forms of correlation and regression coefficients with the EBVs estimated based on the original K−1 were recorded. In response to weighting K by w, the estimated genetic variance changed by 1/w. We found that μ(diag(K)) − μ(offdiag(K)) influences the genetic variance. As such, α did not change the genetic variance, and increasing β increased the estimated genetic variance. Weighting K−1 by w was equivalent to weighting K by 1/w. Using the weighted K−1 together with its corresponding h2, EBVs remained unchanged, which shows the importance of using variance components that are compatible with the K−1. Increasing βI added to K−1 increased the estimated genetic variance, and the effect of α11′ was minor. We found that larger variation of diag(K−1) and higher concentration of offdiag(K−1) around the mean (0) are responsible for lower h2 estimate and variance of EBVs.

Introduction1 Applying the appropriate statistical method to genome wide association studies (GWAS(is one of the major factors influencing the identify chromosome regions effect of quantitative traits. The single-step genomic best linear unbiased prediction (ssGBLUP) approach, a quite common procedure in GWAS, has the advantage of simultaneously using the phenotypes of genotyped and non-genotyped animals, pedigrees, and genotypes; therefore, there is no need to calculate pseudo-phenotypes. It has been reported that the use of ssGBLUP procedure increased the accuracy of genetic evaluation in many contexts and species compared with pedigree-based BLUP. However, the ssGBLUP assumes that all SNPs explain the same amount of genetic variance, which is unlikely in the case of traits whose major genes or QTL are segregating. The weighted single-step genome wide association studies (WssGWAS) approach allows the use of different weights for each SNP according to their trait-relevant importance and improves the accuracy of genetic evaluation and the precision of estimates of SNP effects. Thus, The aim of the present study was to compare the explained genetic variance from multi-step Bayes B (MS-BayesB) method in the different values of π with weighted single-step genome wide association study (WssGWAS(method related to some economically important traits in 920 Japanese quails. Materials and Methods For each bird, a total of three traits including body weight gain (BWG), feed intake (FI) and feed conversion ratio (FCR) were recorded and by using Illumnia iSelect 4K Japanese quail SNP Bead chip. For associations between traits and effective SNPs using the GenSel and BLUPF90 family software. The effects of markers and the genomic estimated breeding values of the traits were obtained by five iterations of WssGWAS. The proportion of additive genetic variance (agv) for each of 1.5-Mb genomic window (adjacent SNPs) was used to identify informative genomic regions and candidate genes, accounting for more than 1% of the agv. Also, to estimate SNP marker effects, the Bayes-B method was used (Meuwissen et al., 2009) with set π 0.90, 0.95, 0.99 The Bayes-B method assumes that some proportion (π) of SNP markers has zero effects. The posterior distributions of the parameters and effects were obtained using Gibbs sampling. We performed a Markov chain Monte Carlo (MCMC) simulation of 41,000 rounds with Gibbs sampling, of which the first 1000 iterations were discarded as burn-in. To estimate posterior means and variances of marker effects, Metropolis-Hastings samples were run for 10 iterations. The QTL windows were identified and located for candidate genes using the Coturnix_japonica_2.0 assembly. DAVID v6.8 Functional Annotation Tool (Huang et al. 2009) was used for gene ontology (GO) enrichment in order to detect biological terms associated with genomic regions and gene networks identified in the analysis. Enrichment analysis of gene function was performed using implementation of the Bonferroni test of overrepresentation. Results and Discussion These unknown genotype individuals can supply additional information to improve the statistical power of QTL detection. Sample size can influence the power of GWAS. In general, the results showed that the BayesA method performed better in explained additive genetic variance compared to BayesB method with π=90. A total of 15 significant windows over 1% explained genetic variance on 10 chromosomes were found for the BWG and explained 23.1% of agv. For FI, we identified 14 informative windows across 9 chromosomes, and explained 28.3% of the agv. Also, for the FCR, 12 significant windows were identified on 9 chromosomes and explained 27.4% of agv. The detected candidate genes in genomic regions played an important role in muscle development, feed intake and residual feed intake. Results of this study showed that use single-step Bayesian methods of phenotype, genotype and pedigree information simultaneously, had outperform in comparison than other multi-step BayesB method. Moreover, considering the identification of new genome regions and the key role of the mentioned genes in development of body weight and feed efficiency, the WssGWAS method can be validated for GWAS for economic traits in Japanese quail. Conclusions In the present study, we identified a wide range of genomic regions associated with body weight gain and feed efficiency traits. The findings of this study provide an important foundation for future fine-mapping studies to more precisely elucidate the mutations affecting production traits in Japanese quail. Future studies should establish causative links between candidate variants and economically important phenotypes using functional analyses. [ABSTRACT FROM AUTHOR]

