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Over the past 50 years a large number of methods have been proposed for estimating heritability from twin studies. The present paper describes the most commonly cited of these estimates as a first step in evaluating their usefulness. A critical review will then follow.
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Whole genome sequences (WGS) enable discovery of rare variants which may contribute to missing heritability of coronary artery disease (CAD). To measure their contribution, we apply the GREML-LDMS-I approach to WGS of 4949 cases and 17,494 controls of European ancestry from the NHLBI TOPMed program. We estimate CAD heritability at 34.3% assuming a prevalence of 8.2%. Ultra-rare (minor allele frequency ≤ 0.1%) variants with low linkage disequilibrium (LD) score contribute ~50% of the heritability. We also investigate CAD heritability enrichment using a diverse set of functional annotations: i) constraint; ii) predicted protein-altering impact; iii) cis-regulatory elements from a cell-specific chromatin atlas of the human coronary; and iv) annotation principal components representing a wide range of functional processes. We observe marked enrichment of CAD heritability for most functional annotations. These results reveal the predominant role of ultra-rare variants in low LD on the heritability of CAD. Moreover, they highlight several functional processes including cell type-specific regulatory mechanisms as key drivers of CAD genetic risk.
The genetic architecture of complex traits spans a continuum of polygenicity, yet it remains unclear how differences in polygenicity relate to the functional localization of SNP heritability across the genome. We use a MiXeR-based framework to partition heritability across 74 functional annotations covering exonic, intronic, and intergenic regions for 34 complex traits and introduce a likelihood-based annotation contribution score that quantifies annotation-specific impact on heritability. Exons account for a minority of heritability, and their contribution decreases with increasing polygenicity, from an average of 22% in less-polygenic somatic diseases and biomarkers to 13% in highly polygenic psychiatric and cognitive phenotypes. Intergenic fractions show the opposite trend, whereas intronic fractions remain relatively stable. Analysis of the broader set of functional annotations also reveals systematic differences along the polygenicity axis: highly polygenic traits show stronger contributions from comparative genomics and variant-effect scores, whereas less-polygenic traits show stronger contributions from promoter, transcription, and chromatin annotations. Together, these results indicate that the functional partitioning of heritability systematically varies with polygenicity, shifting from gene-proximal regulatory architectures to architectures shaped by numerous dispersed regulatory effects.
Personality test data from the California Psychological Inventory were collected on 99 pairs of identical and 99 pairs of fraternal adult male twins. Heritabilities were comuted for all 18 scales and compared to the heritabilities for "pure" scales with overlapping items omitted. Two of the pure scales, Responsibility and Femininity, had zero heritabilities, whereas all of the full scales had moderate to high heritabilities. It was concluded that item overlap has contributed significantly to previous failures to find evidence for the differential heritability of personality traits as measured by the CPI. CPI items were classified into genetic or environmental categories and separate factor analyses of items in these categories revealed more differences than similarities in factor structure. The genetic personality factors included Conversational Poise, Compulsiveness, and Social Ease. Environmental factors included Confidence in Leadership, Impulse Control, Philosophical Attitudes, Intellectual Interest, and Exhibitionism. Compared to the genetic factors, each of the environmental factors accounted for only a very small percentage of the variance.
Serum prostate-specific antigen (PSA) is widely used for prostate cancer screening. While the genetics of PSA levels have been studied to enhance screening accuracy, the genetic basis of PSA velocity, the rate of PSA change over time, remains unclear. The Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial, a large, randomized study with longitudinal PSA data (15,260 cancer-free males, averaging 5.34 samples per subject) and genome-wide genotype data, provides a unique opportunity to estimate PSA velocity heritability. We developed a mixed model to jointly estimate the heritability of PSA levels at age 54 and PSA velocity. To accommodate the large dataset, we implemented 2 efficient computational approaches: a partitioning and meta-analysis strategy using average information restricted maximum likelihood (AI-REML) and a fast restricted Haseman-Elston (REHE) regression method. Simulations showed that both methods yield unbiased estimates of both heritability metrics, with AI-REML providing smaller variability in the estimation of velocity heritability than REHE. Applying AI-REML to PLCO data, we estimated heritability at 0.32 (s.e. = 0.07) for baseline PSA and 0.45 (s.e. = 0.18) for PSA velocity. These findings reveal a substantial genetic contribution to PSA velocity, supporting future genome-wide studies to identify variants affecting PSA dynamics and improve PSA-based screening.
