Review: Balancing Selection for Deleterious Alleles in Livestock

Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.

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Highly efficient CRISPR gene editing in yeast enabled by double selection

10.1101/262808 ◽

2018 ◽

Author(s):

Philippe C Després ◽

Alexandre K Dubé ◽

Lou Nielly-Thibault ◽

Nozomu Yachie ◽

Christian R Landry

Keyword(s):

High Frequency ◽

Large Scale ◽

Gene Editing ◽

Chromosomal Translocations ◽

Selection Strategy ◽

Loss Of Function ◽

Base Editing ◽

Fitness Effects ◽

Genetics And Genomics ◽

Selection For

AbstractCRISPR-Cas9 loss of function (LOF) and base editing screens are powerful tools in genetics and genomics. Yeast is one of the main models in genetics and genomics, yet large-scale approaches remain to be developed in this species because of low mutagenesis rates without donor DNA. We developed a double selection strategy based on co-selection that increases LOF mutation rates, both for CRISPR-Cas9 and the Target-AID base editor. We constructed the pDYSCKO vector, which is amenable to high throughput double selection for both approaches. Using modeling, we show that this improvement provides the required increased in detection power to measure the fitness effects of thousands of mutations in typical yeast pooled screens. We also show that multiplex genome editing with Cas9 causes programmable chromosomal translocations at high frequency, suggesting that multiplex editing should be performed with caution and that base-editors could be preferable tools for LOF screens.

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Impaired SorLA maturation and trafficking as a new mechanism for SORL1 missense variants in Alzheimer disease

Acta Neuropathologica Communications ◽

10.1186/s40478-021-01294-4 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Anne Rovelet-Lecrux ◽

Sebastien Feuillette ◽

Laetitia Miguel ◽

Catherine Schramm ◽

Ségolène Pernet ◽

...

Keyword(s):

3D Structure ◽

Hek293 Cells ◽

Pathophysiological Mechanism ◽

Loss Of Function ◽

Missense Variants ◽

Major Player ◽

Functional Consequences ◽

Endosomal System ◽

The Impact ◽

Clear Increase

AbstractThe SorLA protein, encoded by the SORL1 gene, is a major player in Alzheimer’s disease (AD) pathophysiology. Functional and genetic studies demonstrated that SorLA deficiency results in increased production of Aβ peptides, and thus a higher risk of AD. A large number of SORL1 missense variants have been identified in AD patients, but their functional consequences remain largely undefined. Here, we identified a new pathophysiological mechanism, by which rare SORL1 missense variants identified in AD patients result in altered maturation and trafficking of the SorLA protein. An initial screening, based on the overexpression of 70 SorLA variants in HEK293 cells, revealed that 15 of them (S114R, R332W, G543E, S564G, S577P, R654W, R729W, D806N, Y934C, D1535N, D1545E, P1654L, Y1816C, W1862C, P1914S) induced a maturation and trafficking-deficient phenotype. Three of these variants (R332W, S577P, and R654W) and two maturation-competent variants (S124R and N371T) were further studied in details in CRISPR/Cas9-modified hiPSCs. When expressed at endogenous levels, the R332W, S577P, and R654W SorLA variants also showed a maturation defective profile. We further demonstrated that these variants were largely retained in the endoplasmic reticulum, resulting in a reduction in the delivery of SorLA mature protein to the plasma membrane and to the endosomal system. Importantly, expression of the R332W and R654W variants in hiPSCs was associated with a clear increase of Aβ secretion, demonstrating a loss-of-function effect of these SorLA variants regarding this ultimate readout, and a direct link with AD pathophysiology. Furthermore, structural analysis of the impact of missense variants on SorLA protein suggested that impaired cellular trafficking of SorLA protein could be due to subtle variations of the protein 3D structure resulting from changes in the interatomic interactions.

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Impaired SorLA maturation and trafficking as a new mechanism for SORL1 missense variants in Alzheimer disease

10.1101/2021.06.18.448296 ◽

2021 ◽

Author(s):

Anne Rovelet-Lecrux ◽

Sebastien Feuillette ◽

Laetitia Miguel ◽

Catherine Schramm ◽

Segolene Pernet ◽

...