Family-based methods are a potentially powerful tool to identify trait-defining genetic variants in extended families, particularly when used to complement conventional association analysis. We utilized two-point linkage analysis and single variant association analysis to evaluate whole exome sequencing (WES) data from 1205 Hispanic Americans (78 families) from the Insulin Resistance Atherosclerosis Family Study. WES identified 211,612 variants above the minor allele frequency threshold of ≥0.005. These variants were tested for linkage and/or association with 50 cardiometabolic traits after quality control checks. Two-point linkage analysis yielded 10,580,600 logarithm of the odds (LOD) scores with 1148 LOD scores ≥3, 183 LOD scores ≥4, and 29 LOD scores ≥5. The maximal novel LOD score was 5.50 for rs2289043:T>C, in UNC5C with subcutaneous adipose tissue volume. Association analysis identified 13 variants attaining genome-wide significance (P T in APOA5 and triglyceride levels (P  =  3.67 × 10-10 ). Overall, there was a 5.2-fold increase in the number of informative variants detected by WES compared to exome chip analysis in this population, nearly 30% of which were novel variants relative to the Database of Single Nucleotide Polymorphisms (dbSNP) build 138. Thus, integration of results from two-point linkage and single-variant association analysis from WES data enabled identification of novel signals potentially contributing to cardiometabolic traits.

The role of HER2 in canine mammary tumors is not completely elucidated, and the contradictory results published so far may be, in part, explained by the genetic variability recognized in the canine HER2 gene. Single nucleotide polymorphism (SNPs) in HER2 were recently associated with less aggressive canine mammary tumor histotypes. This study assesses the relationship between SNPs rs24537329 and rs24537331 in canine HER2 gene and clinicopathological characteristics and outcome of mammary tumors in a group of 206 female dogs. Allelic variants were observed in 69.8% and 52.7% of the dogs for SNP rs24537329 and rs24537331, respectively. Our results demonstrated that SNP rs24537331 was associated with decreased tumoral necrosis (HR: 3.09; p = 0.012) and with longer disease-specific overall survival (HR: 2.59; p = 0.013). However, no statistically significant associations were found between SNP rs24537329 and the tumors’ clinicopathological characteristics or survival. Our data suggest that SNP rs24537331 may have a protective effect in canine mammary tumors, allowing the identification of a subgroup of animals prone to develop less aggressive forms of the disease. This study emphasizes the importance of the genetic tests associated with clinical images and histological examinations when assessing CMT outcomes.

A capacity for rapid adaptation should enhance the persistence of populations subject to temporal and spatial heterogeneity in natural selection, but examples from nature remain scarce. Plectritis congesta (Caprifoliaceae) is a winter annual that exhibits local adaptation to browsing by ungulates and hypothesized to show context‐dependent trade‐offs in traits affecting success in competition versus resistance or tolerance to browsing. We grew P. congesta from 44 insular populations historically exposed or naïve to ungulates in common gardens to (1) quantify genetic, plastic and competitive effects on phenotype; (2) estimate a capacity for rapid adaptation (evolvability); and (3) test whether traits favoured by selection with ungulates present were selected against in their absence. Plants from browsed populations bolted and flowered later, had smaller inflorescences, were less fecund and half as tall as plants from naïve populations on average, replicating patterns in nature. Estimated evolvabilities (3–36%) and narrow‐sense heritabilities (h2; 0.13–0.32) imply that differences in trait values as large as reported here can arise in 2–18 generations in an average population. Phenotypic plasticity was substantial, varied by browsing history and fruit phenotype and increased with competition. Fecundity increased with plasticity in flowering height given competition (0.47 ± 0.02 florets/cm, β ± se), but 23–77% faster in naïve plants bearing winged fruits (0.53 ± 0.04) than exposed‐wingless plants (0.43 ± 0.03) or exposed‐winged and naïve‐wingless plants (0.30 ± 0.03, each case). Our results support the hypothesis that context‐dependent variation in natural selection in P. congesta populations has conferred a substantial capacity for adaptation in response to selection in traits affecting success in competition versus resistance or tolerance to browsing in the absence versus presence of ungulates, respectively. Theory suggests that conserving adaptive capacity in P. congesta will require land managers to maintain spatial heterogeneity in natural selection, prevent local extinctions and maintain gene flow. [ABSTRACT FROM AUTHOR]

Postsurgical thrombotic microangiopathy (TMA) is a complication associated with significant morbidity and mortality. Still, the pathophysiological underlying mechanism of postsurgical TMA, a diagnosis often overlooked in postoperative patients with acute kidney injury and thrombocytopenia, is largely unknown. Here, we report the case of a 56-year-old male that developed anuric acute kidney injury, Coombs-negative hemolysis, and thrombocytopenia after surgical aortic arch replacement. Massive ex vivo complement activation on the endothelium, a rare complement gene variant in C2, at-risk haplotype MCPggaac, and excellent response to therapeutic complement inhibition, points to the pivotal role of complement in the pathophysiology of disease. Moreover, the importance of a multidisciplinary team approach in (postsurgical) thrombocytopenia is emphasized. [ABSTRACT FROM AUTHOR]

Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on 2 theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g. epistatic variance) in population genomics. [ABSTRACT FROM AUTHOR]