scholarly journals Deleterious Mutation Accumulation in Arabidopsis thaliana Pollen Genes: A Role for a Recent Relaxation of Selection

2019 ◽  
Vol 11 (7) ◽  
pp. 1939-1951 ◽  
Author(s):  
Mark C Harrison ◽  
Eamonn B Mallon ◽  
Dave Twell ◽  
Robert L Hammond
Keyword(s):  
Arabidopsis Thaliana ◽  
Tissue Specificity ◽  
Deleterious Mutation ◽  
Rapid Evolution ◽  
Relative Strength ◽  
Pollen Competition ◽  
Deleterious Mutations ◽  
Deleterious Alleles ◽  
Polymorphism Data ◽  
Plant Pollen

Abstract In many studies, sex-related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 Myr, A. thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity, and a dilution of masking in diploid expressed, sporophytic genes. In this study, we have investigated the relative strength of selection on pollen genes compared with sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible, positive selection was stronger on pollen genes than sporophytic genes for A. thaliana and 2) current polymorphism data indicate that selection is weaker on pollen genes compared with sporophytic genes. This weaker selection on pollen genes can in part be explained by their higher tissue specificity, which in outbreeding plants can be outweighed by the effects of haploid expression and pollen competition. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared with sporophytic genes.

scholarly journals Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection

2015 ◽  
Author(s):  
MC Harrison ◽  
EB Mallon ◽  
D Twell ◽  
RL Hammond
Keyword(s):  
Arabidopsis Thaliana ◽  
Life History ◽  
Deleterious Mutation ◽  
Rapid Evolution ◽  
Relative Strength ◽  
Pollen Competition ◽  
Deleterious Mutations ◽  
Deleterious Alleles ◽  
Polymorphism Data ◽  
Plant Pollen

AbstractIn many studies sex related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 million years A.thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. In this study we have investigated the relative strength of selection on pollen genes compared to sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible positive selection was stronger on pollen genes than sporophytic genes for A. thaliana; 2) current polymorphism data indicate selection is weaker on pollen genes compared to sporophytic genes. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared to sporophytic genes.

Tissue specificity of expression of heat shock gene ATHSP70-10 in Arabidopsis thaliana seedlings under normal and stress conditions

2020 ◽  
Vol 2020 (3) ◽  
pp. 37-47
Author(s):  
L.Ye. Kozeko ◽  
◽  
E.L. Kordyum ◽  
Keyword(s):  
Arabidopsis Thaliana ◽  
Heat Shock ◽  
Water Deficit ◽  
Tissue Specificity ◽  
Abiotic Factors ◽  
Root Apex ◽  
Stress Conditions ◽  
Heat Shock Gene ◽  
Organ Specificity ◽  
Pcr Analysis

Mitochondrial heat shock proteins of HSP70 family support protein homeostasis in mitochondria under normal and stress conditions. They provide folding and complex assembly of proteins encoded by mitochondrial genome, as well as import of cytosolic proteins to mitochondria, their folding and protection against aggregation. There are reports about organ-specificity of mitochondrial HSP70 synthesis in plants. However, tissue specificity of their functioning remains incompletely characterized. This problem was studied for mitochondrial AtHSP70-10 in Arabidopsis thaliana seedlings using a transgenic line with uidA signal gene under normal conditions, as well as high temperature and water deficit. Under normal conditions, histochemical GUS-staining revealed the expression of AtHSP70-10 in cotyledon and leaf hydathodes, stipules, central cylinder in root differentiation and mature zones, as well as weak staining in root apex and root-shoot junction zone. RT-PCR analysis of wild-type seedlings exposed to 37°C showed rapid upregulation of AtHSP70-10, which reached the highest level within 2 h. In addition, the gradual development of water deficit for 5 days caused an increase in transcription of this gene, which became more pronounced after 3 days and reached a maximum after 5 days of dehydration. Histochemical analysis showed complete preservation of tissue localization of AtHSP70-10 expression under both abiotic factors. The data obtained indicate the specific functioning of mitochondrial chaperone AtHSP70-10 in certain plant cellular structures.

scholarly journals The Effect of Deleterious Alleles on Adaptation in Asexual Populations

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 395-411 ◽  
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.

scholarly journals Harmful mutation load in the mitochondrial genomes of cattle breeds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Genetic Diseases ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals The mutation load under tetrasomic inheritance and its consequences for the evolution of the selfing rate in autotetraploid species

1999 ◽  
Vol 74 (1) ◽  
pp. 31-42 ◽  
Author(s):  
J. RONFORT
Keyword(s):  
Inbreeding Depression ◽  
Deleterious Mutation ◽  
Stable State ◽  
Approximate Solutions ◽  
Balance Model ◽  
Deleterious Mutations ◽  
Selfing Rate ◽  
Mutation Load ◽  
Mean Fitness ◽  
The Mean

