Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana

Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.

Genetic variations at 10q26 regions near FGFR2 gene and its association with non-syndromic cleft lip with or without cleft palate

OBJECTIVES

In our study, we focussed on three SNPs in the non-coding regions near FGFR2 gene, as studies on non-coding variants in the genome are the novel trends to identify the susceptible loci for nonsyndromic cleft lip with or without cleft palate (NSCL/P). FGFR2 gene is selected as a candidate gene based on knock out animal models and the role played in syndromic forms of clefting. FGFR2 gene also plays an important role in FGF signaling pathway during craniofacial development.

METHODS

In the present study 148 case-parent triads were assessed for three SNPs rs10749408, rs11199874 and rs10788165 near FGFR2 gene by using TaqMan allelic discrimination method. Transmission disequilibrium test (TDT) was used to find the allelic association. Linkage disequilibrium (LD) between the markers was analysed using Haploview program 4.2. Haplotype transmission effects were estimated using FAMHAP package. The possible parent-of-origin effects were assessed by likelihood based approach.

RESULTS

TDT analysis of three SNPs failed to show significant transmission disortion from heterozygous parents to the affected child and are not associated with NSCL/P. Linkage disequilibrium analysis showed strong LD between rs11199874 and rs10788165 SNPs. In the haplotype TDT analysis, GG haplotype of rs11199874-rs10788165 showed significant undertransmission to affected child. No significant parent-of-origin effects were observed.

CONCLUSION

The present study on noncoding variants near FGFR2 gene is not associated with NSCL/P. As the numbers of triads included in the study are less, further studies are needed including large sample size to find association with NSCL/P.

中国人群Hedgehog通路基因与非综合征型唇腭裂的亲源效应

OBJECTIVE

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect, affecting 1.4 per 1 000 live births, and multiple genetic and environmental risk factors influencing its risk. All the known genetic risk factors accounted for a small proportion of the heritability. Several authors have suggested parent-of-origin effects (PoO) may play an important role in the etiology of this complex and heterogeneous malformation. To clarify the genetic association between PTCH1, PTCH2, SHH and SMO in hedgehog (HH) pathway and NSCL/P, as well as testing for potential PoO effects in Chinese case-parent trios.

METHODS

We tested for transmission disequilibrium tests (TDT) and PoO effects using 83 common single nucleotide polymorphic (SNP) markers of HH pathway genes from 806 NSCL/P case-parent trios. These trios were drawn from an international consortium established for a genome-wide association studies (GWAS) of non-syndromic oral clefts of multiple ethnicities. DNA samples were collected from each trio. Single marker and haplotype based analysis were performed both in TDT tests and PoO effects. SNPs were excluded if they (ⅰ) had a call rate of < 95%, (ⅱ) had a minor allele frequency (MAF) of < 0.05, (ⅲ) had Mendelian errors over all trios of >5%, (ⅳ) had a genotype distribution in the parents that deviated from the Hardy-Weinberg equilibrium (HWE) (P < 0.000 1). The process was done using Plink (version 1.07, <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml</a>). TDT test was performed in Plink v1.07. A log-linear model was used to explore PoO effects using Haplin v6.2.1 as implemented in R package v3.4.2. Significance level was assessed using the Bonferroni correction.

RESULTS

A total of 18 SNPs were dropped due to low MAF, thus leaving 65 SNPs available for the analysis. Thus the Bonferroni threshold was 7.7×10^-4 (0.05/65). Nominal significant association with NSCL/P was found at a SNP (rs4448343 in PTCH1, P=0.023) and six haplotypes (rs10512249-rs4448343, rs1461208-rs7786445, rs10512249-rs4448343, rs16909865-rs10512249-rs4448343, rs1461208-rs7786445-rs12698335, and rs288756-rs288758-rs1151790, P < 0.05). A total of six haplotypes (rs288765-rs1233563, rs12537550-rs11765352, rs872723-rs288765-rs1233563, rs288765-rs1233563-rs288756, rs6459952-rs12537550-rs11765352, and rs12537550-rs11765352-rs6971211) showed PoO effect (P < 0.05). None of the results remained significant after the Bonferroni correction (P>7.7×10^-4).

