A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains

The classic diallel takes a set of parents and produces offspring from all possible mating pairs. Phenotype values among the offspring can then be related back to their respective parentage. When the parents are diploid, sexed, and inbred, the diallel can characterize aggregate effects of genetic background on a phenotype, revealing effects of strain dosage, heterosis, parent of origin, epistasis, and sex-specific versions thereof. However, its analysis is traditionally intricate, unforgiving of unplanned missing information, and highly sensitive to imbalance, making the diallel unapproachable to many geneticists. Nonetheless, imbalanced and incomplete diallels arise frequently, albeit unintentionally, as by-products of larger-scale experiments that collect F1 data, for example, pilot studies or multiparent breeding efforts such as the Collaborative Cross or the Arabidopsis MAGIC lines. We present a general Bayesian model for analyzing diallel data on dioecious diploid inbred strains that cleanly decomposes the observed patterns of variation into biologically intuitive components, simultaneously models and accommodates outliers, and provides shrinkage estimates of effects that automatically incorporate uncertainty due to imbalance, missing data, and small sample size. We further present a model selection procedure for weighing evidence for or against the inclusion of those components in a predictive model. We evaluate our method through simulation and apply it to incomplete diallel data on the founders and F1's of the Collaborative Cross, robustly characterizing the genetic architecture of 48 phenotypes

Genetic Architecture of Skewed X Inactivation in the Laboratory Mouse

X chromosome inactivation (XCI) is the mammalian mechanism of dosage compensation that balances X-linked gene expression between the sexes. Early during female development, each cell of the embryo proper independently inactivates one of its two parental X-chromosomes. In mice, the choice of which X chromosome is inactivated is affected by the genotype of a cis-acting locus, the X-chromosome controlling element (Xce). Xce has been localized to a 1.9 Mb interval within the X-inactivation center (Xic), yet its molecular identity and mechanism of action remain unknown. We combined genotype and sequence data for mouse stocks with detailed phenotyping of ten inbred strains and with the development of a statistical model that incorporates phenotyping data from multiple sources to disentangle sources of XCI phenotypic variance in natural female populations on X inactivation. We have reduced the Xce candidate 10-fold to a 176 kb region located approximately 500 kb proximal to Xist. We propose that structural variation in this interval explains the presence of multiple functional Xce alleles in the genus Mus. We have identified a new allele, Xcee present in Mus musculus and a possible sixth functional allele in Mus spicilegus. We have also confirmed a parent-of-origin effect on X inactivation choice and provide evidence that maternal inheritance magnifies the skewing associated with strong Xce alleles. Based on the phylogenetic analysis of 155 laboratory strains and wild mice we conclude that Xcea is either a derived allele that arose concurrently with the domestication of fancy mice but prior the derivation of most classical inbred strains or a rare allele in the wild. Furthermore, we have found that despite the presence of multiple haplotypes in the wild Mus musculus domesticus has only one functional Xce allele, Xceb. Lastly, we conclude that each mouse taxa examined has a different functional Xce allele

Developmental Bias in Cleavage-Stage Mouse Blastomeres

The cleavage stage mouse embryo is composed of superficially equivalent blastomeres that will generate both the embryonic inner cell mass (ICM) and the supportive trophectoderm (TE). However, it remains unsettled whether the contribution of each blastomere to these two lineages can be accounted for by chance. Addressing the question of blastomere cell fate may be of practical importance, as preimplantation genetic diagnosis (PGD) requires removal of blastomeres from the early human embryo. To determine if blastomere allocation to the two earliest lineages is random, we developed and utilized a recombination-mediated, non-invasive combinatorial fluorescent labeling method for embryonic lineage tracing

Genetics of Adverse Reactions to Haloperidol in a Mouse Diallel: A Drug–Placebo Experiment and Bayesian Causal Analysis

Haloperidol is an efficacious antipsychotic drug that has serious, unpredictable motor side effects that limit its utility and cause noncompliance in many patients. Using a drug–placebo diallel of the eight founder strains of the Collaborative Cross and their F1 hybrids, we characterized aggregate effects of genetics, sex, parent of origin, and their combinations on haloperidol response. Treating matched pairs of both sexes with drug or placebo, we measured changes in the following: open field activity, inclined screen rigidity, orofacial movements, prepulse inhibition of the acoustic startle response, plasma and brain drug level measurements, and body weight. To understand the genetic architecture of haloperidol response we introduce new statistical methodology linking heritable variation with causal effect of drug treatment. Our new estimators, “difference of models” and “multiple-impute matched pairs”, are motivated by the Neyman–Rubin potential outcomes framework and extend our existing Bayesian hierarchical model for the diallel (Lenarcic et al. 2012). Drug-induced rigidity after chronic treatment was affected by mainly additive genetics and parent-of-origin effects (accounting for 28% and 14.8% of the variance), with NZO/HILtJ and 129S1/SvlmJ contributions tending to increase this side effect. Locomotor activity after acute treatment, by contrast, was more affected by strain-specific inbreeding (12.8%). In addition to drug response phenotypes, we examined diallel effects on behavior before treatment and found not only effects of additive genetics (10.2–53.2%) but also strong effects of epistasis (10.64–25.2%). In particular: prepulse inhibition showed additivity and epistasis in about equal proportions (26.1% and 23.7%); there was evidence of nonreciprocal epistasis in pretreatment activity and rigidity; and we estimated a range of effects on body weight that replicate those found in our previous work. Our results provide the first quantitative description of the genetic architecture of haloperidol response in mice and indicate that additive, dominance-like inbreeding and parent-of-origin effects contribute strongly to treatment effect heterogeneity for this drug

The <i>Xce</i> allelic series.

