Inheritance of hypodontia in Kerry Blue Terrier dogs

Integral segregation analysis, which earlier proved efficient in studying complex hereditary diseases in humans and have been introduced in animal genetics for several years, was used to analyze the inheritance of hypodontia by premolars in Kerry Blue Terrier dogs. Dental formulas have been determined in 598 out of 911 animals united into a single large, complex pedigree. The results of integrated segregation analysis indicated heterogeneous genetic control of different forms of hypodontia. The geneses of different premolars in dogs have been demonstrated to be described by different models of inheritance: the absence of the second premolars can be described by the recessive major-gene model, whereas the agenesis of the fourth premolars have a more complex genetic mechanism and cannot be described by the model of a simple major-gene control.     

Inheritance of litter size at birth in the Brazilian grass mouse (Akodon cursor,Sigmodontinae, Rodentia)

By means of complex segregation analysis we studied the inheritance of litter size in two large pedigrees of captive-bred colonies of the Brazilian grass mouse Akodon cursor. Genetic analysis has revealed a highly significant influence of genetic factors on the variation of litter size (heritability, h2, was estimated as 0.44). The inheritance followed the classical polygene model: neither the major-gene model nor the polygene with unequal contribution model described the data significantly better.     

Segregation analysis of phenotypic components of learning disabilities. I. Nonword memory and digit span

Dyslexia is a common and complex disorder with evidence for a genetic component. Multiple loci (i.e., quantitative-trait loci [QTLs]) are likely to be involved, but the number is unknown. Diagnosis is complicated by the lack of a standard protocol, and many diagnostic measures have been proposed as understanding of the component processes has evolved. One or more genes may, in turn, influence these measures. To date, little work has been done to evaluate the mode of inheritance of individual component-as opposed to composite-phenotypes, beyond family or twin correlation studies that initially demonstrate evidence for a genetic basis of such components. Here we use two approaches to segregation analysis in 102 nuclear families to estimate genetic models for component phenotypes associated with dyslexia: digit span and a nonword-repetition task. Both measures are related to phonological skills, one of the key component processes in dyslexia. We use oligogenic-trait segregation analysis to estimate the number of QTLs contributing to each phenotype, and we use complex segregation analysis to identify the most parsimonious inheritance models. We provide evidence in support of both a major-gene mode of inheritance for the nonword-repetition task, with approximately 2.4 contributing QTLs, and for a genetic basis of digit span, with approximately 1.9 contributing QTLs. Results obtained by reciprocal adjustment of measures suggest that genes contributing to digit span may contribute to the nonword-repetition score but that there are additional QTLs involved in nonword repetition. Our study adds to existing studies of the genetic basis of composite phenotypes related to dyslexia, by providing evidence for major-gene modes of inheritance of these single-measure component phenotypes.     

Complex segregation analysis of autism.

A complex segregation analysis of autism in 185 Utah families was carried out using the mixed model. The 209 affected individuals in these families represent nearly complete ascertainment of the autistic cases born in Utah between 1965 and 1984. The sibling recurrence risk for autism was 4.5% (95% confidence limits 2.8%-6.2%). Likelihoods were maximized for major-gene models, a polygenic model, a sibling-effect model, and a mixed model consisting of major-gene and shared-sibling effects. The analysis provided no evidence for major-locus inheritance of autism. Subdivision of the sample according to the probands' IQ levels showed that sibling recurrence risk did not vary consistently with IQ level. A segregation analysis of families in which the proband had an IQ less than 50 also failed to provide evidence for a major locus. However, because of the etiologic heterogeneity of this disorder, genetic analysis of other meaningful subsets of families could prove informative.     

Complex segregation analysis of dilated cardiomyopathy (DCM) in Irish wolfhounds

The objective of the present study was to analyse the mode of inheritance for dilated cardiomyopathy (DCM) in Irish wolfhounds using regressive logistic models by testing for mechanisms of genetic transmission. Insights from this spontaneous animal model should aid importantly in understanding basic pathogenic mechanisms with regard to genetics and molecular biology of DCM in humans. Moreover, a procedure for the simultaneous prediction of breeding values and the estimation of genotype probabilities for DCM is expected to markedly improve breeding programmes. Results of cardiovascular examinations of 1018 dogs carried out between 1987 and 2003 by one veterinarian were analysed. Data of 878 dogs from 531 litters in 147 different kennels were used for complex segregation analyses. Pedigree information was available for more than 15 generations. Male dogs were affected significantly more often by DCM than female dogs. The segregation analysis showed that among all other tested models a mixed monogenic-polygenic model including a sex-dependent allele effect best explained the segregation of affected animals in the pedigrees. A pure monogenic inheritance of DCM could be significantly rejected in favour of the major gene and most general model. The gene action of the major gene was significantly different between female and male dogs.     

