Heritability of brachydactyly type A3 in children, adolescents, and young adults from an endogamous population in eastern Nepal

Brachymesophalangia-V (BMP-V), a short and broad middle phalanx of the fifth digit, is the most common of all skeletal anomalies of the hand. When this feature appears alone, it is clinically known as brachydactyly type A3 (BDA3). A high prevalence of BDA3 has been observed among the children of the Jirel ethnic group in eastern Nepal. As part of the Jiri Growth Study, a hand-wrist radiograph is taken annually of each child to assess skeletal development. For this study the most recent radiographs of 1,357 Jirel children, adolescents, and young adults (676 boys, 681 girls), age 3-20 years, were examined for the presence or absence of BDA3, to report the prevalence and estimate the heritability of BDA3 in the Jirel population. The overall prevalence of BDA3 in this sample was 10.5% (12.9% of the males and 8.9% of the females were classified as BDA3 affected). The additive genetic heritability of BDA3 was statistically significant in this sample (h2 +/- SE = 0.87 +/- 0.16, p < 0.0001). This study is the first to estimate the prevalence and heritability of BDA3 in a large South Asian family-based sample.     

Genetic and phenotypic aspects of foot lesion scores in sheep of different breeds and ages

Footrot is a costly endemic disease of sheep. This study investigates the potential to decrease its prevalence through selective breeding for decreased lesion score. Pedigreed mule and Scottish Blackface (SBF) ewes were scored for lesions on each hoof on a 0 to 4 scale for up to 2 (SBF ewes) or 4 (mules) times over 2 years. One score was obtained for SBF lambs. An animal was deemed to have lesions (severe lesions) if at least one hoof had a score of at least 1 (2). The prevalence of lesions was 34% in lambs, 17% in SBF ewes and 51% in mules. The heritability of lesions (severe lesions) analysed as repeated measurements of the same trait in a threshold model was 0.19 (0.26) in SBF ewes and 0.12 (0.19) in mules. Estimates for the sum and maximum of scores as well as the number of feet affected were much lower, as were estimates for permanent animal effects (i.e. non-genetic effects associated with an animal). When successive scores on the same animal were analysed as correlated traits, heritability estimates for most traits tended to be higher, except for severe footrot in mules where estimates varied greatly over time. The phenotypic correlations between successive scores in SBF ewes were close to 0, genetic correlations were moderately positive (0.18 to 0.55). Correlations in mules were generally of a similar size, but some genetic correlations were higher (up to 0.92). There was a clear trend for heritabilities for lesions and severe lesions to increase with higher prevalence of lesions, even when analysed in a threshold model. Heritability estimates for traits that combine scores over several events in mules, identifying the more persistently affected animals, ranged from 0.12 to 0.23 with the highest estimates for the average number of feet that were (severely) affected in animals scored for a minimum at two events. The heritability of all lesion traits in lambs was estimated as 0. It is concluded that selection for lower lesions is possible in ewes but not lambs, and that a simple binary score at an animal level is at least as effective as a comprehensive score at hoof level. Given the low repeatability of lesion scores, repeated measures over time will improve effectiveness of selection. Selection across environments (flocks, seasons) with different prevalences of lesions scores will need to take account of variation in the heritability.     

Phenotypic and genetic trends of patellar luxation in Dutch Flat‐Coated Retrievers