The genetic architecture of complex traits spans a continuum of polygenicity, yet it remains unclear how differences in polygenicity relate to the functional localization of SNP heritability across the genome. We use a MiXeR-based framework to partition heritability across exonic, intronic, and intergenic regions for 34 traits and introduce a likelihood-based annotation contribution score that quantifies annotation-specific impact on heritability. Exons explain a minority of heritability, and their contribution decreases with increasing polygenicity, from an average of 22% in less polygenic somatic diseases and biomarkers to 13% in highly polygenic psychiatric and cognitive phenotypes. Intergenic fractions show the opposite trend, whereas intronic fractions remain relatively stable. Analysis of a broader set of functional annotations reveals systematic differences along the polygenicity axis: highly polygenic traits show stronger contributions from comparative genomics and variant-effect scores, whereas less polygenic traits show stronger contributions in promoter, transcription, and chromatin annotations. Together, these results indicate that the functional partitioning of heritability systematically varies with polygenicity, pointing to a shift from gene-proximal regulatory architectures to architectures shaped by numerous dispersed regulatory effects as a key determinant of differences in polygenicity across traits.
Here, we report the successful implementation of heritable virus-induced genome editing (VIGE) in tomato (Solanum lycopersicum). We generated three transgenic tomato lines expressing Streptococcus pyogenes Cas9 (SpCas9) under the control of Cauliflower mosaic virus 35S (35S), S. lycopersicum ribosomal protein S5A (SlRPS5A), or S. lycopersicum YAO promoters (SlYAO). These three lines were tested for somatic and heritable editing using the tobacco rattle virus (TRV)-based system carrying guide RNAs (gRNAs) fused with mobile RNA sequences. TRV with gRNA targeted to Phytoene desaturase (SlPDS) and Downy mildew resistance 6 (SlDMR6) genes fused to mobile RNA sequences showed significant somatic editing efficiency in all three tomato lines expressing SpCas9. However, the progenies from the SlYAO promoter-driven SpCas9 tomato infected with TRV with gRNA targeted to SlDMR6 fused to the mobile RNA sequence resulted in monoallelic mutations with a frequency of 3%. Optimization of environmental conditions, such as reduced light intensity, significantly increased heritable editing frequencies, from 0% to 86% at the SlPDS and from 3% to 100% at the SlDMR6, including biallelic mutations. These findings underscore the use of appropriate promoters to express Cas nucleases and optimized environmental conditions to enhance heritable genome editing efficiency in tomato using VIGE. Furthermore, our method enables the generation of mutants without additional tissue culture or transformation once a SpCas9-expressing tomato line is established.
Vegetable grafting is a horticultural technique employed to develop specialized plant varieties by effectively enhancing resistance to both biotic and abiotic stresses, as well as improving fruit quality and yield. However, these advantageous traits are generally non-heritable. The MSH1 gene induced heritable enhancement-through-grafting (HEG) effect on growth vigor, demonstrating promising application potential. In this study, we employed the msh1 mutant tomato as a rootstock to induce heritable superior traits and combined this approach with hybridization techniques to enhance tomato cultivars. Three Slmsh1 mutants were generated using CRISPR/Cas9 which exhibited a dwarf phenotype with whitened spots. By grafting several distinct inbred lines onto Slmsh1, we observed significant HEG, drought stress tolerance, and fruit quality. Under drought conditions, Slmsh1-grafted tomato seedlings exhibited increased biomass and enhanced drought tolerance through the regulation of antioxidant enzyme activities. Differential expression and methylation analyses of the graft progeny revealed that these heritable enhanced traits (HETs) are likely attributable to epigenetic modifications in the expression of ROS-scavenging- and hormone-related genes. Furthermore, to explore practical applications, we crossed inbred lines with HETs and evaluated the growth, yield, and fruit quality of the resulting hybrid combinations. The results indicated that these hybrid combinations improved fruit yield and quality, enhancing the total soluble solids, soluble sugar, and soluble protein content. These findings suggest that Slmsh1-grafted progenies enhanced plant biomass and drought resistance, while their hybrid combinations positively influenced root growth, yield, and fruit quality, providing new insights into the synergistic integration of genome editing and conventional breeding.
Heritable translocation and dominant lethal tests were conducted with random-bred Swiss albino male mice. The animals were provided drinking water containing triethylenemelamine (TEM) for 4 weeks, and were then mated for 3 successive weeks for analysis of dominant lethality and production of F1 progeny. Potential translocation carriers among F1 males were selected after two breedings and confirmed by cytogenetic analysis. Translocation heterozygotes were obtained in offspring of the TEM-treated groups, but not in the control groups. In F1 males produced from the first week of mating, the frequencies of translocations were 0, 1.78 6.2 and 10.0% for the control group and groups receiving TEM at 0.0125, 0.025 and 0.050 mg/kg/day, respectively, and in those produced from the third week of mating, the values were 0 and 2.1%, respectively, for the control group and the group receiving TEM at 0.050 mg/kg/day. F1 males from the second week of mating were not studied for the induction of heritable translocations. TEM-induced dominant lethality and heritable translocations were most prominent in the first week of mating after 4 weeks of treatment. In addition, heritable translocations appeared to be a more sensitive endpoint than dominant lethal mutations for the measurement of mutagenic effects of TEM.