Keyword(s):

Protein Structure ◽

Alzheimer Disease ◽

Hek293 Cells ◽

Pathophysiological Mechanism ◽

Loss Of Function ◽

Missense Variants ◽

Major Player ◽

Functional Consequences ◽

Sorl1 Gene ◽

The Impact

The SorLA protein, encoded by the SORL1 gene, is a major player in Alzheimer disease (AD) pathophysiology. Functional and genetic studies demonstrated that SorLA deficiency results in increased production of Aβ peptides, and thus a higher risk of AD. A large number of SORL1 missense variants have been identified in AD patients, but their functional consequences remain largely undefined. Here, we identified a new pathophysiological mechanism, by which rare SORL1 missense variants identified in AD patients result in altered maturation and trafficking of SorLA protein. An initial screening, based on the overexpression of 71 SorLA variants in HEK293 cells, revealed that 15 of them (S114R, R332W, G543E, S564G, S577P, R654W, R729W, D806N, Y934C, D1535N, D1545E, P1654L, Y1816C, W1862C, P1914S) induced a maturation and trafficking-deficient phenotype. Three of these variations (R332W, S577P, and R654W) and two maturation-competent variations (S124R and N371T) were further studied in details in CRISPR/Cas9-modified hiPSCs. When expressed at endogenous levels, the R332W, S577P, and R654W SorLA variants also showed a maturation defective profile. We further demonstrated that these variants were largely retained in the endoplasmic reticulum, resulting in a reduction in the delivery of SorLA mature protein to the plasma membrane and to the endosomal system. Importantly, expression of the R332W and R654W variants in hiPSCs were associated with a clear increase of Aβ secretion, demonstrating a loss-of-function effect of these SorLA variants regarding this ultimate readout, and a direct link with AD pathophysiology. Finally, structural analysis of the impact of missense variations on SorLA protein structure indicated that impaired cellular trafficking of SorLA protein could be due to subtle variations of the protein structure resulting from changes in the interatomic interactions.

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Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2023018118 ◽

2021 ◽

Vol 118 (49) ◽

pp. e2023018118

Author(s):

Anubhab Khan ◽

Kaushalkumar Patel ◽

Harsh Shukla ◽

Ashwin Viswanathan ◽

Tom van der Valk ◽

...

Keyword(s):

Inbreeding Depression ◽

Purifying Selection ◽

Isolated Population ◽

Loss Of Function ◽

Mutation Load ◽

Genetic Rescue ◽

Frequency Distributions ◽

Recessive Mutations ◽

Deleterious Alleles ◽

Large Populations

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small–isolated and two large–connected populations in India. As expected, the small–isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large–connected (FROH = 0.35 and FROH = 0.46) populations. The small–isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small–isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small–isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small–isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

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Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

10.1101/2021.05.18.444660 ◽

2021 ◽

Author(s):

Anubhab Khan ◽

Kaushalkumar Patel ◽

Harsh Shukla ◽

Ashwin Viswanathan ◽

Tom van der Valk ◽

...

Keyword(s):

Inbreeding Depression ◽

Purifying Selection ◽

Isolated Population ◽

Loss Of Function ◽

Mutation Load ◽

Genetic Rescue ◽

Frequency Distributions ◽

Recessive Mutations ◽

Deleterious Alleles ◽

Large Populations

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used genome sequencing of 57 tigers to estimate individual inbreeding and mutation loads in a small-isolated, and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH=0.57) than the large-connected (FROH=0.35 and FROH=0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at high frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of (a) high mutation load; (b) purging and (c) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation should offset any possible impacts of inbreeding depression.

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Comparison of predicted and actual consequences of missense mutations

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1511585112 ◽

2015 ◽

Vol 112 (37) ◽

pp. E5189-E5198 ◽

Cited By ~ 118

Author(s):

Lisa A. Miosge ◽

Matthew A. Field ◽

Yovina Sontani ◽

Vicky Cho ◽

Simon Johnson ◽

...

