The Addition of Epistatic Genetic Effects Increases Genomic Prediction Accuracy for Reproduction and Production Traits in Duroc Pigs Using Genomic Models

Background: Genomic selection has been implemented in livestock genetic evaluations for years. However, currently most genomic selection models only consider the additive effects associated with SNP markers and nonadditive genetic effects have been for the most part ignored. Methods: Production traits for 26,735 to 27,647 Duroc pigs and reproductive traits for 5,338 sows were used, including off-test body weight (WT), off-test back fat (BF), off-test loin muscle depth (MS), number born alive (NBA), number born dead (NBD), and number weaned (NW). All animals were genotyped with the PorcineSNP60K Bead Chip. Variance components were estimated using a linear mixed model that includes inbreeding coefficient, additive, dominance, additive-by-additive, additive-by-dominance, dominance-by-dominance effect, and common litter environmental effect. Genomic prediction performance, including all nonadditive genetic effects, was compared with a reduced model that included only additive genetic effect. Results: Significant estimates of additive-by-additive effect variance were observed for NBA, BF, and WT (31%, 9%, and 10%, respectively). Production traits showed significant large estimates of additive-by-dominance variance (9%-23%). MS also showed large estimate of dominance-by-dominance variance (10%). Dominance effect variance estimates were low for all traits (0%-2%). Compared to the reduced model, prediction accuracies using the full model, including nonadditive effects, increased significantly by 12%, 12%, and 1% for NBA, WT, and MS, respectively. A strong dominance association signal with BF was identified near AK5.Conclusions: Sizable estimates of epistatic effects were found for the reproduction and production traits, while the dominance effect was relatively small for all traits yet significant for all production traits. Including nonadditive effects, especially epistatic effects in the genomic prediction model, significantly improved prediction accuracy for NBA, WT, and MS.

Optimization of BSA-seq experiment for QTL mapping

Deep sequencing-based bulked segregant analysis (BSA-seq) has become a popular approach for quantitative trait loci (QTL) mapping in recent years. Effective statistical methods for BSA-seq have been developed, but how to design a suitable experiment for BSA-seq remains unclear. In this paper, we show in theory how the major experimental factors (including population size, pool proportion, pool balance, and generation) and the intrinsic factors of a QTL (including heritability and degree of dominance) affect the power of QTL detection and the precision of QTL mapping in BSA-seq. Increasing population size can improve the power and precision, depending on the QTL heritability. The best proportion of each pool in the population is around 0.25. So, 0.25 is generally applicable in BSA-seq. Small pool proportion can greatly reduce the power and precision. Imbalance of pool pair in size also causes decrease of the power and precision. Additive effect is more important than dominance effect for QTL mapping. Increasing the generation of filial population produced by selfing can significantly increase the power and precision, especially from F2 to F3. These findings enable researchers to optimize the experimental design for BSA-seq. A web-based program named BSA-seq Design Tool is available at http://124.71.74.135/BSA-seqDesignTool/ and https://github.com/huanglikun/BSA-seqDesignTool.

Bilingual Language Control Flexibly Adapts to Cultural Context

How does bilingual language control adapt to the cultural context? We address this question by looking at the pattern of switch cost and reversed language dominance effect, which are suggested to separately reflect reactive and proactive language control mechanisms, in the contexts with culturally-neutral pictures (i. e., baseline context) or culturally-biased pictures (i.e., congruent context where culture matched the language to be spoken or incongruent context where culture mismatched the language to be spoken). Results showed an asymmetric switch cost with larger costs for L2 in the congruent context as compared with the baseline and incongruent contexts, but the reversed language dominance effect was not changed across contexts, suggesting that cultural context plays a critical role in modulating reactive but not proactive language control. These findings reveal the dynamic nature of language control in bilinguals and have important implications for the current models of bilingual language control.

Assessing the evidence for asymmetrical language switch costs and reversed language dominance effects - a meta analysis

Two seemingly counterintuitive phenomena – asymmetrical language switch costs and the reversed language dominance effect – prove to be particularly controversial in the literature on language control. Asymmetrical language switch costs refer to the larger costs for switching into the dominant language compared to switching into the less dominant language, both relative to staying in either one language. The reversed language dominance effect refers to longer reaction times when in the more dominant of the two languages in situations that require frequent language switching (i.e., mixed-language blocks). The asymmetrical language switch costs are commonly taken as an index for processes of transient, reactive inhibitory language control, whereas the reversed language dominance effect is taken as an index for sustained, proactive inhibitory language control. In the present meta-analysis, we set out to establish the empirical evidence for these two phenomena using a Bayesian linear mixed effects modelling approach. Despite the observation of both phenomena in some studies, our results suggest that overall, there is little evidence for the generality and robustness of these two effects, and this holds true even when conditions – such as language proficiency and preparation time manipulations – were included as moderators of these phenomena. We conclude that asymmetrical switch costs and the reversed language dominance effect are important for theory development, but their utility for theory testing is limited due to their lack of robustness and the absence of confirmed moderatory variables.

