A statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci

Modification of Experimental Design and Statistical Method for Mapping Imprinted QTLs Based on Immortalized F2 Population

Genomic imprinting is an epigenetic phenomenon, which plays important roles in the growth and development of animals and plants. Immortalized F₂ (imF₂) populations generated by random cross between recombinant inbred (RI) or doubled haploid (DH) lines have been proved to have significant advantages for mapping imprinted quantitative trait loci (iQTLs), and statistical methods for this purpose have been proposed. In this paper, we propose a special type of imF₂ population (R-imF₂) for iQTL mapping, which is developed by random reciprocal cross between RI/DH lines. We also propose two modified iQTL mapping methods: two-step point mapping (PM-2) and two-step composite point mapping (CPM-2). Simulation studies indicated that: (i) R-imF₂ cannot improve the results of iQTL mapping, but the experimental design can probably reduce the workload of population construction; (ii) PM-2 can increase the precision of estimating the position and effects of a single iQTL; and (iii) CPM-2 can precisely map not only iQTLs, but also non-imprinted QTLs. The modified experimental design and statistical methods will facilitate and promote the study of iQTL mapping.

Mapping of imprinted quantitative trait loci using immortalized F2 populations

Mapping of imprinted quantitative trait loci (iQTLs) is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM) and composite interval mapping (CIM) based on conventional low-density genetic maps and point mapping (PM) and composite point mapping (CPM) based on ultrahigh-density genetic maps, using an immortalized F2 (imF2) population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM) are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.

Statistical dissection of cyto-nuclear epistasis subject to genomic imprinting in line crosses

Cytoplasm contains important metabolism reaction organelles such as mitochondria and chloroplast (in plant). In particular, mitochondria contains special DNA information which can be passed to offsprings through maternal gametes, and has been confirmed to play a pivotal role in nuclear activities. Experimental evidences have documented the importance of cyto-nuclear interactions in affecting important biological traits. While studies have also pointed out the role of interaction between imprinting nuclear DNA and cytoplasm, no statistical method has been developed to efficiently model such effect and further quantify its effect size. In this work, we developed an efficient statistical model for genome-wide estimating and testing the cytoplasmic effect, nuclear DNA imprinting effect as well as the interaction between them under reciprocal backcross and F2 designs derived from inbred lines. Parameters are estimated under maximum likelihood framework implemented with the EM algorithm. Extensive simulations show good performance in a variety of scenarios. The utility of the method is demonstrated by analyzing a published data set in an F2 family derived from C3H/HeJBir and C57BL/6 J mouse strains. Important cyto-nuclear interactions were identified. Our approach provides a quantitative framework for identifying and estimating cyto-nuclear interactions subject to genomic imprinting involved in the genetic control of complex traits.

A computational framework for the inheritance pattern of genomic imprinting for complex traits

Genetic imprinting, by which the expression of a gene depends on the parental origin of its alleles, may be subjected to reprogramming through each generation. Currently, such reprogramming is limited to qualitative description only, lacking more precise quantitative estimation for its extent, pattern and mechanism. Here, we present a computational framework for analyzing the magnitude of genetic imprinting and its transgenerational inheritance mode. This quantitative model is based on the breeding scheme of reciprocal backcrosses between reciprocal F(1) hybrids and original inbred parents, in which the transmission of genetic imprinting across generations can be tracked. We define a series of quantitative genetic parameters that describe the extent and transmission mode of genetic imprinting and further estimate and test these parameters within a genetic mapping framework using a new powerful computational algorithm. The model and algorithm described will enable geneticists to identify and map imprinted quantitative trait loci and dictate a comprehensive atlas of developmental and epigenetic mechanisms related to genetic imprinting. We illustrate the new discovery of the role of genetic imprinting in regulating hyperoxic acute lung injury survival time using a mouse reciprocal backcross design.

Characterization of genomic imprinting effects and patterns with parametric accelerated failure time model

Genomic imprinting, a genetic phenomenon of non-equivalent allele expression that depends on parental origins, has been ubiquitously observed in nature. It does not only control the traits of growth and development but also may be responsible for survival traits. Based on the accelerated failure time model, we construct a general parametric model for mapping the imprinted QTL (iQTL). Within the framework of interval mapping, maximum likelihood estimation of iQTL parameters is implemented via EM algorithm. The imprinting patterns of the detected iQTL are statistically tested according to a series of null hypotheses. BIC model selection criterion is employed to choose an optimal baseline hazard function with maximum likelihood and parsimonious parameters. Simulations are used to validate the proposed mapping procedure. A published dataset from a mouse model system was used to illustrate the proposed framework. Results show that among the five commonly used survival distributions, Log-logistic distribution is the optimal baseline hazard function for mapping QTL of hyperoxic acute lung injury (HALI) survival; under the log-logistic distribution, four QTLs were identified, in which only one QTL was inherited in Mendelian fashion, whereas others were imprinted in different imprinting patterns.

Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits

Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE–QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0–9 cM; genomic region of 5.0–10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait’s phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.

A model for transgenerational imprinting variation in complex traits

Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs) based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture model framework, this strategy provides a path to trace the parental origin of alleles from previous generations. The imprinting effects of iQTLs and their interactions with other traditionally defined genetic effects, expressed in different generations, are estimated and tested by implementing the EM algorithm. The strategy was used to map iQTLs responsible for survival time with four reciprocal F populations and test whether and how the detected iQTLs inherit their imprinting effects into the next generation. The new strategy will provide a tool for quantifying the role of imprinting effects in the creation and maintenance of phenotypic diversity and elucidating a comprehensive picture of the genetic architecture of complex traits and diseases.

Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here, we extend an algorithmic model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed differently due to their parental origin. The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from three SNPs, OPRKG36T (with two alleles G and T), OPRKA843G (with alleles A and G), and OPRKC846T (with alleles C and T), at the kappa-opioid receptor, triggers a significant effect on pain sensitivity, but with expression significantly depending on the parent from which it is inherited (p = 0.008). With a tremendous advance in SNP identification and automated screening, the model founded on haplotype discovery and statistical inference may provide a useful tool for genetic analysis of any quantitative trait with complex inheritance.

Genetic dissection of complex endosperm traits

The endosperm of plants is a major source of food, feed and industrial raw materials. The genetic analysis of endosperm traits poses numerous challenges due to the endosperm's complex genetic composition and unique physical and developmental properties. Modern molecular techniques and statistical methods have greatly improved the mapping of quantitative trait loci underlying endosperm traits and have led to revolutionary insights regarding epistatic and epigenetic effects. This article describes the current state of the methodologies used in the genetic dissection of endosperm traits and highlights practical issues and statistical concepts and procedures.

Computing genetic imprinting expressed by haplotypes

Different expression of maternally and paternally inherited alleles at certain genes is called genetic imprinting. Despite its great importance in trait formation, development, and evolution, it remains unclear how genetic imprinting operates in a complex network of interactive genes located throughout the genome. Genetic mapping has proven to be a powerful tool that can estimate the distribution and effects of imprinted genes. While traditional mapping models attempt to detect imprinted quantitative trait loci based on a linkage map constructed from molecular markers, we have developed a statistical model for estimating the imprinting effects of haplotypes composed of multiple sequenced single-nucleotide polymorphisms. The new model provides a characterization of the difference in the effect of maternally and paternally derived haplotypes, which can be used as a tool for genetic association studies at the candidate gene or genome-wide level. The model was used to map imprinted haplotype effects on body mass index in a random sample from a natural human population, leading to the detection of significant imprinted effects at the haplotype level. The new model will be useful for characterizing the genetic architecture of complex quantitative traits at the nucleotide level.

A Statistical Variance Components Framework for Mapping Imprinted Quantitative Trait Locus in Experimental Crosses

Current methods for mapping imprinted quantitative trait locus (iQTL) with inbred line crosses assume fixed QTL effects. When an iQTL segregates in experimental line crosses, combining different line crosses with similar genetic background can improve the accuracy of iQTLs inference. In this article, we develop a general interval-based statistical variance components framework to map iQTLs underlying complex traits by combining different backcross line crosses. We propose a new iQTL variance partition method based on the nature of marker alleles shared identical-by-decent (IBD) in inbred lines. Maternal effect is adjusted when testing imprinting. Efficient estimation methods with the maximum likelihood and the restricted maximum likelihood are derived and compared. Statistical properties of the proposed mapping strategy are evaluated through extensive simulations under different sampling designs. An extension to multiple QTL analysis is given. The proposed method will greatly facilitate genetic dissection of imprinted complex traits in inbred line crosses.

A statistical model for estimating maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development

Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs) that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants.

Reciprocally imprinted genes and the response to selection on one sex

We explore the theoretical consequences of limiting selection to males for the evolution of imprinted genes. We find that the efficiency of male-limited selection depends on the pattern of imprinting at an imprinted locus. When selection is strong, the maternally expressed pattern of imprinting allows faster genetic change than the reciprocal, paternally expressed pattern. When selection is relatively weak, the pattern of imprinting that permits a greater rate of genetic response to selection depends on the frequency of the favored allele: the paternally expressed pattern permits faster genetic change than does the maternally expressed pattern at low frequencies of a favored allele; at higher frequencies of a favored allele, however, the maternally expressed pattern is again more conducive to a genetic response. To our knowledge, this is the first theoretical description of a difference between the two reciprocal patterns of imprinting. The selective efficiency bias we identify between the two patterns of imprinting has implications for natural and livestock populations, which we discuss.

Functional mapping imprinted quantitative trait loci underlying developmental characteristics

Background

Genomic imprinting, a phenomenon referring to nonequivalent expression of alleles depending on their parental origins, has been widely observed in nature. It has been shown recently that the epigenetic modification of an imprinted gene can be detected through a genetic mapping approach. Such an approach is developed based on traditional quantitative trait loci (QTL) mapping focusing on single trait analysis. Recent studies have shown that most imprinted genes in mammals play an important role in controlling embryonic growth and post-natal development. For a developmental character such as growth, current approach is less efficient in dissecting the dynamic genetic effect of imprinted genes during individual ontology.

Results

Functional mapping has been emerging as a powerful framework for mapping quantitative trait loci underlying complex traits showing developmental characteristics. To understand the genetic architecture of dynamic imprinted traits, we propose a mapping strategy by integrating the functional mapping approach with genomic imprinting. We demonstrate the approach through mapping imprinted QTL controlling growth trajectories in an inbred F₂ population. The statistical behavior of the approach is shown through simulation studies, in which the parameters can be estimated with reasonable precision under different simulation scenarios. The utility of the approach is illustrated through real data analysis in an F₂ family derived from LG/J and SM/J mouse stains. Three maternally imprinted QTLs are identified as regulating the growth trajectory of mouse body weight.

Conclusion

The functional iQTL mapping approach developed here provides a quantitative and testable framework for assessing the interplay between imprinted genes and a developmental process, and will have important implications for elucidating the genetic architecture of imprinted traits.

Genetic dissection of cytonuclear epistasis in line crosses

Dissection of cytonuclear interactions is fundamentally important for understanding the genetic architecture of complex traits. Here we propose a mating design based on reciprocal crosses and extend the existing QTL mapping method to evaluate the contribution of cytoplasm and QTL x cytoplasm interactions to the phenotypic variation. Efficiency of the design and method is demonstrated via simulated data.