CONCLUSION

Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.

PHLDA2 gene polymorphisms and risk of HELLP syndrome and severe preeclampsia

OBJECTIVE

Pleckstrin homology-like domain, family A, member 2 (PHLDA2) is a maternally expressed imprinted gene. Loss of imprinting in PHLDA2 is associated with abnormal placental development and fetal growth restriction. Our objective was to determine whether genetic variation in PHLDA2 is also associated with risk of HELLP syndrome and preeclampsia (PE) with severe features.

STUDY DESIGN

Case (n = 162) and control (n = 33) mother-father-child triads were recruited using an internet-based method. Medical records were reviewed to verify clinical diagnosis of self-reported cases. DNA was genotyped for three polymorphisms in the PHLDA2 gene using TaqMan assays: rs13390, rs1056819, rs2583435.

MAIN OUTCOME MEASURES

To examine the association between minor alleles and haplotypes with HELLP syndrome and PE with severe features, relative risks and 95% confidence intervals were estimated using log-linear models, adjusting for the correlation between familial genotypes, using HAPLIN.

RESULTS

There was no association identified between PHLDA2 gene polymorphisms or haplotypes and HELLP syndrome and PE with severe features. No parent-of-origin effects were observed.

CONCLUSION

Genetic variation in the PHLDA2 gene is not associated with HELLP syndrome or PE with severe features.

Two Powerful Tests for Parent-of-Origin Effects at Quantitative Trait Loci on the X Chromosome

Parent-of-origin effects, which describe an occurrence where the expression of a gene depends on its parental origin, are an important phenomenon in epigenetics. Statistical methods for detecting parent-of-origin effects on autosomes have been investigated for 20 years, but the development of statistical methods for detecting parent-of-origin effects on the X chromosome is relatively new. In the literature, a class of Q-XPAT-type tests are the only tests for the parent-of-origin effects for quantitative traits on the X chromosome. In this paper, we propose two simple and powerful classes of tests to detect parent-of-origin effects for quantitative trait values on the X chromosome. The proposed tests can accommodate complete and incomplete nuclear families with any number of daughters. The simulation study shows that our proposed tests produce empirical type I error rates that are close to their respective nominal levels, as well as powers that are larger than those of the Q-XPAT-type tests. The proposed tests are applied to a real data set on Turner's syndrome, and the proposed tests give a more significant finding than the Q-C-XPAT test.

Maternal regulation of chromosomal imprinting in animals

Chromosomal imprinting requires an epigenetic system that "imprints" one of the two parental chromosomes such that it results in a heritable (cell-to-cell) change in behavior of the "imprinted" chromosome. Imprinting takes place when the parental genomes are separate, which occurs during gamete formation in the respective germ-lines and post-fertilization during the period when the parental pro-nuclei lie separately within the ooplasm of the zygote. In the mouse, chromosomal imprinting is regulated by germ-line specific DNA methylation. But the methylation machinery in the respective germ-lines does not discriminate between imprinted and non-imprinted regions. As a consequence, the mouse oocyte nucleus contains over a thousand oocyte-specific germ-line differentially methylated regions (gDMRs). Upon fertilization, the sperm provides a few hundred sperm-specific gDMRs of its own. Combined, there are around 1600 imprinted and non-imprinted gDMRs in the pro-nuclei of the newly fertilized zygote. It is a remarkable fact that beginning in the maternal ooplasm, there are mechanisms that manage to preserve DNA methylation at ~ 26 known imprinted gDMRs in the face of the ongoing genome-wide DNA de-methylation that characterizes pre-implantation development. Specificity is achieved through the binding of KRAB-zinc finger proteins to their cognate recognition sequences within the gDMRs of imprinted genes. This in turn nucleates the assembly of localized heterochromatin-like complexes that preserve methylation at imprinted gDMRs through recruitment of the maintenance methyl transferase Dnmt1. These studies have shown that a germ-line imprint may cause parent-of-origin-specific behavior only if "licensed" by mechanisms that operate post-fertilization. Study of the germ-line and post-fertilization contributions to the imprinting of chromosomes in classical insect systems (Coccidae and Sciaridae) show that the ooplasm is the likely site where imprinting takes place. By comparing molecular and genetic studies across these three species, we suggest that mechanisms which operate post-fertilization play a key role in chromosomal imprinting phenomena in animals and conserved components of heterochromatin are shared by these mechanisms.