Methodologies for segregation analysis and QTL mapping in plants

Most characters of biological interest and economic importance are quantitative traits. To uncover the genetic architecture of quantitative traits, two approaches have become popular in China. One is the establishment of an analytical model for mixed major-gene plus polygenes inheritance and the other the discovery of quantitative trait locus (QTL). Here we review our progress employing these two approaches. First, we proposed joint segregation analysis of multiple generations for mixed major-gene plus polygenes inheritance. Second, we extended the multilocus method of Lander and Green (1987), Jiang and Zeng (1997) to a more generalized approach. Our methodology handles distorted, dominant and missing markers, including the effect of linked segregation distortion loci on the estimation of map distance. Finally, we developed several QTL mapping methods. In the Bayesian shrinkage estimation (BSE) method, we suggested a method to test the significance of QTL effects and studied the effect of the prior distribution of the variance of QTL effect on QTL mapping. To reduce running time, a penalized maximum likelihood method was adopted. To mine novel genes in crop inbred lines generated in the course of normal crop breeding work, three methods were introduced. If a well-documented genealogical history of the lines is available, two-stage variance component analysis and multi-QTL Haseman-Elston regression were suggested; if unavailable, multiple loci in silico mapping was proposed.     

Power of the joint segregation analysis method for testing mixed major-gene and polygene inheritance models of quantitative traits

Understanding the genetic architecture of quantitative traits can greatly assist the design of strategies for their manipulation in plant-breeding programs. For a number of traits, genetic variation can be the result of segregation of a few major genes and many polygenes (minor genes). The joint segregation analysis (JSA) is a maximum-likelihood approach for fitting segregation models through the simultaneous use of phenotypic information from multiple generations. Our objective in this paper was to use computer simulation to quantify the power of the JSA method for testing the mixed-inheritance model for quantitative traits when it was applied to the six basic generations: both parents (P₁ and P₂), F₁, F₂, and both backcross generations (B₁ and B₂) derived from crossing the F₁ to each parent. A total of 1968 genetic model-experiment scenarios were considered in the simulation study to quantify the power of the method. Factors that interacted to influence the power of the JSA method to correctly detect genetic models were: (1) whether there were one or two major genes in combination with polygenes, (2) the heritability of the major genes and polygenes, (3) the level of dispersion of the major genes and polygenes between the two parents, and (4) the number of individuals examined in each generation (population size). The greatest levels of power were observed for the genetic models defined with simple inheritance; e.g., the power was greater than 90% for the one major gene model, regardless of the population size and major-gene heritability. Lower levels of power were observed for the genetic models with complex inheritance (major genes and polygenes), low heritability, small population sizes and a large dispersion of favourable genes among the two parents; e.g., the power was less than 5% for the two major-gene model with a heritability value of 0.3 and population sizes of 100 individuals. The JSA methodology was then applied to a previously studied sorghum data-set to investigate the genetic control of the putative drought resistance-trait osmotic adjustment in three crosses. The previous study concluded that there were two major genes segregating for osmotic adjustment in the three crosses. Application of the JSA method resulted in a change in the proposed genetic model. The presence of the two major genes was confirmed with the addition of an unspecified number of polygenes. Received: 18 August 2000 / Accepted: 9 March 2001     

Inheritance of litter size at birth in farmed arctic foxes (Alopex lagopus, Canidae, Carnivora)

Natural populations of the arctic fox (Alopex lagopus, Canidae, Carnivora) differ drastically in their reproductive strategy. Coastal foxes, which depend on stable food resources, produce litters of moderate size. Inland foxes feed on small rodents, whose populations are characterized by cycling fluctuation. In the years with low food supply, inland fox populations have a very low rate of reproduction. In the years with high food supply, they undergo a population explosion. To gain insight into the genetic basis of the reproductive strategy of this species, we performed complex segregation analysis of the litter size in the extended pedigree of the farmed arctic foxes involving 20,665 interrelated animals. Complex segregation analysis was performed using a mixed model assuming that the trait was under control of a major gene and a large number of additive genetic and random factors. To check the significance of any major gene effect, we used Elston-Stewart transmission probability test. Our analysis demonstrated that the inheritance of this trait can be described within the frameworks of a major gene model with recessive control of low litter size. This model was also supported by the pattern of its familial segregation and by comparison of the distributions observed in the population and that expected under our model. We suggest that a system of balanced polymorphism for litter size in the farmed population might have been established in natural populations of arctic foxes as a result of adaptation to the drastic fluctuations in prey availability.     

