Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci

Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae (Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a single Avr locus corresponding to Pc38, Pc39, Pc55, Pc63, Pc70, and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.

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The promise and deceit of genomic selection component analyses

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.1812 ◽

2021 ◽

Vol 288 (1961) ◽

Author(s):

John K. Kelly

Keyword(s):

Allele Frequency ◽

Statistical Power ◽

Field Experiments ◽

Whole Genome Sequence ◽

Frequency Change ◽

Genome Wide ◽

Pooled Sequencing ◽

Frequency Changes ◽

Selection Intensities ◽

Combine Information

Selection component analyses (SCA) relate individual genotype to fitness components such as viability, fecundity and mating success. SCA are based on population genetic models and yield selection estimates directly in terms of predicted allele frequency change. This paper explores the statistical properties of gSCA: experiments that apply SCA to genome-wide scoring of SNPs in field sampled individuals. Computer simulations indicate that gSCA involving a few thousand genotyped samples can detect allele frequency changes of the magnitude that has been documented in field experiments on diverse taxa. To detect selection, imprecise genotyping from low-level sequencing of large samples of individuals provides much greater power than precise genotyping of smaller samples. The simulations also demonstrate the efficacy of ‘haplotype matching’, a method to combine information from a limited collection of whole genome sequence (the reference panel) with the much larger sample of field individuals that are measured for fitness. Pooled sequencing is demonstrated as another way to increase statistical power. Finally, I discuss the interpretation of selection estimates in relation to the Beavis effect, the overestimation of selection intensities at significant loci.

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Estimating the genome-wide contribution of selection to temporal allele frequency change

10.1101/798595 ◽

2019 ◽

Cited By ~ 1

Author(s):

Vince Buffalo ◽

Graham Coop

Keyword(s):

Allele Frequency ◽

Genetic Drift ◽

Genomic Data ◽

Allele Frequencies ◽

Frequency Change ◽

Standing Variation ◽

Genome Wide ◽

Selection Experiments ◽

Frequency Changes ◽

Linked Selection

AbstractRapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult, since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data, e.g. evolve-and-resequence studies. These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one timepoint to be predictive of the changes at later timepoints, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time-points and across replicates. We estimate that at least 17% to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.Significance StatementA long-standing problem in evolutionary biology is to understand the processes that shape the genetic composition of populations. In a population without migration, the two processes that change allele frequencies are selection, which increases beneficial alleles and removes deleterious ones, and genetic drift which randomly changes frequencies as some parents contribute more or less alleles to the next generation. Previous efforts to disentangle these processes have used genomic samples from a single timepoint and models of how selection affects neighboring sites (linked selection). Here, we use genomic data taken through time to quantify the contributions of selection and drift to genome-wide frequency changes. We show selection acts over short timescales in three evolve-and-resequence studies and has a sizable genome-wide impact.

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Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed population

10.1101/2021.10.28.466320 ◽

2021 ◽

Author(s):

Rose M.H. Driscoll ◽

Felix E.G. Beaudry ◽

Elissa J Cosgrove ◽

Reed Bowman ◽

John W Fitzpatrick ◽

...

Keyword(s):

Allele Frequency ◽

Evolutionary Dynamics ◽

Z Chromosome ◽

Frequency Change ◽

Effective Population ◽

Genome Wide ◽

Males And Females ◽

Frequency Changes ◽

Genetic Contributions ◽

The Impact

Sex-biased demography, including sex-biased survival or migration, can impact allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females have similar contributions to autosomal allele frequency change, but males have higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in accounting for genome-wide allele frequency change in wild populations.

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Estimating the genome-wide contribution of selection to temporal allele frequency change

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1919039117 ◽

2020 ◽

Vol 117 (34) ◽

pp. 20672-20680

Author(s):

Vince Buffalo ◽

Graham Coop

Keyword(s):

Allele Frequency ◽

Genetic Drift ◽

Time Course ◽

Frequency Change ◽

Time Points ◽

Standing Variation ◽

Genome Wide ◽

Selection Experiments ◽

Frequency Changes ◽

Linked Selection

Rapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data (e.g., evolve-and-resequence studies). These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one time point to be predictive of the changes at later time points, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time points and across replicates. We estimate that at least 17 to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances, we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.