Keyword(s):

De Novo ◽

Low Frequency ◽

Purifying Selection ◽

Missense Mutations ◽

Loss Of Function ◽

Immune Genes ◽

Missense Variants ◽

Neutral Mutations

Each person’s genome sequence has thousands of missense variants. Practical interpretation of their functional significance must rely on computational inferences in the absence of exhaustive experimental measurements. Here we analyzed the efficacy of these inferences in 33 de novo missense mutations revealed by sequencing in first-generation progeny of N-ethyl-N-nitrosourea–treated mice, involving 23 essential immune system genes. PolyPhen2, SIFT, MutationAssessor, Panther, CADD, and Condel were used to predict each mutation’s functional importance, whereas the actual effect was measured by breeding and testing homozygotes for the expected in vivo loss-of-function phenotype. Only 20% of mutations predicted to be deleterious by PolyPhen2 (and 15% by CADD) showed a discernible phenotype in individual homozygotes. Half of all possible missense mutations in the same 23 immune genes were predicted to be deleterious, and most of these appear to become subject to purifying selection because few persist between separate mouse substrains, rodents, or primates. Because defects in immune genes could be phenotypically masked in vivo by compensation and environment, we compared inferences by the same tools with the in vitro phenotype of all 2,314 possible missense variants in TP53; 42% of mutations predicted by PolyPhen2 to be deleterious (and 45% by CADD) had little measurable consequence for TP53-promoted transcription. We conclude that for de novo or low-frequency missense mutations found by genome sequencing, half those inferred as deleterious correspond to nearly neutral mutations that have little impact on the clinical phenotype of individual cases but will nevertheless become subject to purifying selection.

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Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection

10.1101/053793 ◽

2016 ◽

Cited By ~ 1

Author(s):

Tobias L. Lenz ◽

Victor Spirin ◽

Daniel M. Jordan ◽

Shamil R. Sunyaev

Keyword(s):

Balancing Selection ◽

Purifying Selection ◽

Physical Distance ◽

Deleterious Mutations ◽

Sequencing Data ◽

Hla Genes ◽

Deleterious Alleles ◽

Whole Exome Sequencing Data ◽

Elevated Frequency ◽

Coding Variants

AbstractDeleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in non-HLA genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases.

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Response to selection for seed yield in six white clover cultivars

Proceedings of the New Zealand Grassland Association ◽

10.33584/jnzg.2004.66.2566 ◽

2004 ◽

pp. 103-110 ◽

Cited By ~ 1

Author(s):

K.H. Widdup ◽

D.R. Woodfield ◽

I.J. Baird ◽

P.T.P. Clifford

Keyword(s):

Seed Production ◽

Seed Yield ◽

White Clover ◽

Trifolium Repens ◽

Leaf Size ◽

Fourth Generation ◽

Selection Strategy ◽

Flowering Pattern ◽

Selection For ◽

The Impact

The successful commercialisation of agronomically superior white clover (Trifolium repens) cultivars is dependent on their seed production potential. Field trials were established in 2000 and repeated in 2003 to determine the impact of selection for increased seed yield. The seed yield of the pre-release cultivar (the base population prior to selection for seed yield and cultivar release, representing generation 0) was compared with the field Nucleus generation of the released cultivar (second generation after selection for seed yield, representing generation 2) and the Basic seed generation (the fourth generation after selection for seed yield, representing generation 4), in six recent cultivars (Grasslands Kopu II, Grasslands Challenge, NuSiral, Grasslands Sustain, Grasslands Demand and Grasslands Prestige). The Nucleus and Basic generations had consistently higher seed yield than the pre-release generation for all cultivars. These increases in seed yield were associated with increases in inflorescence density (inflorescences/m2) and to a lesser extent with increased seed yield/inflorescence. Changes were also evident in flowering pattern with four of the six cultivars having a sharper flowering peak following selection. This improved uniformity was also evident through reduced variability in leaf size of the Nucleus generation compared to the pre-release generation. Grasslands Kopu II had the highest seed yields which were associated with moderately high inflorescence density in combination with high seed yield/ inflorescence. The selection strategy used in the final phase of the development of these cultivars has proven successful in increasing seed yield through refining flowering pattern and production while maintaining the morphology and uniformity of the new cultivar. Keywords: cultivars, genetic improvement, seed production, Trifolium repens, white clover

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Impact of Amoxicillin treatment on E. coli in dairy cow faeces

Access Microbiology ◽

10.1099/acmi.ac2020.po0879 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Caleb Marsh ◽