Evidence, from combined segregation and linkage analysis, that a variant of the angiotensin I-converting enzyme (ACE) gene controls plasma ACE levels.

The hypothesis of a genetic control of plasma angiotensin I-converting enzyme (ACE) level has been suggested both by segregation analysis and by the identification of an insertion/deletion (I/D) polymorphism of the ACE gene, a polymorphism contributing much to the variability of ACE level. To elucidate whether the I/D polymorphism was directly involved in the genetic regulation, plasma ACE activity and genotype for the I/D polymorphism were both measured in a sample of 98 healthy nuclear families. The pattern of familial correlations of ACE level was compatible with a zero correlation between spouses and equal parent-offspring and sib-sib correlations (.24 +/- .04). A segregation analysis indicated that this familial resemblance could be entirely explained by the transmission of a codominant major gene. The I/D polymorphism was associated with marked differences of ACE levels, although these differences were less pronounced than those observed in the segregation analysis. After adjustment for the polymorphism effects, the residual heritability (.280 +/- .096) was significant. Finally, a combined segregation and linkage analysis provided evidence that the major-gene effect was due to a variant of the ACE gene, in strong linkage disequilibrium with the I/D polymorphism. The marker allele I appeared always associated with the major-gene allele s characterized by lower ACE levels. The frequency of allele I was .431 +/- .025, and that of major allele s was .557 +/- .041. The major gene had codominant effects equal to 1.3 residual SDs and accounted for 44% of the total variability of ACE level, as compared with 28% for the I/D polymorphism.(ABSTRACT TRUNCATED AT 250 WORDS)     

Inheritance of dermatoglyphic asymmetry in 500 Indian pedigrees: complex segregation analysis

The major aim of this study is to determine the mode of inheritance of asymmetry of quantitative dermatoglyphic traits based on principal factors through the application of complex segregation (genetic model fitting) analyses on a large ethnically homogeneous sample of 500 Indian pedigrees (2435 individuals) of two generations. By segregation analysis of the traits- PC1_FA both Mendelian and Environmental models were rejected (< 0.001) with the General model, i.e. that despite presence of significant inheritance (rejection of Environmental model), the nature of inheritance is more complex, than Mendelian one. Although a little genetic effect was observed due to familial correlations on asymmetry traits, no evidence was found of major gene contribution to be involved, but this does not contradict the notion postulated by several earlier authors that asymmetry (fluctuating) provides a measure of developmental instability in human.     

Polymorphism of dental formula and segregation of its variants in a pedigree of Kerry Blue Terrier dogs

Polymorphism of the dental formula was analyzed in a complex pedigree of Kerry Blue Terrier. A lack of one or more lower premolars was observed in some dogs. Two different patterns of missing teeth were identified. One pattern consisted in agenesis of a second premolar, often in combination with agenesis of neighbor teeth, including the fourth premolar. In the second pattern, agenesis of a fourth premolar was expressed as an isolated abnormality. It was shown previously that the first pattern is inherited as a recessive trait with near complete penetrance. In this work, the major-gene control was demonstrated for the second pattern. This abnormality develops in 70–80% of mutant homozygotes and in no more than 20% of heterozygotes and wild-type homozygotes. It was shown that the two dentition abnormalities are controlled by different genes, which were designated LPA2 and LPA4 (Lower Premolar Agenesis).     

Identification of risk loci for necrotizing meningoencephalitis in Pug dogs

Due to their unique population structure, purebred dogs have emerged as a key model for the study of complex genetic disorders. To evaluate the utility of a newly available high-density canine whole-genome array with >170,000 single nucleotide polymorphisms (SNPs), genome-wide association was performed on a small number of case and control dogs to determine disease susceptibility loci in canine necrotizing meningoencephalitis (NME), a disorder with known non-Mendelian inheritance that shares clinical similarities with atypical variants of multiple sclerosis in humans. Genotyping of 30 NME-affected Pug dogs and 68 healthy control Pugs identified 2 loci associated with NME, including a region within dog leukocyte antigen class II on chromosome 12 that remained significant after Bonferroni correction. Our results support the utility of this high-density SNP array, confirm that dogs are a powerful model for mapping complex genetic disorders and provide important preliminary data to support in depth genetic analysis of NME in numerous affected breeds.     

