scholarly journals The genome-wide rate and spectrum of spontaneous mutations differs between haploid and diploid yeast

2018 ◽  
Author(s):  
Nathaniel P. Sharp ◽  
Linnea Sandell ◽  
Christopher G. James ◽  
Sarah P. Otto
Keyword(s):  
Structural Changes ◽  
Wide Spectrum ◽  
Doubled Haploids ◽  
Rate Variation ◽  
Spontaneous Mutations ◽  
Single Nucleotide ◽  
Homologous Chromosomes ◽  
Genome Wide ◽  
Dna Replication And Repair ◽  
Genomic Regions

AbstractBy altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report the first direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploid and diploid forms of the budding yeast. Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that diploidy masks the effects of recessive alleles. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to particular single-nucleotide mutations in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids are Saccharomyces cerevisiae not simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.

scholarly journals The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast

2018 ◽  
Vol 115 (22) ◽  
pp. E5046-E5055 ◽  
Author(s):  
Nathaniel P. Sharp ◽  
Linnea Sandell ◽  
Christopher G. James ◽  
Sarah P. Otto
Keyword(s):  
Structural Changes ◽  
Wide Spectrum ◽  
Doubled Haploids ◽  
Rate Variation ◽  
Spontaneous Mutations ◽  
Single Nucleotide ◽  
Homologous Chromosomes ◽  
Genome Wide ◽  
Dna Replication And Repair ◽  
Genomic Regions

By altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report a direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploids and diploids following a mutation-accumulation experiment in the budding yeast Saccharomyces cerevisiae. Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide mutations (SNMs) and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that mutations would have weaker effects, due to masking, in diploids. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to SNMs in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids, we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids are not simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.

scholarly journals Emerging Technologies for Genome-Wide Profiling of DNA Breakage

2021 ◽  
Vol 11 ◽  
Author(s):  
Matthew J. Rybin ◽  
Melina Ramic ◽  
Natalie R. Ricciardi ◽  
Philipp Kapranov ◽  
Claes Wahlestedt ◽  
...  
Keyword(s):  
Genome Instability ◽  
Dna Double Strand Breaks ◽  
Single Nucleotide ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Nucleotide Resolution ◽  
Genomic Regions

Genome instability is associated with myriad human diseases and is a well-known feature of both cancer and neurodegenerative disease. Until recently, the ability to assess DNA damage—the principal driver of genome instability—was limited to relatively imprecise methods or restricted to studying predefined genomic regions. Recently, new techniques for detecting DNA double strand breaks (DSBs) and single strand breaks (SSBs) with next-generation sequencing on a genome-wide scale with single nucleotide resolution have emerged. With these new tools, efforts are underway to define the “breakome” in normal aging and disease. Here, we compare the relative strengths and weaknesses of these technologies and their potential application to studying neurodegenerative diseases.

scholarly journals Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 170 ◽  
Author(s):  
Zengkui Lu ◽  
Yaojing Yue ◽  
Chao Yuan ◽  
Jianbin Liu ◽  
Zhiqiang Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Muscle Development ◽  
Genome Wide Association Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Economic Trait ◽  
Significance Levels ◽  
Genomic Regions ◽  
Selection Of

Body weight is an important economic trait for sheep and it is vital for their successful production and breeding. Therefore, identifying the genomic regions and biological pathways that contribute to understanding variability in body weight traits is significant for selection purposes. In this study, the genome-wide associations of birth, weaning, yearling, and adult weights of 460 fine-wool sheep were determined using resequencing technology. The results showed that 113 single nucleotide polymorphisms (SNPs) reached the genome-wide significance levels for the four body weight traits and 30 genes were annotated effectively, including AADACL3, VGF, NPC1, and SERPINA12. The genes annotated by these SNPs significantly enriched 78 gene ontology terms and 25 signaling pathways, and were found to mainly participate in skeletal muscle development and lipid metabolism. These genes can be used as candidate genes for body weight in sheep, and provide useful information for the production and genomic selection of Chinese fine-wool sheep.

scholarly journals Population Differentiation at the HLA Genes

2017 ◽  
Author(s):  
Débora Y. C. Brandt ◽  
Jônatas César ◽  
Jérôme Goudet ◽  
Diogo Meyer
Keyword(s):  
Population Differentiation ◽  
Balancing Selection ◽  
Global Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Hla Genes ◽  
Genome Wide ◽  
Different Populations ◽  
Genomic Regions

ABSTRACTBalancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle this issue, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. However, this result depends on accounting for the differences in allele frequency between selected and putatively neutral sites. Our finding of reduced differentiation at SNPs within HLA genes suggests a predominant role of shared selective pressures among populations at a global scale. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. This pattern was reproduced in simulations of overdominant selection. We conclude that population differentiation at the HLA genes is generally lower than genome-wide, but it may be higher for recently diverged population pairs, and that this pattern can be explained by a simple overdominance regime.

scholarly journals Genome-wide association for mapping QTLs linked to protein and oil contents in soybean

2017 ◽  
Vol 52 (10) ◽  
pp. 896-904
Author(s):  
Douglas Antônio Dias ◽  
Leandra Regina Texeira Polo ◽  
Fabiane Lazzari ◽  
Glacy Jaqueline da Silva ◽  
Ivan Schuster
Keyword(s):  
Protein Content ◽  
Oil Content ◽  
Near Infrared ◽  
Snp Markers ◽  
Regression Analyses ◽  
Nucleotide Polymorphism ◽  
Near Infrared Reflectance ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Genomic Regions

Abstract: The objective of this work was to identify single-nucleotide polymorphism (SNP) markers linked with quantitative trait loci (QTLs) associated with increased contents of protein and oil in soybean. A total of 169 Brazilian soybean varieties, genotyped with 6,000 SNP markers, were evaluated. Protein and oil contents were obtained with the near-infrared reflectance method. Correlation and multiple linear regression analyses were used to identify linkage disequilibrium between SNP markers and the QTLs associated with the two characteristics. Seven QTLs were found to be associated with protein content, on six chromosomes (2, 6, 11, 12, 13, and 16), explaining 60.9% of the variation in this trait. For oil content, eight QTLs were identified on six chromosomes (1, 4, 5, 6, 17, and 19), explaining 78.3% of the variation in the trait. The correlation between the number of loci containing favorable alleles and the evaluated characteristics was 0.49 for protein content and 0.60 for oil content. The molecular markers identified are mapped in genomic regions containing QTLs previously mapped for both characteristics, which reinforces the association between these regions and the genetic control of oil and protein contents in soybean.

scholarly journals Selection on a pleiotropic color gene block underpins early differentiation between two warbler species

2019 ◽  
Author(s):  
Silu Wang ◽  
Sievert Rohwer ◽  
Devin R. de Zwaan ◽  
David P. L Toews ◽  
Irby J. Lovette ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Basis ◽  
Early Stage ◽  
Population Substructure ◽  
Carotenoid Pigment ◽  
Single Nucleotide ◽  
Gene Block ◽  
Genome Wide ◽  
Genomic Regions ◽  
Divergence With Gene Flow

AbstractWhen one species gradually splits into two, divergent selection on specific traits can cause peaks of differentiation in the genomic regions encoding those traits. Whether speciation is initiated by strong selection on a few genomic regions with large effects or by more diffused selection on many regions with small effects remains controversial. Differentiated phenotypes between differentiating lineages are commonly involved in reproductive isolation, thus their genetic underpinnings are key to the genomics architecture of speciation. When two species hybridize, recombination over multiple generations can help reveal the genetic regions responsible for the differentiated phenotypes against a genomic background that has been homogenized via backcrossing and introgression. We used admixture mapping to investigate genomic differentiation and the genetic basis of differentiated plumage features (relative melanin and carotenoid pigment) between hybridizing sister species in the early stage of speciation: Townsend’s (Setophaga townsendi) and Hermit warblers (S. occidentalis). We found a few narrow and dispersed divergent regions between allopatric parental populations, consistent with the ‘divergence with gene flow’ model of speciation. One of the divergent peaks involves three genes known to affect pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). After controlling for population substructure, we found that a single nucleotide polymorphism (SNP) inside the intron of RALY displays a strong pleiotropic association with cheek, crown, and breast coloration. In addition, we detect selection on the ASIP-RALY gene block, as the geographic cline of the RALY marker of this gene block has remained narrower than the plumage cline, which remained narrower than expected under neutral diffusion over two decades. Despite extensive gene flow between these species across much of the genome, the selection on ASIP-RALY gene block maintains stable genotypic and plumage difference between species allowing further differentiation to accumulate via linkage to its flanking genetic region or linkage-disequilibrium genome-wide.