Single-locus equilibrium frequencies of a partially recessive deleterious mutation under the mutation–selection balance model are derived for partially selfing autotetraploid populations. Assuming multiplicative fitness interactions among loci, approximate solutions for the mean fitness and inbreeding depression values are also derived for the multiple locus case and compared with expectations for the diploid model. As in diploids, purging of deleterious mutations through consanguineous matings occurs in autotetraploid populations, i.e. the equilibrium mutation load is a decreasing function of the selfing rate. However, the variation of inbreeding depression with the selfing rate depends strongly on the dominance coefficients associated with the three heterozygous genotypes. Inbreeding depression can either increase or decrease with the selfing rate, and does not always vary monotonically. Expected issues for the evolution of the selfing rate consequently differ depending on the dominance coefficients. In some cases, expectations for the evolution of the selfing rate resemble expectations in diploids; but particular sets of dominance coefficients can be found that lead to either complete selfing or intermediate selfing rates as unique evolutionary stable state.

scholarly journals Sex-dependent dominance maintains migration supergene in rainbow trout

2018 ◽  
Author(s):  
Devon E. Pearse ◽  
Nicola J. Barson ◽  
Torfinn Nome ◽  
Guangtu Gao ◽  
Matthew A. Campbell ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Sex Chromosomes ◽  
Sexual Conflict ◽  
Genetic Basis ◽  
Deleterious Mutation ◽  
Deleterious Mutations ◽  
Heteromorphic Sex Chromosomes ◽  
Males And Females ◽  
Shared Genetic ◽  
Environmental Dependence

AbstractTraits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.

scholarly journals Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data

2016 ◽  
Author(s):  
Paula Tataru ◽  
Maéva Mollion ◽  
Sylvain Glemin ◽  
Thomas Bataillon
Keyword(s):  
Molecular Evolution ◽  
Evolutionary Genetics ◽  
Deleterious Mutations ◽  
Probabilistic Framework ◽  
Evolutionary Trajectory ◽  
Beneficial Mutations ◽  
Fitness Effects ◽  
Polymorphism Data ◽  
Inference Methods ◽  
Biased Estimates

ABSTRACTThe distribution of fitness effects (DFE) encompasses deleterious, neutral and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (α). Inference of DFE and α from patterns of polymorphism (SFS) and divergence data has been a longstanding goal of evolutionary genetics. A widespread assumption shared by numerous methods developed so far to infer DFE and α from such data is that beneficial mutations contribute only negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and α is only predicted by contrasting the SFS with divergence data from an outgroup. Here, we develop a hierarchical probabilistic framework that extends on previous methods and also can infer DFE and α from polymorphism data alone. We use extensive simulations to examine the performance of our method. We show that both a full DFE, comprising both deleterious and beneficial mutations, and α can be inferred without resorting to divergence data. We demonstrate that inference of DFE from polymorphism data alone can in fact provide more reliable estimates, as it does not rely on strong assumptions about a shared DFE between the outgroup and ingroup species used to obtain the SFS and divergence data. We also show that not accounting for the contribution of beneficial mutations to polymorphism data leads to substantially biased estimates of the DFE and α. We illustrate these points using our newly developed framework, while also comparing to one of the most widely used inference methods available.

scholarly journals Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene

Development ◽  
1999 ◽  
Vol 126 (4) ◽  
pp. 711-721 ◽  
Author(s):  
Q. Tian ◽  
J.W. Reed
Keyword(s):  
Arabidopsis Thaliana ◽  
Lateral Root ◽  
Tissue Specificity ◽  
Plant Hormone ◽  
Root Formation ◽  
Auxin Transport ◽  
Feedback Regulation ◽  
Loss Of Function ◽  
Leaf Formation ◽  
Induced Genes

The plant hormone auxin controls many aspects of development and acts in part by inducing expression of various genes. Arabidopsis thaliana semidominant shy2 (short hypocotyl) mutations cause leaf formation in dark-grown plants, suggesting that SHY2 has an important role in regulating development. Here we show that the SHY2 gene encodes IAA3, a previously known member of the Aux/IAA family of auxin-induced genes. Dominant shy2 mutations cause amino acid changes in domain II, conserved among all members of this family. We isolated loss-of-function shy2 alleles including a putative null mutation. Gain-of-function and loss-of-function shy2 mutations affect auxin-dependent root growth, lateral root formation, and timing of gravitropism, indicating that SHY2/IAA3 regulates multiple auxin responses in roots. The phenotypes suggest that SHY2/IAA3 may activate some auxin responses and repress others. Models invoking tissue-specificity, feedback regulation, or control of auxin transport may explain these results.

scholarly journals Inbreeding depression due to mildly deleterious mutations in finite populations: size does matter

2000 ◽  
Vol 75 (1) ◽  
pp. 75-81 ◽  
Author(s):  
THOMAS BATAILLON ◽  
MARK KIRKPATRICK
Keyword(s):  
Population Size ◽  
Inbreeding Depression ◽  
Deleterious Mutation ◽  
Large Population ◽  
Genetic Load ◽  
Breeding Systems ◽  
Deleterious Mutations ◽  
Single Locus Analysis ◽  
Population Sizes ◽  
Inbreeding Rate

We studied the effects of population size on the inbreeding depression and genetic load caused by deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as population size becomes smaller and/or the rate of inbreeding increases. This pattern contrasts with that for the load, which increases as population size becomes smaller but decreases as inbreeding rate goes up. The depression and load both approach asymptotic limits when the population size becomes very large or very small. Numerical results show that the transition between the small and the large population regimes is quite rapid, and occurs largely over a range of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may bias some estimates of the genomic rate of deleterious mutation. These effects could also be important in the evolution of breeding systems in hermaphroditic organisms and in the conservation of endangered populations.

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