Canine patellar luxation has been described in various dog breeds, with high prevalence especially in smaller dogs. Most dogs suffer from medial displacement of the patella, although in larger dogs lateral displacement is also seen. A sex predisposition has been described for females. Patellar luxation is considered a polygenic, multifactorial disorder. From 1990 to 2007, in total 3834 Flat‐Coated Retrievers were screened; 23.6% of those animals were affected with patellar luxation. Lateral displacement of the patella was most common in this breed (61% of cases), whereas medial (31% of cases) and lateral and medial (8% of cases) were less common. Unilateral involvement (51% of cases) was just as often observed as was bilateral involvement (49% of cases). Females were more often affected with patellar luxation (30% of all tested females) than were males (17% of all tested males). The heritability of patellar luxation was 0.17 ± 0.03 in this population, and breeding with one affected parent increased the prevalence of patellar luxation in offspring by 45% compared to that with two unaffected parents. Since the start of the screening program, there was an initial decrease from 28% to 18% in incidence, but this stagnated thereafter. The annual average estimated breeding values followed the same pattern. With approximately one quarter of the Dutch Flat‐Coated Retrievers being affected with patellar luxation, this population shows unusually high prevalence compared with reports in other large‐breed dogs. The heritability for patellar luxation in this population was moderate (0.17), indicating that environmental factors play a large role in the manifestation of the disorder. A screening program reduced the prevalence of patellar luxation in this breed, but improvement has recently stagnated. Inclusion of breeding values in the screening program could improve its effectiveness.     

Optimal control of hepatitis C antiviral treatment programme delivery for prevention amongst a population of injecting drug users

In most developed countries, HCV is primarily transmitted by injecting drug users (IDUs). HCV antiviral treatment is effective, and deemed cost-effective for those with no re-infection risk. However, few active IDUs are currently treated. Previous modelling studies have shown antiviral treatment for active IDUs could reduce HCV prevalence, and there is emerging interest in developing targeted IDU treatment programmes. However, the optimal timing and scale-up of treatment is unknown, given the real-world constraints commonly existing for health programmes. We explore how the optimal programme is affected by a variety of policy objectives, budget constraints, and prevalence settings. We develop a model of HCV transmission and treatment amongst active IDUs, determine the optimal treatment programme strategy over 10 years for two baseline chronic HCV prevalence scenarios (30% and 45%), a range of maximum annual budgets (￡50,000-300,000 per 1,000 IDUs), and a variety of objectives: minimising health service costs and health utility losses; minimising prevalence at 10 years; minimising health service costs and health utility losses with a final time prevalence target; minimising health service costs with a final time prevalence target but neglecting health utility losses. The largest programme allowed for a given budget is the programme which minimises both prevalence at 10 years, and HCV health utility loss and heath service costs, with higher budgets resulting in greater cost-effectiveness (measured by cost per QALY gained compared to no treatment). However, if the objective is to achieve a 20% relative prevalence reduction at 10 years, while minimising both health service costs and losses in health utility, the optimal treatment strategy is an immediate expansion of coverage over 5-8 years, and is less cost-effective. By contrast, if the objective is only to minimise costs to the health service while attaining the 20% prevalence reduction, the programme is deferred until the final years of the decade, and is the least cost-effective of the scenarios.     

Implications of multilocus inheritance for gene-disease association studies

The impact of multilocus inheritance on the power of candidate gene association studies and the parameters derived therefrom is considered. Both case-control and family-based control designs are included. When the background heritability H (i.e., residual correlation) among sibs for the disease in question is high, the power of multiplex affected sibships versus singletons is diminished compared with the situation when background heritability is low. Thus, multiplex families for association studies are most advantageous for low heritability disorders. Estimates of genotype relative risk (GRR) are also distorted in multiplex sibships compared with singletons based on background heritability. In a case-control study, GRR is inflated in multiplex families, with the degree of inflation decreasing with background heritability. By contrast, in a TDT (parental control) study, GRR is deflated in multiplex families, with the degree of deflation increasing with background heritability (and no deflation when H is 0). Considering identical twins, the difference in genotype frequencies between concordant versus discordant MZ twin pairs for the candidate gene is large when the heritability is low, but modest when the heritability is high.     

Inheritance of hypodontia in twins

The aim of this study was to establish prevalence of hypodontia in the twin sample and to assess the degree of its heritability. A study was performed in a sample of 96 twin pairs, 38 pairs being monozygotic (MZ) and 58 pairs dizygotic (DZ), from north-west Croatia. The sample included 25.82% of all twins born in the region during a ten-year period. The twin zygosity was determined according to the WHO recommendations (1996). A revised Holzinger's index (Hc') according to Allen was applied to calculate the degree of heritability. Hypodontia was found in 22 out of the total of 192 twins analyzed (11.5%). Among 96 pairs of twins, hypodontia was observed in 17 pairs (7 MZ and 10 DZ pairs). Among the MZ, 4 pairs were found to be concordant for hypodontia, among the DZ one pair only. The heritability index was 0825. A prevalence of hypodontia in twins observed in this study is significantly higher than in the general population. A high index of heritability (Hc' = 0.825) points to a high genetic determination.     