scholarly journals Genetics of recombination rate variation in the pig

2020 ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Chromosome Length ◽  
Rate Variation ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions ◽  
Iterative Peeling ◽  
Recombination Rate Variation

AbstractBackgroundIn this paper, we estimated recombination rate variation within the genome and between individuals in the pig using multiocus iterative peeling for 150,000 pigs across nine genotyped pedigrees. We used this to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig.ResultsOur results confirmed known features of the pig recombination landscape, including differences in chromosome length, and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, the lines also showed differences in average genome-wide recombination rate. The heritability of genome-wide recombination was low but non-zero (on average 0.07 for females and 0.05 for males). We found three genomic regions associated with recombination rate, one of them harbouring the RNF212 gene, previously associated with recombination rate in several other species.ConclusionOur results from the pig agree with the picture of recombination rate variation in vertebrates, with low but nonzero heritability, and a major locus that is homologous to one detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

Use of single-step genome-wide association studies for prospecting genomic regions related to milk production and milk quality of buffalo

2018 ◽  
Vol 85 (4) ◽  
pp. 402-406 ◽  
Author(s):  
Camila da Costa Barros ◽  
Daniel Jordan de Abreu Santos ◽  
Rusbel Raul Aspilcueta-Borquis ◽  
Gregório Miguel Ferreira de Camargo ◽  
Francisco Ribeiro de Araújo Neto ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Fat ◽  
Association Studies ◽  
Single Step ◽  
Milk Quality ◽  
Genome Wide Association Studies ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Genomic Regions

The aim of this research communication was to identify chromosome regions and genes that could be related to milk yield (MY), milk fat (%F) and protein percentage (%P) in Brazilian buffalo cows using information from genotyped and non-genotyped animals. We used the 90 K Axiom® Buffalo Genotyping array. A repeatability model was used. An iterative process was performed to calculate the weights of markers as a function of the squared effects of Single Nucleotide Polymorphism (SNP) and allele frequencies. The 10 SNPs with the largest effects for MY, %F and %P were studied and they explained 7·48, 9·94 and 6·56% of the genetic variance, respectively. These regions harbor genes with biological functions that could be related to the traits analyzed. The identification of such regions and genes will contribute to a better understanding of their influence on milk production and milk quality traits of buffaloes.

scholarly journals Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing

2020 ◽  
Author(s):  
Kazunari Matsudaira ◽  
Takafumi Ishida
Keyword(s):  
Amplicon Sequencing ◽  
Single Nucleotide ◽  
Reduced Representation ◽  
Island Species ◽  
Genome Wide ◽  
Distribution Ranges ◽  
Natural Hybridisation ◽  
Quality Filtering ◽  
Divergence Pattern ◽  
Genomic Regions

AbstractGibbons in the genus Hylobates, which live in Southeast Asia, show great diversity, comprising seven to nine species. Natural hybridisation has been observed in the species contact zones, although the roles played by hybridisation and introgression in the evolution of these species remain unclear. To uncover the divergence history and the contributions of hybridisation and introgression to the evolution of Hylobates, random amplicon sequencing-direct (GRAS-Di) analysis was employed to genotype 47 gibbons, representing eight species from three genera. After quality filtering, over 300,000 autosomal single-nucleotide variant (SNV) sites were identified. The SNV-based autosomal phylogeny, together with the mitochondrial phylogeny, supported a divergence pattern beginning approximately 4.3 million years ago. First, the mainland species, H. pileatus and H. lar, consecutively diverged from the Sundaic island species. Second, H. moloch, in Java (and likely H. klossii, in the Mentawai Islands) diverged from the other species. Third, H. muelleri, in Borneo, and H. agilis/H. albibarbis, in Sumatra and southwestern Borneo, diverged. Lastly, H. agilis and H. albibarbis diverged from each other. The Patterson’s D-statistics indicated significant introgression between H. lar and H. pileatus, between H. lar and H. agilis, and between H. albibarbis and H. muelleri, and weak introgression was identified between H. moloch and H. albibarbis, and between H. moloch and H. muelleri abbotti, suggesting incomplete reproductive barriers among Hylobates species and that hybridisation and introgression occur whenever the distribution ranges contact. Some candidates for introgressed genomic regions were detected, and the functions of these would be revealed by further genome-wide studies.

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