Correction: Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

AbstractDeleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring by crossing two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.Author SummaryA key long-term goal of biology is understanding the genetic basis of phenotypic variation. Although most new mutations are likely disadvantageous, their prevalence and importance in explaining patterns of phenotypic variation is controversial and not well understood. In this study we combine whole genome-sequencing and field evaluation of a maize mapping population to investigate the contribution of deleterious mutations to phenotype. We show that a priori prediction of deleterious alleles correlates well with effect sizes for grain yield and that variants predicted to be more damaging are on average more recessive. We develop a simple model allowing for variation in the heterozygous effects of deleterious mutations and demonstrate its improved ability to predict both phenotypes and hybrid vigor. Our results help reconcile alternative explanations for hybrid vigor and highlight the use of leveraging evolutionary history to facilitate breeding for crop improvement.

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Self-other agreement in disgust sensitivity

10.31234/osf.io/dymqk ◽

2019 ◽

Author(s):

Annika Karinen ◽

Joshua M. Tybur ◽

Reinout E. de Vries

Keyword(s):

Personality Traits ◽

Political Attitudes ◽

Romantic Partners ◽

Disgust Sensitivity ◽

Trait Variation ◽

Self And Other ◽

Self Reports ◽

Moral Disgust ◽

Sexual Disgust ◽

Moral Condemnation

A broad literature indicates that pathogen, sexual, and moral disgust sensitivity relate to, among other things, political attitudes, moral condemnation, and symptoms of psychopathology. As such, instruments measuring disgust sensitivity have been widely used across subfields of psychology. Yet, surprisingly little work has examined whether self-reports in disgust sensitivity reflect systematic trait variation. Here, we present the first study to examine self-other agreement in pathogen, sexual, and moral disgust sensitivity. Romantic partners (n1 = 290), friends (n2 = 212) and acquaintances (n3 = 140) rated each other on these three domains of disgust sensitivity and on the HEXACO personality dimensions. Correlations between dyad partners’ self- and other-ratings were calculated to estimate the magnitude of self-other agreement. We found self-other agreement in all domains of disgust sensitivity (r’s of .36, .46, and .66 for moral, pathogen, and sexual disgust sensitivity, respectively), with this agreement only slightly inferred from personality perceptions (percentages mediated by HEXACO were 15%, 7%, and 33% for pathogen, sexual, and moral disgust sensitivity, respectively). These results suggest that pathogen, sexual, and moral disgust sensitivity reflect systematic trait variation that is detectable by others and distinct from broader personality traits.

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Adaptive trait variation in the federally endangered Lindera melissifolia (Lauraceae), as it relates to genotype and genotype-environment interaction1

The Journal of the Torrey Botanical Society ◽

10.3159/torrey-d-18-00056.1 ◽

2019 ◽

Vol 146 (3) ◽

pp. 166

Author(s):

Tracy S. Hawkins ◽

Craig S. Echt ◽

Margaret S. Devall ◽

Paul B. Hamel ◽

A. Dan Wilson ◽

...

Keyword(s):

Trait Variation ◽

Adaptive Trait

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Faculty Opinions recommendation of Engineering quantitative trait variation for crop improvement by genome editing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.731219358.793541326 ◽

2018 ◽

Author(s):

Wolfgang Busch

Keyword(s):

Genome Editing ◽

Quantitative Trait ◽

Crop Improvement ◽

Trait Variation

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Faculty Opinions recommendation of Engineering quantitative trait variation for crop improvement by genome editing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.731219358.793537506 ◽

2017 ◽

Author(s):

François Parcy

Keyword(s):

Genome Editing ◽

Quantitative Trait ◽

Crop Improvement ◽

Trait Variation

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Intraspecific trait variation alters the outcome of competition in freshwater ciliates

Ecology and Evolution ◽

10.1002/ece3.7828 ◽

2021 ◽

Author(s):

Sabine Flöder ◽

Joanne Yong ◽

Toni Klauschies ◽

Ursula Gaedke ◽

Tobias Poprick ◽

...

Keyword(s):

Trait Variation ◽

Intraspecific Trait Variation ◽

Freshwater Ciliates

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The Effect of Deleterious Alleles on Adaptation in Asexual Populations

Genetics ◽

10.1093/genetics/162.1.395 ◽

2002 ◽

Vol 162 (1) ◽

pp. 395-411 ◽

Cited By ~ 2

Author(s):

Toby Johnson ◽

Nick H Barton

Keyword(s):

Selective Sweep ◽

Deleterious Mutation ◽

Short Interval ◽

Selective Advantage ◽

Asexual Population ◽

Restrictive Assumption ◽

Deleterious Alleles ◽

Fixation Probabilities ◽

Asexual Populations ◽

Beneficial Allele

Abstract We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.

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Intraspecific trait variation drives grassland species richness and productivity under changing precipitation

Ecosphere ◽

10.1002/ecs2.3707 ◽

2021 ◽

Vol 12 (8) ◽

Author(s):

Meifeng Deng ◽

Weixing Liu ◽

Ping Li ◽

Lin Jiang ◽

Shaopeng Li ◽

...

Keyword(s):

Species Richness ◽

Trait Variation ◽

Grassland Species ◽

Intraspecific Trait Variation

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The Probability of Fixation in Populations of Changing Size

Genetics ◽

10.1093/genetics/146.2.723 ◽

1997 ◽

Vol 146 (2) ◽

pp. 723-733 ◽

Cited By ~ 33

Author(s):

Sarah P Otto ◽

Michael C Whitlock

Keyword(s):

Diffusion Equation ◽

Adaptive Evolution ◽

Process Model ◽

Branching Process ◽

Approximate Solutions ◽

Logistic Growth ◽

Beneficial Mutations ◽

Demographic Models ◽

Deleterious Alleles ◽

Probability Of Fixation

The rate of adaptive evolution of a population ultimately depends on the rate of incorporation of beneficial mutations. Even beneficial mutations may, however, be lost from a population since mutant individuals may, by chance, fail to reproduce. In this paper, we calculate the probability of fixation of beneficial mutations that occur in populations of changing size. We examine a number of demographic models, including a population whose size changes once, a population experiencing exponential growth or decline, one that is experiencing logistic growth or decline, and a population that fluctuates in size. The results are based on a branching process model but are shown to be approximate solutions to the diffusion equation describing changes in the probability of fixation over time. Using the diffusion equation, the probability of fixation of deleterious alleles can also be determined for populations that are changing in size. The results developed in this paper can be used to estimate the fixation flux, defined as the rate at which beneficial alleles fix within a population. The fixation flux measures the rate of adaptive evolution of a population and, as we shall see, depends strongly on changes that occur in population size.

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