Proactive language control during bilingual sentence production

Aims and objectives/purpose/research questions: While evidence for proactive language control processes has been found during single word production, very little and conflicting evidence has been observed for such control processes during sentence production. So, the main goal of this study was to investigate whether proactive language control can occur during sentence production. Design/methodology/approach: To investigate proactive language control during sentence production, we relied on a description task in single and mixed language blocks. Data and analysis: Mixing costs and the reversed language dominance effect of language intrusions and filled pauses were used to examine proactive language control. Findings/conclusions: Evidence for proactive language control during sentence production came from the mixing cost effect observed with both language intrusions and filled pauses. Whereas no reversed language dominance effect was observed in mixed language blocks, a significant difference in language pattern was observed between single and mixed language blocks, indicating that proactive language control of the first language might be implemented in mixed language blocks during sentence production. Originality: Unlike the vast majority of studies investigating language control, this study relied on sentence production instead of single word production. Moreover, to the best of our knowledge, this is the first study to examine filled pauses to gain insight into language control. Significance/implications: These data indicate that proactive language control can be implemented during bilingual sentence production.

Endogenous Spatial Attention Modulates the Magnitude of the Colavita Visual Dominance Effect

The Colavita effect refers to the phenomenon wherein people tend to not respond to an auditory stimulus when a visual stimulus is simultaneously presented. Although previous studies have shown that endogenous modality attention influences the Colavita effect, whether the Colavita effect is influenced by endogenous spatial attention remains unknown. In the present study, we established endogenous spatial cues to investigate whether the size of the Colavita effect changes under visual or auditory cues. We measured three indexes to investigate the effect of endogenous spatial attention on the size of the Colavita effect. These three indexes were developed based on the following observations in bimodal trials: (a) The proportion of the “only vision” response was significantly higher than that of the “only audition” response; (b) the proportion of the “vision precedes audition” response was significantly higher than that of the “audition precedes vision” response; and (c) the reaction time difference of the “vision precedes audition” response was significantly higher than that of the “audition precedes vision” response. Our results showed that the Colavita effect was always influenced by endogenous spatial attention and that its size was larger at the cued location than at the uncued location; the cue modality (visual vs. auditory) had no effect on the size of the Colavita effect. Taken together, the present results shed light on how endogenous spatial attention affects the Colavita effect.

Genetic Variance Components in Cotton by Generation Mean Analysis

The mode of gene action for the expression of quantitative traits is decided by the predominance of variances due to additive, dominance and epistasis gene effects. In this experiment, involving four F1 crosses (TCH1716 x TCB37, TCH1705-101 x TCB209, KC2 x TCB26 and TSH0250 x DB3) of upland cotton, inheritance of major yield components by Generation Mean Analysis was investigated. The investigation revealed that both additive and dominance gene effects were involved in the expression of most of the yield contributing traits. One or more types of epistatic interaction effects were prevalent for all the characters and thus played a major role in the control of the characters. The inheritance of the traits was found to be complex in lieu of the low heritability estimates and genetic advance over mean. For seed cotton yield per plant, the dominance x dominance interaction effect was positively significant for all the crosses, the additive x dominance effect was positively significant only in cross 1 and the dominance main effect showed negative significant in all crosses. The dominance (h) and dominance x dominance (l) effects were of opposite signs in all the crosses indicating the presence of duplicate epistasis in all the crosses. To harness additive gene effects for improvement of some of the traits, breeding methods with postponement of selection to later generation should be adopted.

Which Class Matters? Juxtaposing Multiple Class Environments as Frames-of-Reference for Academic Self-Concept Formation

Equally able students have lower academic self-concept in high achieving schools or classes, a phenomenon known as the big fish little pond effect (BFLPE). The class (more so than the school) has been shown to be the pivotal frame-of-reference for academic self-concept formation—a local dominance effect. However, many school systems worldwide employ forms of course-by-course tracking, thus exposing students to multiple class environments. Due to the high correlation between multiple student environments, the frame-of-reference used for academic self-concept formation in course-by-course tracked systems is unclear to date. We addressed this unresolved issue by using data from a comprehensive survey that measured the entire population of Austrian eighth-grade students in the domain of mathematics in 2012. General secondary school students were in the core subjects (i.e., mathematics, German, and English) grouped according to ability, whereas regular class composition was the same in all other subjects. Using cross-classified multilevel models, we regressed math self-concept on average math achievement of students’ school, math class, and regular class. Consistent with the local dominance effect, we found the BFLPE on the school level to be weak after controlling for the class levels. We found a stronger BFLPE on the regular class level and the strongest BFLPE on the math class level. Our study demonstrates the importance of multiple class environments as frames-of-reference for academic self-concept formation.

Hand preference for the visual and auditory modalities in humans

The sensory dominance effect refers to the phenomenon that one sensory modality more frequently receives preferential processing (and eventually dominates consciousness and behavior) over and above other modalities. On the other hand, hand dominance is an innate aspect of the human motor system. To investigate how the sensory dominance effect interacts with hand dominance, we applied the adapted Colavita paradigm and recruited a large cohort of healthy right-handed participants (n = 119). While the visual dominance effect in bimodal trials was observed for the whole group (n = 119), about half of the right-handers (48%) showed a visual preference, i.e., their dominant hand effect manifested in responding to the visual stimuli. By contrast, 39% of the right-handers exhibited an auditory preference, i.e., the dominant hand effect occurred for the auditory responses. The remaining participants (13%) did not show any dominant hand preference for either visual or auditory responses. For the first time, the current behavioral data revealed that human beings possess a characteristic and persistent preferential link between different sensory modalities and the dominant vs. non-dominant hand. Whenever this preferential link between the sensory and the motor system was adopted, one dominance effect peaks upon the other dominance effect’s best performance.