<p>Panel A shows the order of <i>Xce</i> allele strength. Panel B shows hypothetical distribution and mean XCI ratio skewing in female populations that are either homozygous or heterozygous for <i>Xce</i> alleles.</p

The <i>Xce</i> candidate interval based on historical data.

<p>Panel A is a phylogenetic tree that reflects the sequence divergence within the Chadwick candidate interval for inbred mouse strains with known <i>Xce</i> alleles. Inbred strains with a number one superscript have both MDA and Sanger sequencing information available, while mouse strains with a number two superscript have only MDA genotype data available. Inbred strains with no number are assumed to have identical genotypes to a closely related strain that has been genotyped. Blue and green shading denotes the subspecific origin of the Chadwick interval for each strain (<i>M. m. domesticus</i> and <i>M. m. castaneus</i>, respectively). Panel B is a physical map that shows the locations of the previous <i>Xce</i> candidate intervals <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Chadwick1" target="_blank">[26]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Cattanach8" target="_blank">[57]</a>. Below the historical candidate intervals are the results of the SDP analyses using inbred strains selected from Panel A (See Methods). Tick marks represent SDPs classified as consistent (black), inconsistent (red), and partially consistent (gray). SNPs that retain consistent SDPs after inclusion of ALS/LtJ, LEWES/EiJ, PERA/EiJ, SJL/J, TIRANO/EiJ, WSB/EiJ, and ZALENDE/EiJ in the analysis are shown as blue tick marks above consistent SDPs. Our new maximum candidate interval is shown in gray below the tick marks. The minimum candidate interval is shown in black, while regions excluded are shown in red.</p

Maternal inheritance magnifies XCI skewing.

<p>Shown is allele-specific expression from reciprocal F1 <i>Xce</i> heterozygotes. The X-axis is partitioned according to <i>Xce</i> allele pairs. The Y-axis is the ratio of allele-specific expression from the X chromosome harboring the stronger <i>Xce</i> allele. Ratios were determined using either RNAseq or pyrosequencing.</p

Natural history of <i>Xce</i>.

<p>Panel A shows a three-dimensional PCA plot based on hybridization intensity of ten MegaMUGA probes (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen-1003853-g004" target="_blank">Figure 4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853.s014" target="_blank">Table S10</a>) within the refined <i>Xce</i> candidate interval. Mouse strains with known <i>Xce</i> alleles are shown as large spheres, while predicted mouse strains and wild-mice are shown as smaller spheres. Mouse samples are shaded according to <i>Xce</i> allele or <i>Xce</i> haplotype: Known <i>Xce^a</i> allele, black; predicted <i>Xce^a</i> allele, gray; known <i>Xce^b</i> allele, blue; predicted <i>Xce^b</i> allele, light blue; known <i>Xce^c</i> allele, green; predicted <i>Xce^c</i> allele, light green; known <i>Xce^d</i> allele, orange; predicted <i>Xce^d</i> allele, yellow; known <i>Xce^d</i> allele, orange; predicted <i>Xce^d</i> allele, yellow; known <i>Xce^e</i> allele, red; predicted <i>Xce^e</i> allele, pink; known <i>Xce^f</i> allele, magenta. Panel B shows a phylogenetic tree based on 18 MDA SNP probes within the new <i>Xce</i> candidate interval. The topography of the tree accurately reflects the genetic relationship between the <i>Xce</i> alleles, however because of the limited number of SNP used to generate the tree and the ascertainment bias of the SNPs present on the MDA <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Yang1" target="_blank">[40]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Keane1" target="_blank">[41]</a>, the tree is misleading with respect to the true genetic distance between <i>Xce</i> haplotypes (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853.s004" target="_blank">Figure S4</a> for a more accurate representation of branch lengths). Open circles represent classical inbred strains with unknown <i>Xce</i> alleles; filled circles represent wild-derived or wild-caught mice with unknown <i>Xce</i> alleles; open squares represent classical inbred strains phenotyped for <i>Xce</i>; filled squares represent wild-derived strains with known <i>Xce</i> alleles. Strains with whole genome sequence data are shown with a star. We color coded the specific or subspecific origin of the candidate interval for the four major branches of the tree: red, <i>M. m. musculus</i>; blue, <i>M. m. domesticus</i>; green, <i>M. m. castaneus</i>, orange, <i>M. spretus</i>, pink, <i>Mus spicilegus </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Yalcin1" target="_blank">[53]</a>.</p

Sequence analysis of the candidate interval.

<p>In panel A, the candidate interval is show as a thick black bar. Below the candidate interval is a dotplot generated from pairwise sequence concordance in the mm9 genome assembly. Diagonal lines slanting down from left to right are duplications, while diagonal lines slanting up from left to right are inversions. Above the dotplot are arrows that show the four duplications (SD1-4) and inversion (I5) identified. Panel B is a phylogenetic tree that depicts the relationship between the duplications. The phylogenetic tree was generated using the CLUSTALW2 alignment software <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Larkin1" target="_blank">[71]</a>. Also shown are the ten MegaMUGA markers used for the PCA analysis and their positions in relation to the segmental duplications. Shown in panel C are probe hybridization plots for two of these markers, UNC31159403 and XiD2 (all plots are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853.s002" target="_blank">Figure S2</a>). The axes represent hybridization intensities for probes tracking alternative alleles at each marker. The colors correspond to the different functional <i>Xce</i> alleles: gray <i>Xce^a</i>; blue <i>Xce^b</i>; red <i>Xce^e</i>; green <i>Xce^c</i>; yellow <i>Xce^d</i>. Note that these plots do not agree with the expectations for standard biallelic variants. Typically biallelic variant plots show three distinct clusters representing homozygous A, homozygous B, or heterozygous A/B.</p