Investigation of parent-of-origin effects induced by fenofibrate treatment on triglycerides levels

Background

Genome-wide association studies performed on triglycerides (TGs) have not accounted for epigenetic mechanisms that may partially explain trait heritability.

Results

Parent-of-origin (POO) effect association analyses using an agnostic approach or a candidate approach were performed for pretreatment TG levels, posttreatment TG levels, and pre- and posttreatment TG-level differences in the real GAW20 family data set. We detected 22 genetic variants with suggestive POO effects with at least 1 phenotype (P ≤ 10^− 5). We evaluated the association of these 22 significant genetic variants showing POO effects with close DNA methylation probes associated with TGs. A total of 18 DNA methylation probes located in the vicinity of the 22 SNPs were associated with at least 1 phenotype and 6 SNP-probe pairs were associated with DNA methylation probes at the nominal level of P < 0.05, among which 1 pair presented evidence of POO effect. Our analyses identified a paternal effect of SNP rs301621 on the difference between pre- and posttreatment TG levels (P = 1.2 × 10^− 5). This same SNP showed evidence for a maternal effect on methylation levels of a nearby probe (cg10206250; P = 0.01). Using a causal inference test we established that the observed POO effect of rs301621 was not mediated by DNA methylation at cg10206250.

Conclusions

We performed POO effect association analyses of SNPs with TGs, as well as association analyses of SNPs with DNA methylation probes. These analyses, which were followed by a causal inference test, established that the paternal effect at the SNP rs301621 is induced by treatment and is not mediated by methylation level at cg10206250.

Differential Allelic Expression of HTR1B in Suicide Victims: Genetic and Epigenetic Effect of the Cis-Acting Variants

OBJECTIVES

In the present study, we tested the allelic imbalance of the C861G single nucleotide polymorphism (SNP) of HTR1B in the frontal cortex of suicide victims.

METHODS

The study was conducted using 3 sets of samples. First, C861G allele-specific mRNA levels in the frontal cortex were compared between suicide (n = 13) and nonsuicide controls (n = 13) from the Stanley Medical Research postmortem brain collection. Second, we tested common variants in the HTR1B promoter for linkage disequilibrium (LD) with the C861G variant in an unrelated sample of suicide attempters (SA; n = 38) and non-SA (NSA; n = 42). Finally, we performed a family-based association study of the C861G and promoter variants in 162 nuclear families using suicidal behavior severity scores as phenotype.

RESULTS

We observed no alterations in the C/G expression ratio in suicide victims compared to nonsuicide controls (p = 0.370). When comparing the LD between the C861G and cis-acting SNPs, we did not find any differences in SA and NSA. There was no association between preferential transmission of cis-acting SNPs and suicidal behavior severity scores in both maternal and paternal meiosis.

CONCLUSIONS

We found several promoter variants in LD that may potentially influence the allelic imbalance in the C861G variant. However, no evidence of allelic imbalance nor parent-of-origin effects of the C861G variant was observed in suicidal behavior. Further research is required to assess this marker in larger cohorts.

A powerful parent-of-origin effects test for qualitative traits on X chromosome in general pedigrees

Background

Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of methods have been proposed to test for parent-of-origin effects on autosomes based on nuclear families and general pedigrees. Although these parent-of-origin effects tests on autosomes have been available for more than 15 years, there has been no statistical test developed to test for parent-of-origin effects on X chromosome, until the parental-asymmetry test on X chromosome (XPAT) and its extensions were recently proposed. However, these methods on X chromosome are only applicable to nuclear families and thus are not suitable for general pedigrees.