Prevalence of neural tube defects in South Australia, 1966-91: effectiveness and impact of prenatal diagnosis.

OBJECTIVE--To determine trends in total prevalence of neural tube defects in South Australia during 1966-91, the impact of prenatal diagnosis on birth prevalence, and the effectiveness of prenatal screening for neural tube defects in 1986-91. DESIGN--All births and terminations of pregnancy affected by neural tube defects and information on prenatal screening were ascertained from multiple sources including the South Australian perinatal and abortion statistics collections, birth defects register, and state maternal serum alpha fetoprotein screening programme. SETTING--Southern Australia. SUBJECTS--All 1058 births and terminations of pregnancy affected by neural tube defects in 1966-91. MAIN OUTCOME MEASURES--Total prevalence and birth prevalence of individual and all neural tube defects. The proportion of screened cases detected prenatally. RESULTS--Total prevalence of neural tube defects during 1966-91 was 2.01/1000 births with no upward or downward trend. However, birth prevalence fell significantly (by 5.1% a year), with an 84% reduction from 2.29/1000 births in 1966 to 0.35/1000 in 1991 (relative risk = 0.16, 95% confidence interval 0.07 to 0.34). The fall was 96% for anencephaly and 82% for spina bifida. 85% of defects, both open and closed, were detected before 28 weeks'' gestation in women screened by serum alpha fetoprotein or mid-trimester ultrasonography, or both, in 1986-91 (99.0% for anencephaly and 75.7% for spina bifida). CONCLUSIONS--While the total prevalence of neural tube defects in South Australia remained stable, prenatal diagnosis and termination of pregnancy resulted in an 84% fall in birth prevalence during 1966-91. Screening detected over four fifths of cases in 1986-91.     

Variation in the hematocrit of a passerine bird across life stages is mainly of environmental origin

The heritability of the hematocrit in adult, breeding pied flycatchers Ficedula hypoleuca is examined in a southern European population across seven years to see the consistency, or lack thereof, of patterns found with the trait at fledgling age where no significant heritability could be detected. While the across-years repeatability of the trait in adult, breeding birds was low but significant, heritabilities based on adult parent-adult offspring regressions controlling for assortative mating and full-sibling comparisons did not differ significantly from zero. Neither were heritability estimates affected by selection on fledgling hematocrit, as it was unrelated to local recruitment. There was no relationship between fledgling and adult hematocrit, suggesting that both behave as phenotypically plastic, different traits. This is the first study testing for the heritability of a physiological trait in birds with data from adult, free-ranging individuals.     

Disease and Polygenic Architecture: Avoid Trio Design and Appropriately Account for Unscreened Control Subjects for Common Disease

Genome-wide association studies (GWASs) are an optimal design for discovery of disease risk loci for diseases whose underlying genetic architecture includes many common causal loci of small effect (a polygenic architecture). We consider two designs that deserve careful consideration if the true underlying genetic architecture of the trait is polygenic: parent-offspring trios and unscreened control subjects. We assess these designs in terms of quantification of the total contribution of genome-wide genetic markers to disease risk (SNP heritability) and power to detect an associated risk allele. First, we show that trio designs should be avoided when: (1) the disease has a lifetime risk > 1%; (2) trio probands are ascertained from families with more than one affected sibling under which scenario the SNP heritability can drop by more than 50% and power can drop as much as from 0.9 to 0.15 for a sample of 20,000 subjects; or (3) assortative mating occurs (spouse correlation of the underlying liability to the disorder), which decreases the SNP heritability but not the power to detect a single locus in the trio design. Some studies use unscreened rather than screened control subjects because these can be easier to collect; we show that the estimated SNP heritability should then be scaled by dividing by (1 − K × u)² for disorders with population prevalence K and proportion of unscreened control subjects u. When omitting to scale appropriately, the SNP heritability of, for example, major depressive disorder (K = 0.15) would be underestimated by 28% when none of the control subjects are screened.     