Imogen Whigham ◽

Ginny Sherwin ◽

Michael Jones

Keyword(s):

Drug Resistance ◽

Dairy Cow ◽

Low Frequency ◽

Multi Drug Resistance ◽

E Coli ◽

Disk Diffusion Testing ◽

Resistant Infection ◽

Selection For ◽

The Uk ◽

The Impact

Introduction: There has been a global drive for increased antimicrobial stewardship. In the UK, this drive has focused on decreased usage of antimicrobials, specifically HP-CIAs. It is well known that antimicrobials are selection drivers for antimicrobial resistance. How a given dose will impact the prevalence of resistance in a microbiome, and therefore the associated risk of a resistant infection is less understood. Questions also remain around the impact of antimicrobial therapy on resistance across a herd, if selection occurs within an animal receiving treatment, what is the potential risk of this resistance spreading throughout other animals? Methods: E. COLI ISOLATION Tryptone Bile X-Glucuronide (TBX) media was used for selective growth of non – toxigenic E. coli from dairy cow faeces. SUSCEPTIBILITY TESTING EUCAST Disk Diffusion testing guidelines were followed to determine susceptibility of faecal isolates to a panel of 8 antimicrobials from 5 different classes. ISOLATE FINGERPRINTING To determine clonality of faecal isolates ERIC-PCR was used as an efficient method to provide a genomic fingerprint. Results This work is ongoing. Current work suggests that low frequency Amoxicillin treatment has no significant selection for resistance. However, there appears to be some instances of co-selection for Streptomycin, Tetracycline and Sulphonamide resistance, and several multi drug resistance isolates have been identified. More work needs to be done to confirm the impact of low frequency Amoxicillin treatment on E. coli resistance and identify the mechanism behind suspected co-selection and multi drug resistance.

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The impact of artificial selection for Wolbachia-mediated dengue virus blocking on phage WO

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0009637 ◽

2021 ◽

Vol 15 (7) ◽

pp. e0009637

Author(s):

Heverton L. C. Dutra ◽

Suzanne A. Ford ◽

Scott L. Allen ◽

Sarah R. Bordenstein ◽

Stephen F. Chenoweth ◽

...

Keyword(s):

Artificial Selection ◽

Chromosome 1 ◽

Cascading Effects ◽

Intrinsic Factors ◽

Deleterious Alleles ◽

Potential Link ◽

Selection For ◽

Elevated Frequency ◽

Virus Blocking ◽

The Impact

Wolbachia is currently at the forefront of global efforts to control arbovirus transmission from the vector Aedes aegypti. The use of Wolbachia relies on two phenotypes—cytoplasmic incompatibility (CI), conferred by cifA and cifB genes in prophage WO, and Wolbachia-mediated pathogen blocking (WMPB). These traits allow for local, self-sustaining reductions in transmission of dengue (DENV) following release of Wolbachia-infected A. aegypti. Here, aided by previous artificial selection experiment that generated Low and High pathogen blocking lines, we examined the potential link between WMPB and phage WO. We found no evidence that Wolbachia or phage WO relative densities predict DENV blocking strength across selected lines. However, selection resulted in reduced phage WO relative density for the Low WMPB line. The Low blocking line was previously shown to have reduced fitness as a result of selection. Through subsequent genomic analyses, we demonstrate that SNP variation underpinning selection for low blocking led to elevated frequency of potential deleterious SNPs on chromosome 1. The key region on chromosome 1 contains genes relating to cell cycle regulation, oxidative stress, transcriptional pausing, among others, that may have cascading effects on Wolbachia intracellular environment. We hypothesize that reduction in phage WO may be driven by changes in the loci directly under selection for blocking, or by the accumulation of predicted deleterious alleles in linkage disequilibrium with blocking loci resulting from hitchhiking. For the Low line with fewer phage WO, we also detected reduced expression of cifA and cifB CI genes, with patterns of expression varying between somatic and reproductive tissues. In conclusion, we propose that artificial selection for WMPB trait had corresponding impacts on phage WO densities, and also the transcription of CI-causing genes. Future studies may include a more detailed analysis of the regions the A. aegypti chromosome 1’s ability to affect WMPB and other Wolbachia-associated intrinsic factors such as phage WO.

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