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Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities

10.22541/au.160672149.99010965/v1 ◽

2020 ◽

Author(s):

Ricardo Pereira ◽

Thiago Lima ◽

N Pierce ◽

Lin Chao ◽

Ronald Burton

Keyword(s):

Allele Frequency ◽

Experimental Evolution ◽

Nuclear Genome ◽

Population Divergence ◽

Hybrid Breakdown ◽

Parental Allele ◽

Genome Wide ◽

Frequency Changes ◽

Efficiency Of Selection ◽

Genomic Regions

Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genome, causing inviability, sterility or low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, it is unclear whether mitonuclear incompatibilities involve few or many regions in the nuclear genome. We employ an experimental evolution approach starting with unfit F2 interpopulation hybrids of the copepod Tigriopus californicus, in which compatible and incompatible nuclear alleles compete in a fixed mitochondrial background. After about nine generations, we observe a generalized increase in population size and in survivorship, suggesting efficiency of selection against maladaptive phenotypes. Whole genome sequencing of evolved populations showed some consistent allele frequency changes across the three replicates of each reciprocal cross, but markedly different patterns between mitochondrial background. In only a few regions (~6.5% of the genome), the same parental allele was overrepresented irrespective of the mitochondrial background. About 33% of the genome shows allele frequency changes consistent with divergent selection, with the location of these genomic regions strongly differing between mitochondrial backgrounds. The dominant allele matches the mitochondrial background in 87 and 89% of these genomic regions, consistent with mitonuclear coadaptation. These results suggest that mitonuclear incompatibilities have a complex polygenic architecture that differs between populations, potentially generating genome wide barriers to gene flow between closely related taxa.

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Genome-Wide Detection of Allele Frequency Change and Quantitative Trait Loci for Respiratory Disease and Immune-Related Traits in Landrace Pigs Selected for Mycoplasmal Pneumonia of Swine Resistance

10.21203/rs.3.rs-133661/v1 ◽

2021 ◽

Author(s):

Yoshinobu Uemoto ◽

Kasumi Ichinoseki ◽

Toshimi Matsumoto ◽

Nozomi Oka ◽

Hironori Takamori ◽

...

Keyword(s):

Disease Resistance ◽

Allele Frequency ◽

Respiratory Disease ◽

Quantitative Trait ◽

Association Studies ◽

Frequency Change ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Mycoplasmal Pneumonia ◽

Frequency Changes

Abstract Background: The genetic improvement of disease resistance in pig has been well-received. Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for understanding the genomic background of disease resistance and to apply marker-assisted selection. The objective of this study was to understand the influence of genomic factors on respiratory disease and immune-related traits in MPS-selected pigs.Results: A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip, and were then used for genomic analyses. First, we performed genome-wide association studies (GWAS) to detect a novel QTL for a total of 22 performance, respiratory disease, and immune-related traits using additive and nonadditive genetic effects. Second, we evaluated the changes in allele frequency due to selection for MPS resistance and compared the putative selected regions with the detected QTL. GWAS detected a total of 11 genome-wide significant single nucleotide polymorphisms (SNPs) with an additive effect in five traits and a total of three significant SNPs with a nonadditive effect in three traits. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic region among traits, only five of these detected QTL regions overlapped among traits. Changes in allele frequencies at the many putative selected regions were spread across the whole genome and overlapped with the detected QTL. Some of these selected regions were the ones that contained the detected QTL for MPS score and other traits.Conclusion: These results suggest that a closed-line breeding population is a useful target population to refine and confirm QTL regions by integrating the results of GWAS and allele frequency changes. The study provides new insights into the genomic factors that affect respiratory disease and immune-related traits in pigs.

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