Heritability of phenotypic udder traits to improve resilience to mastitis in Texel ewes

There are no estimates of the heritability of phenotypic udder traits in suckler sheep, which produce meat lambs, and whether these are associated with resilience to mastitis. Mastitis is a common disease which damages the mammary gland and reduces productivity. The aims of this study were to investigate the feasibility of collecting udder phenotypes, their heritability and their association with mastitis in suckler ewes. Udder and teat conformation, teat lesions, intramammary masses (IMM) and litter size were recorded from 10 Texel flocks in Great Britain between 2012 and 2014; 968 records were collected. Pedigree data were obtained from an online pedigree recording system. Univariate quantitative genetic parameters were estimated using animal and sire models. Linear mixed models were used to analyse continuous traits and generalised linear mixed models were used to analyse binary traits. Continuous traits had higher heritabilities than binary with teat placement and teat length heritability (h²) highest at 0.35 (SD 0.04) and 0.42 (SD 0.04), respectively. Udder width, drop and separation heritabilities were lower and varied with udder volume. The heritabilities of IMM and teat lesions (sire model) were 0.18 (SD 0.12) and 0.17 (SD 0.11), respectively. All heritabilities were sufficiently high to be in a selection programme to increase resilience to mastitis in the population of Texel sheep. Further studies are required to investigate genetic relationships between traits and to determine whether udder traits predict IMM, and the potential benefits from including traits in a selection programme to increase resilience to chronic mastitis.     

Heritability and segregation analysis of deafness in U.S. Dalmatians

Hereditary loss of hearing affects many breeds of the domestic dog, but the Dalmatian has the highest prevalence. Approximately 30% are affected in the United States (U.S.) population. It is widely accepted that a relationship exists between deafness and pigmentation in the dog and also in other animals. While the Dalmatian exemplifies this relationship, the genetic origin and mode of inheritance of deafness in this breed are unknown. The goals of this study were to: (1) estimate the heritability of deafness in an extended kindred of U.S. Dalmatians and (2) determine, through complex segregation analysis, whether there is a major segregating locus that has a large effect on the expression of deafness. A kindred of 266 Dalmatians was assembled, of which 199 had been diagnosed using the brainstem auditory evoked response to determine auditory status. Of these, 74.4% (N = 148) had normal hearing, 18.1% (N = 36) were unilaterally deaf, and 7.5% (N = 15) were bilaterally deaf. A heritability of 0.73 was estimated considering deafness a dichotomous trait and 0.75 considering it as a trichotomous trait. Although deafness in the Dalmatian is clearly heritable, the evidence for the presence of a single major gene affecting the disorder is not persuasive.     

Combining Ability and Heritability Analysis of Bolting Character of Non heading Chinese Cabbage

Combining ability and heritability of bolting character of four non heading Chinese cabbage inbred lines were analyzed using Griffing diallel cross I. The results showed that the general combining ability of inbred lines M11 1 2 and M11 1 4 were better, with as bolting resistant potential parental material. The broad sense heritability and narrow sense heritability of bolting character were 9742% and 9141% respectively, and mainly affected by additive genes.So,the selection of bolting characters in non heading Chinese cabbage was effective in early generations.     

Dominance and environmental variances: their effect on heritabilities estimated from twin data

A method for partitioning genetic variance estimated from twin data into additive and dominance variances was presented using Falconer's variance component model. The effects of dominance and environmental variances on a number of heritability estimates were also reviewed. A heritability estimate, based on the analysis of variance and the genetic variance estimates presented by HASEMAN and ELSTON and CHRISTIAN et al. which utilizes all available information from twin data, was proposed and discussed. This estimate seems to be the least affected by fluctuations in the magnitudes of dominance and environmental variances.     