Genomic correlates of impulsivity have been identified in several genome-wide association studies (GWAS) using cross-sectional designs, but no studies have investigated the molecular genetic correlates of impulsivity phenotypes using longitudinally constructed traits. In 3860 unrelated European participants in the Avon Longitudinal Study of Parents and Children (ALSPAC), we constructed longitudinal phenotypes for delay discounting and impulsive personality traits (as measured by the UPPS-P impulsive behavior scales) via assessment at ages 24, 26, and 28. We conducted GWASs of impulsivity using both cross-sectional and longitudinal phenotypes, estimated heritability and their phenotypic and genetic correlations, and evaluated their association with recently-developed polygenic risk scores (PRSs) for the impulsivity indicators themselves and also related psychiatric conditions. Latent growth curve modeling revealed a stable intercept over time for all impulsivity phenotypes. High genetic correlation of cross-sectional measures over time suggested a stable genetic component for delay discounting (rg = 0.53-0.99) and sensation seeking (rg = 0.99). Heritability estimates of the stable longitudinal phenotypes substantively improved as compared to their cross-sectional counterparts, revealing a significant SNP-heritability for delay discounting (0.22; p = 0.03) and sensation seeking (0.35; p = 0.0007). Consistent with previous reports, GWAS and gene-based analyses revealed associations between specific longitudinal impulsivity indicators and CADM2 and NCAM1 genes. The PRSs for the impulsivity indicators and disorders related to self-regulation were also significantly associated with longitudinal impulsivity traits. Finally, we validated the associations between longitudinal impulsivity phenotypes and their PRSs in an independent 13-wave longitudinal study (n = 1019) and the benefit of longitudinal phenotypes in simulation studies. In this first longitudinal genetic study of impulsivity traits, the results revealed stable genomic correlates of delay discounting and sensation seeking over time and further validated the utility of recently-developed PRSs, both in relation to the observed traits and in connecting them to psychiatric disorders. More generally, these findings support using latent intercepts as novel longitudinal phenotypes to boost signal for heritability and genomic correlates of mechanisms contributing to psychiatric disease liability.
Heritabilities of 11 quasi-continuous skeletal traits were estimated in randombred house mice of three separate ages (1, 3, and 5 months). Three separate methods--regression, maximum likelihood correlation, and Falconer's Method--were used to obtain heritabilities for each of the separate age groups. Significant differences in the incidences of seven of the skeletal traits were found among ages, but they did not affect the heritability estimates, these estimates being pooled over ages. Heritabilities calcuated from female parents were consistently higher (by about 13%) than those from male parents, indicating the presence of maternal effects. Mid-parent estimates made by all three methods gave very similar mean levels (0.17--0.20). Although low, this level compared favorably with that expected on the basis of previously estimated rates of accumulation of genetic variance. Maternal effects estimated from full sib correlations averaged 0.08.
The origin of the word heritability remains unknown. Its usage has evolved through three stages, becoming more restrictive in its meaning along the way. In the initial stage, 1832 and possibly earlier, heritability was used to denote the hereditary transmission of characteristics or material things, simply having the capability (legally or biologically) of being inherited. The second stage, beginning around the turn of this century, followed Johannsen's classical definition of nongenetic or environmental fluctuations distinct from genotypic differences, and usage closely approximated "broad sense heritability" and Johannsen's Erblichkeit. Finally, in 1936, we come to the modern day usage of narrow sense heritability, the ratio of additive genetic variance to the total phenotypic variance within a population, and credit Dr. J.L. Lush with its origin.
