scholarly journals Effects of marker type and filtering criteria on Q ST - F ST comparisons

2019 ◽  
Vol 6 (11) ◽  
pp. 190666 ◽  
Author(s):  
Zitong Li ◽  
Ari Löytynoja ◽  
Antoine Fraimout ◽  
Juha Merilä
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Differentiation ◽  
Empirical Data ◽  
Simulated Data ◽  
Pungitius Pungitius ◽  
Marker Selection ◽  
Marker Type ◽  
Genomic Location ◽  
Minor Alleles ◽  
Trait Differentiation

Comparative studies of quantitative and neutral genetic differentiation ( Q ST - F ST tests) provide means to detect adaptive population differentiation. However, Q ST - F ST tests can be overly liberal if the markers used deflate F ST below its expectation, or overly conservative if methodological biases lead to inflated F ST estimates. We investigated how marker type and filtering criteria for marker selection influence Q ST - F ST comparisons through their effects on F ST using simulations and empirical data on over 18 000 in silico genotyped microsatellites and 3.8 million single-locus polymorphism (SNP) loci from four populations of nine-spined sticklebacks ( Pungitius pungitius ). Empirical and simulated data revealed that F ST decreased with increasing marker variability, and was generally higher with SNPs than with microsatellites. The estimated baseline F ST levels were also sensitive to filtering criteria for SNPs: both minor alleles and linkage disequilibrium (LD) pruning influenced F ST estimation, as did marker ascertainment. However, in the case of stickleback data used here where Q ST is high, the choice of marker type, their genomic location, ascertainment and filtering made little difference to outcomes of Q ST - F ST tests. Nevertheless, we recommend that Q ST - F ST tests using microsatellites should discard the most variable loci, and those using SNPs should pay attention to marker ascertainment and properly account for LD before filtering SNPs. This may be especially important when level of quantitative trait differentiation is low and levels of neutral differentiation high.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

scholarly journals An evaluation of the interpretability and predictive performance of the BayesR model for genomic prediction

2020 ◽  
Author(s):  
Fanny Mollandin ◽  
Andrea Rau ◽  
Pascal Croiseau
Keyword(s):  
Linkage Disequilibrium ◽  
Qtl Mapping ◽  
Effect Size ◽  
Genomic Prediction ◽  
Simulated Data ◽  
Predictive Performance ◽  
Real Data ◽  
Sliding Windows ◽  
Size Classes ◽  
The Impact

ABSTRACTTechnological advances and decreasing costs have led to the rise of increasingly dense genotyping data, making feasible the identification of potential causal markers. Custom genotyping chips, which combine medium-density genotypes with a custom genotype panel, can capitalize on these candidates to potentially yield improved accuracy and interpretability in genomic prediction. A particularly promising model to this end is BayesR, which divides markers into four effect size classes. BayesR has been shown to yield accurate predictions and promise for quantitative trait loci (QTL) mapping in real data applications, but an extensive benchmarking in simulated data is currently lacking. Based on a set of real genotypes, we generated simulated data under a variety of genetic architectures, phenotype heritabilities, and we evaluated the impact of excluding or including causal markers among the genotypes. We define several statistical criteria for QTL mapping, including several based on sliding windows to account for linkage disequilibrium. We compare and contrast these statistics and their ability to accurately prioritize known causal markers. Overall, we confirm the strong predictive performance for BayesR in moderately to highly heritable traits, particularly for 50k custom data. In cases of low heritability or weak linkage disequilibrium with the causal marker in 50k genotypes, QTL mapping is a challenge, regardless of the criterion used. BayesR is a promising approach to simultaneously obtain accurate predictions and interpretable classifications of SNPs into effect size classes. We illustrated the performance of BayesR in a variety of simulation scenarios, and compared the advantages and limitations of each.

scholarly journals Intragenic Conflict in Phylogenomic Data Sets

2020 ◽  
Vol 37 (11) ◽  
pp. 3380-3388
Author(s):  
Stephen A Smith ◽  
Nathanael Walker-Hale ◽  
Joseph F Walker
Keyword(s):  
Data Analysis ◽  
Empirical Data ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Simulated Data ◽  
Data Sets ◽  
Alignment Error ◽  
Biological Processes ◽  
Simple Method

Abstract Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.