Pollution Breaks Down the Genetic Architecture of Life History Traits in Caenorhabditis elegans

When pollution occurs in an environment, populations present suffer numerous negative and immediate effects on their life history traits. Their evolutionary potential to live in a highly stressful environment will depend on the selection pressure strengths and on the genetic structure, the trait heritability, and the genetic correlations between them. If expression of this structure changes in a stressful environment, it becomes necessary to quantify these changes to estimate the evolutionary potential of the population in this new environment. We studied the genetic structure for survival, fecundity, and early and late growth in isogenic lines of a Caenorhabditis elegans population subject to three different environments: a control environment, an environment polluted with uranium, and a high salt concentration environment. We found a heritability decrease in the polluted environments for fecundity and early growth, two traits that were the most heritable in the control environment. The genetic structure of the traits was particularly affected in the uranium polluted environment, probably due to generally low heritability in this environment. This could prevent selection from acting on traits despite the strong selection pressures exerted on them. Moreover, phenotypic traits were more strongly affected in the salt than in the uranium environment and the heritabilities were also lower in the latter environment. Consequently the decrease in heritability was not proportional to the population fitness reduction in the polluted environments. Our results suggest that pollution can alter the genetic structure of a C. elegans population, and thus modify its evolutionary potential.     

云南香型软米水稻资源农艺性状遗传效应研究

选取5份云南地方香型软米水稻种质资源和6份自育香型软米保持系按5×6不完全双列杂交设计(NCⅡ)配制成30个组合,采用加性-显性-上位性遗传模型,分析云南香型软米11个农艺性状的遗传效应。结果表明,云南香型软米多数农艺性状的遗传主要受加×加上位性效应、加性×环境效应、显性×环境效应的影响,还存在不同程度的加性效应和显性效应,单株产量受基因加性效应、显性效应、加×加上位性效应、加性×环境效应、显性×环境效应的影响;株高、有效穗的遗传率以普通狭义遗传率为主,其他性状的普通狭义遗传率和互作狭义遗传率均达极显著水平;产量构成性状之间存在不同类型和不同程度的遗传相关,多数性状之间以加×加上位性、加性×环境和显性×环境互作效应显著。     

The impact of population structure on genomic prediction in stratified populations

Key message

Impacts of population structure on the evaluation of genomic heritability and prediction were investigated and quantified using high-density markers in diverse panels in rice and maize.

Abstract

Population structure is an important factor affecting estimation of genomic heritability and assessment of genomic prediction in stratified populations. In this study, our first objective was to assess effects of population structure on estimations of genomic heritability using the diversity panels in rice and maize. Results indicate population structure explained 33 and 7.5 % of genomic heritability for rice and maize, respectively, depending on traits, with the remaining heritability explained by within-subpopulation variation. Estimates of within-subpopulation heritability were higher than that derived from quantitative trait loci identified in genome-wide association studies, suggesting 65 % improvement in genetic gains. The second objective was to evaluate effects of population structure on genomic prediction using cross-validation experiments. When population structure exists in both training and validation sets, correcting for population structure led to a significant decrease in accuracy with genomic prediction. In contrast, when prediction was limited to a specific subpopulation, population structure showed little effect on accuracy and within-subpopulation genetic variance dominated predictions. Finally, effects of genomic heritability on genomic prediction were investigated. Accuracies with genomic prediction increased with genomic heritability in both training and validation sets, with the former showing a slightly greater impact. In summary, our results suggest that the population structure contribution to genomic prediction varies based on prediction strategies, and is also affected by the genetic architectures of traits and populations. In practical breeding, these conclusions may be helpful to better understand and utilize the different genetic resources in genomic prediction.     