Results

In this article, we propose the pedigree parental-asymmetry test on X chromosome (XPPAT) statistic to test for parent-of-origin effects in the presence of association, which can accommodate general pedigrees. When there are missing genotypes in some pedigrees, we further develop the Monte Carlo pedigree parental-asymmetry test on X chromosome (XMCPPAT) to test for parent-of-origin effects, by inferring the missing genotypes given the observed genotypes based on a Monte Carlo estimation. An extensive simulation study has been carried out to investigate the type I error rates and the powers of the proposed tests. Our simulation results show that the proposed methods control the size well under the null hypothesis of no parent-of-origin effects. Moreover, XMCPPAT substantially outperforms the existing tests and has a much higher power than XPPAT which only uses complete nuclear families (with both parents) from pedigrees. We also apply the proposed methods to analyze rheumatoid arthritis data for their practical use.

Conclusions

The proposed XPPAT and XMCPPAT test statistics are valid and powerful in detecting parent-of-origin effects on X chromosome for qualitative traits based on general pedigrees and thus are recommended.

Electronic supplementary material

The online version of this article (10.1186/s12859-017-2001-5) contains supplementary material, which is available to authorized users.

Partitioning Phenotypic Variance Due to Parent-of-Origin Effects Using Genomic Relatedness Matrices

We propose a new method, G-REMLadp, to estimate the phenotypic variance explained by parent-of-origin effects (POEs) across the genome. Our method uses restricted maximum likelihood analysis of genome-wide genetic relatedness matrices based on individuals' phased genotypes. Genome-wide SNP data from parent child duos or trios is required to obtain relatedness matrices indexing the parental origin of offspring alleles, as well as offspring phenotype data to partition the trait variation into variance components. To calibrate the power of G-REMLadp to detect non-null POEs when they are present, we provide an analytic approximation derived from Haseman-Elston regression. We also used simulated data to quantify the power and Type I Error rates of G-REMLadp, as well as the sensitivity of its variance component estimates to violations of underlying assumptions. We subsequently applied G-REMLadp to 36 phenotypes in a sample of individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC). We found that the method does not seem to be inherently biased in estimating variance due to POEs, and that substantial correlation between parental genotypes is necessary to generate biased estimates. Our empirical results, power calculations and simulations indicate that sample sizes over 10000 unrelated parent-offspring duos will be necessary to detect POEs explaining < 10% of the variance with moderate power. We conclude that POEs tagged by our genetic relationship matrices are unlikely to explain large proportions of the phenotypic variance (i.e. > 15%) for the 36 traits that we have examined.

Identification of Parent-of-Origin-Dependent QTLs Using Bulk-Segregant Sequencing (Bulk-Seq)

Parent-of-origin effects play important roles in plant reproduction and are often mediated by epigenetic modifications at the histone or DNA level. However, the genetic basis underlying these modifications can be challenging to identify. Here, we describe an approach (Bulk-Seq) that can be used to map loci mediating parent-of-origin-dependent effects using whole-genome sequencing of pools of DNA.

Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation

BACKGROUND

Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes.

RESULTS

We compared genome-wide methylation patterns of sexually-produced, diploid embryos laid by a queen, with parthenogenetically-produced diploid embryos laid by her daughters. Thelytokous embryos inheriting two maternal genomes had fewer hypermethylated genes compared to fertilized embryos, supporting the prediction that fertilized embryos have increased methylation due to inheritance of a paternal genome. However, bisulfite PCR and sequencing of a differentially methylated gene, Stan (GB18207) showed strong allele-specific methylation that was maintained in both fertilized and thelytokous embryos. For this gene, methylation was associated with haplotype, not parent of origin.

CONCLUSIONS

The results of our study are consistent with predictions from the kin theory of genomic imprinting. However, our demonstration of allele-specific methylation based on sequence shows that genome-wide differential methylation studies can potentially confound imprinting and allele-specific methylation. It further suggests that methylation patterns are heritable or that specific sequence motifs are targets for methylation in some genes.