Published studies show that among identical twins, lower birthweight is associated with lower adult intelligence. However, no such relation between birthweight and adult IQ exists among fraternal twins. A likely explanation for the association between birthweight and intelligence among identical twins is the identical twin transfusion syndrome which occurs only between some monochorionic identical twin pairs. The IQ scores from separated identical twins were reanalysed to explore the consequences of identical twin transfusion syndrome for IQ resemblance and heritability. Among 129 published cases of identical twin pairs reared apart, 76 pairs contained some birthweight information. The 76 pairs were separated into three classes: 23 pairs in which there was clear evidence of a substantial birthweight differences (indicating the probable existence of the identical twin transfusion syndrome), 27 pairs in which the information on birthweight was ambiguous (?), and 26 pairs in which there was clear evidence that the twins were similar in birthweight. The reanalyses showed: (1) birthweight differences are positively associated with IQ differences in the total sample of separated identical twins; (2) within the group of 23 twin pairs who showed large birthweight differences, there was a positive relation between birthweight differences and IQ differences; (3) when heritability of IQ is estimated for those twins who do not suffer large birthweight differences, the resemblance (and thus, h2/b) of the separated identical twins' IG is 0-95. Given that the average reliability of the individual IQ test is around 0-95, these data suggest that genetic factors and errors of measurement cause the individual differences in IQ among human beings. Because of the identical twin transfusion syndrome, previous studies of MZ twins have underestimated the effect of genetic factors on IQ. An analysis of the IQs for heavier and lighter birthweight twins suggests that the main effect of the identical twin transfusion syndrome is to lower the IQ of the lighter birthweight twin, rather than to raise the IQ of the more fortunate partner or to influence the IQ of both members. This reanalysis suggests that postnatal cultural and social environment produce little of the total phenotypic variation in IQ found in the normal population. In the future, investigators who use twin studies to estimated heritability must ascertain whether their identical twin pairs suffered from the identical twin transfusion syndrome. Accurate estimates of heritability can only be obtained using identical twins who do not suffer from placental circulation problems. Most likely, the identical twin transfusion syndrome produces anoxia and brain damage during early prenatal development in the smaller identical twin. The anoxia is caused by a lowering of the haemoglobin content of the smaller twin by 35% or more.
Evidence is presented that the heritability of sternopleural chaeta number in Drosophila melanogaster is influenced by the age of the parents such that estimates based upon parents 14 days and older are significantly higher than those from 3-day-old parents. The increase is generally between 60 and 100 per cent when parents with mean ages of 3 days and 21 or 28 days are compared. The age-effect on h2 is more marked with age of mother, but there is a male effect when all comparisons are made between young mothers. The increase is found with estimates of h2 based both on offspring mid-parent regression and on half sib analyses, but may be more marked with the former. The increase in h2 is significantly less when females first mated when young are used than when females kept virgin until just prior to the test of heritability are used as old mothers. Some possible causes for these effects of parental age upon heritability and the expression of quantitative characters are discussed.
T(1;13)70H/+ translocation heretozygous mice were used for assessing heritability values for chiasma frequencies and the epididymal sperm count. The chiasma frequency estimates were based on 15 son-sire pairs, the translocation heterozygotes being maintained in a Swiss random-bred genetic background. The chiasma frequencies were scored separately for the T70H/+ derived multivalent, specific pairing segments within the multivalent and the remaining bivalents. Chiasma counts within these specified parts of the genome were positively correlated. The heritability estimates, significantly greater than zero, ranged from 0.78-0.98, depending on the chromosome segments included. These results indicate a strong genetic control on a cellular basis for the formation of chiasmata in the mouse. Despite significantly positive correlations and regressions between the various chiasma frequencies and the sperm count (for which 29 pairs of observations were available), no significant heritability estimate for the sperm count was obtained. The relation between the chiasma frequency and the sperm count was weakest when the chiasma count was confined to a region of the translocation-caused multivalent in which the absence of a chiasma almost always resulted in the production of an univalent. This indicates that in the translocation heterozygotes used, the overall chiasma frequency has a greater predictive value for the sperm count than autosomal univalence alone.
Ninety-three pairs of monozygotic and 97 pairs of dizygotic middle-aged, American, male twins were studied to estimate the heritability of Type A behavior--a coronary heart disease-prone behavior pattern. Participants were given the interview assessment of Type A behavior. In addition, they completed four psychological test batteries: the Thurstone Temperament Schedule, the Jenkins Activity Survey, the California Psychological Inventory, and the Gough Adjective Check List. Type A behavior measured by interview was found to be nonheritable. Psychological test scales which significantly correlated with Type A behavior, however, generally had significant heritability estimates. Only the Adjective Check List scales, which significantly correlated with Type A, showed nonsignificant heritability estimates. Selected items from these Adjective Check List scales may provide a method for assessment of Type A behavior possibly free from genetic influence.
Heritability (h2) of a serum lipid or a serum lipoprotein concentration is the proportion of variability in that concentration, among individuals, which is associated with heredity. We derive a familiar formula for estimating heritability (h2) from a simple linear model for inheritance. The formula was implied by Fisher (1918) and by Wright (1921); it was derived from a consideration of variances by Jensen (1967), and from a consideration of path coefficients by Rao et al. (1974). The estimate of heritability (ĥ2) is ĥ2 = 2(rMZ - rDZ) for twin studies, where rMZ and rDZ are the sample intraclass correlation coefficients among monozygous and dizygous twins, respectively. We calculate ĥ2 for some published twin data (Heiberg 1974) on serum lipoprotein and serum lipid concentrations.