Selection bias in quantitative trait loci mapping

A simulation study was performed to see whether selection affected quantitative trait loci (QTL) mapping. Populations under random selection, under selection among full-sib families, and under selection within a full-sib family were simulated each with heritability of 0.3, 0.5, and 0.7. They were analyzed with the marker spacing of 10 cM and 20 cM. The accuracy for QTL detection decreased for the populations under selection within full-sib family. Estimates of QTL effects and positions differed (P < .05) from their input values. The problems could be ignored when mapping a QTL for the populations under selection among full-sib families. A large heritability helped reduction of such problems. When the animals were selected within a full-sib family, the QTL was detected for the populations with heritability of 0.5 or larger using the marker spacing of 10 cM, and with heritability of 0.7 using the marker spacing of 20 cM. This study implied that when selection was introduced, the accuracy for QTL detection decreased and the estimates of QTL effects were biased. A caution was warranted on the decision of data (including selected animals to be genotyped) for QTL mapping.     

Changes in the expression of genetic characteristics across cohorts in skeletal deformations of farmed salmonids

Genetic analysis of disorder incidence in farmed animals is challenged by two factors. Disorders in different cohorts and environments could be caused by different factors, leading to changes in heritability and to less than unity genetic correlations across cohorts. Moreover, due to computational limitations, liability scale heritabilities at very low incidence may differ from those estimated at higher incidence. We tested whether these two dilemmas occur in skeletal deformations of farmed salmonids using multigeneration data from the Finnish rainbow trout breeding programme and previous salmonid studies. The results showed that heritability was close to zero in cohorts in which management practices maintained incidence at a low level. When there was a management failure and incidence was unusually high, heritability was elevated. This may be due to computational limitations at very low incidence and/or because deformations are induced by different factors in different cohorts. Most genetic correlations between deformations recorded in different generations were weakly to strongly positive. However, also negative correlations between generations were present, showing that high liability at one time can be genetically connected to low liability at another time. The results emphasise that genetic architecture of binary traits can be influenced by trait expression.     

Heritability of semen characteristics in dogs

Retrospective analysis was performed on semen collected from 24 dogs (parents: 14 Labrador retrievers and 10 Golden retrievers) aged between 16 and 28 months of age. The dogs were part of a large breeding programme but lived in the homes of volunteer families. The semen was subjected to a standardised examination procedure including assessment of: percentage normal motility, sperm concentration, total sperm output, percentage of live normal sperm, and total number of live normal sperm. Semen was subsequently collected from one son of each of the parents when the offspring were aged between 16 and 28 mo (offspring: 14 Labrador retrievers and 10 Golden retrievers), and was subjected to the same examination procedures conducted by the same technician. Examination of breeding records demonstrated that each of the 48 dogs achieved at least one pregnancy within a period of 3 months before to 3 months after the semen collection.There was a weak correlation between parents and offspring for each of the 5 semen parameters, although none of these were statistically significant. Narrow sense heritability measures were low for all parameters except for the heritability of high sperm motility (rN2 = 0.57) and the heritability of low total sperm output (rN2 = 0.57).It is plausible that breeding selection procedures may be useful in dog breeding programmes in an attempt to improve semen quality, although any impact upon fertility is yet to be proven.     

Spatial Aspects of Foot-Pad Dermatitis in Swedish Broilers

This study aimed at analysing spatial and spatio-temporal aspects of foot-pad dermatitis in Swedish broilers. The information on disease prevalence and severity was based on a two-year foot-health surveillance programme where information on producer, breed, feed manufacturer, region, abattoir, date of slaughter and several other variables was recorded. The level of clustering in space was analysed on 2-digit zipcode level using Moran's I test which measures similarity of location. The level of clustering in space was also analysed using the Ipop test, which takes the population at risk into consideration. The examination of time-space interaction was carried out using the Barton method and the Knox method. We found a significant (p<0.001) clustering of regions with respect to foot-pad dermatitis score using Moran's I test, and a significant (p<0.0001) clustering in space also when related to the number of flocks delivered from each region. The flocks with very high prevalence of foot-pad dermatitis were significantly (p<0.05) clustered in both time and space, i.e. the flocks with high prevalence of lesions came from the same geographic area during the same time periods. This information will permit us to focus the control efforts within the foot-health surveillance programme on specific regions in specific time periods, thus making the programme more effective.