Comparison of Novel and Existing Methods for Detection of Linkage Disequilibrium Using Parent-Child Trios in the GAW12 Genetic Isolate Simulated Data

2001 ◽  
Vol 21 (S1) ◽  
pp. S378-S383
Author(s):  
J.E. Bailey-Wilson ◽  
A.J.M. Sorant ◽  
J.D. Malley ◽  
S. Presciuttini ◽  
R.A. Redner ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Simulated Data ◽  
Genetic Isolate ◽  
Parent Child

The effects of halothane susceptibility on some economically important traits in pigs 1. Litter productivity

1985 ◽  
Vol 40 (2) ◽  
pp. 351-358 ◽  
Author(s):  
A. E. Carden ◽  
W. G. Hill ◽  
A. J. Webb
Keyword(s):  
Linkage Disequilibrium ◽  
Maximum Likelihood ◽  
Genetic Differentiation ◽  
Perinatal Mortality ◽  
Litter Size ◽  
Maximum Likelihood Estimates ◽  
Halothane Anaesthesia ◽  
Data Set ◽  
Apparent Influence

ABSTRACTThe effects of susceptibility to halothane anaesthesia on litter productivity were investigated by comparing susceptible and normal females in two sets of data. The first comprised 206 litters from the first five generations of Pietrain/Hampshire synthetic lines selected for and against halothane susceptibility. Susceptible and normal females were mated to boars of their own type. The second data set consisted of 93 litters from the same susceptible and normal females mated to normal boars. Compared with normal contemporaries, litter sizes of susceptible females were reduced by 1·16 (s.e. 0·40) piglets at birth, and 1-76 (s.e. 0·41) at weaning (ca. 1 weeks). Maximum likelihood estimates of the proportions of piglet deaths from birth to weaning as a trait of susceptible v. normal dams were 0·32 v. 014 (P < 0·001). There were no significant differences in piglet weights or perinatal mortality, and no apparent influence of piglet genotype on any trait. The lower litter size of susceptible females at weaning appeared to result from reductions in both numbers born and survival to weaning. The study bears out previous reports of a reduction in litter productivity due to the halothane gene. However, the present differences could have arisen largely from random genetic differentiation between lines, or linkage disequilibrium in the synthetic foundation population.

scholarly journals Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

2020 ◽  
Author(s):  
Ahasanul Hoque ◽  
Jason D. Fiedler ◽  
Mukhlesur Rahman
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Genetic Differentiation ◽  
Genetic Gain ◽  
Mantel Test ◽  
Snp Markers ◽  
Breeding Program ◽  
Neighbor Joining ◽  
Breeding Lines ◽  
The North

Abstract Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6,200 SNP markers Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise F st comparison revealed a great degree of divergence ( F st > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r= 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree assists to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.

scholarly journals Molecular Characterization of Fusarium Head Blight Pathogens Sampled from a Naturally Infected Disease Nursery Used for Wheat Breeding Programs in China

Plant Disease ◽  
2012 ◽  
Vol 96 (9) ◽  
pp. 1280-1285 ◽  
Author(s):  
K. D. Puri ◽  
E. S. Saucedo ◽  
S. Zhong
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Differentiation ◽  
Fusarium Head Blight ◽  
Random Mating ◽  
Variable Number Tandem Repeat ◽  
Distinct Species ◽  
Wheat Breeding ◽  
Variable Number ◽  
Head Blight ◽  
Pairwise Linkage Disequilibrium

Fusarium head blight (FHB) is an important disease of wheat and barley worldwide. The disease is primarily caused by members of the Fusarium graminearum species complex, consisting of at least 14 phylogenetically distinct species. To determine the population structure of the FHB pathogens in a naturally infected disease nursery located at Jianyang, Fujian province, China, 160 isolates of the F. graminearum complex were recovered from symptomatic wheat spike samples collected in two consecutive years (2008 and 2009) and characterized using species- and chemotype-specific polymerase chain reaction as well as variable number tandem repeat (VNTR) markers. All isolates analyzed were identified as F. asiaticum except for one isolate, which was identified as F. avenaceum. Among the 159 F. asiaticum isolates, 126 (79%) isolates were of the nivalenol (NIV) type while 29 (18%) isolates were of the 15-acetyl deoxynivalenol type and only 4 (3%) isolates were of the 3-acetyl deoxynivalenol type. The 10 VNTR markers revealed 124 distinct haplotypes and 76 polymorphic alleles across the whole population. The two subpopulations (FA-08 and FA-09) grouped based on the year of collection exhibited low genetic differentiation (Fst = 0.032) and high gene flow (Nm = 15.13). However, a significant genetic differentiation was found within the NIV-type isolates as revealed by the Structure software. The pairwise linkage disequilibrium tests did not support the hypothesis of random mating in the population because half (48.8%) of the locus pairs showed a linkage disequilibrium (P > 0.05). Our results suggest that FHB in this nursery was caused by a genetically homogenous and non-random mating population of F. asiaticum in 2008 and 2009, which consisted of all three trichothecene types with various levels of aggressiveness.

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