病理性近视的家系研究

为了探讨我国病理性近视的遗传模式,对90个病理性近视大家系进行了分离分析。简单分离分析采用先验法和SEGRAN-B软件,进行拟合优度卡方检验,比较实际分离比与理论分离比的符合程度;复合分离分析运用SAGE-REGD软件进行孟德尔遗传模型(主基因、显性、隐性、共显性)和非孟德尔遗传模型(非传递、环境、一般)的拟合。结果显示,婚配类型为A*N的家系符合常染色体显性遗传,散发概率为13．8％,婚配类型为N*N的家系符合常染色体隐性遗传,散发概率为16．3％,但常染色体显性遗传不能除外,复合分离分析接受孟德尔遗传的显性、隐性、共显性和主基因模型,共显性模型的可能性最大,基因频率为0．21442999。因此,我国病理性近视存在常染色体显性和隐性遗传模式,并有一定比例的散发病例,具有遗传异质性。     

家族高发性2型糖尿病的遗传模式研究

对1999～2000年门诊及住院的家族高发性2型糖尿病患者为先证者的136个大家系进行研究,以探讨该病的遗传模式。对家系人群采用Falconer 法估算遗传率,用Penrose法进行多基因分析,并用S.A.G.E-REGD软件拟合A型回归Logistic模型进行复合分离分析的方法,对家族高发性2型糖尿病家系进行研究。结果表明,136个大家系的2型糖尿病遗传率为94.07%±5.84%,提示在这些家系中可能有显性主基因存在。多基因分析研究表明,在该人群中,2型糖尿病因性别不同而存在两种遗传模式。复合分离分析拒绝单纯环境模型、非传递模型、共显性模型,接受隐性模型和显性模型,但隐性模型为最佳遗传模式。因此,2型糖尿病具有高度的遗传性和遗传异质性,总体表现为多因子遗传,在部分遗传背景较一致的家系人群中可能存在由主要基因决定的常染色体显性遗传。 Abstract:This study is to explore the genetic model of type 2 diabetes mellitus (type 2 DM) among the hereditary family.One hundred and thirty-six pedigrees of familial type 2 DM were studied.The heritability of type 2 DM was estimated according to Falconer's method and the multi-factorial inheritance analyzed according to Penrose's method.Complex segregation analysis was performed using S.A.G.E-REGD.The heritability of familial type 2 DM was 9407%±5.84%.Dominant major gene might influence the genesis of type 2 DM.Analysis of multi-factorial inheritance indicated that there be two genetic patterns respectively in male and female populations.By complex segregation analysis,environment,non-transmitted and co-dominant inheritance were rejected.Autosomal dominant (AD) inheritance and autosomal recessive (AR) inheritance was accepted but AR inheritance was the best pattern.This study suggested that type 2 DM had significant heritability and genetic heterogeneity,which appeared to be a disease of multi-factorial inheritance generally and autosomal dominant (AD) inheritance in part of pedigrees.     

Chromatographic components of β-hexosaminidase in I-cell disease (Mucolipidosis II)

Summary Modes of inheritance of congenital glaucoma have been studied. Two methods of analysis, complex segregation analysis and frequency of congenital glaucoma in second- and third-degree relatives, did not permit one to retain a unitary mode of inheritance of this malformation.Genetic heterogeneity of congenital glaucoma is proposed. Recurrence risks and guidelines for genetic counseling in specified situations are given.     

New models of inheritance of complex characteristics and their use in segregation analysis of idiopathic scoliosis]

New methods of segregation analysis of alternative traits have been developed. These methods make it possible to take into account the sex and age specificity of the disease manifestation. Hence, they extend the range of genetic hypotheses to be tested and ensure the correct analysis of inheritance of complex pathologies in humans. Segregation analysis of idiopathic scoliosis performed in this study demonstrates the possibilities of the new methods. Based on pedigrees of 93 probands, it has been demonstrated for the first time that the inheritance of severe (degrees II to IV) forms of this disease can be described by a model that assumes a dominant major gene with incomplete, sex- and age-dependent penetrances of all genotypes. According to this model, severe forms of idiopathic scoliosis do not develop if the mutant allele is absent (the penetrance of genotype A1A1 is zero). The probabilities of the disease for subjects with genotypes A1A2 and A2A2 are similar and approximately equal to 0.3 and 0.5 for males and females, respectively. Mild (degree I) forms of idiopathic scoliosis are heterogeneous. A progressive disease may be expected only in the patients that carry the mutant allele.     

Identification and estimation of a QTL model and its effects

 A joint segregation analysis of a genetic system and the effects of QTLs based on the six populations P₁, F₁, P₂, B₁, B₂ and F₂ is proposed in this paper. The major steps were as follows. Firstly, under the supposition that the segregating population was composed of component distributions controlled by a major gene(s) and modified by both polygenes and environments, four groups and 17 types of genetic models, including a one major-gene model, a two major-gene model, a polygene model, and a mixed one-major gene and polygene model, were set up. Secondly, the joint maximum-likelihood function was constructed from the six generations so as to estimate the parameters of component distributions through an EM algorithm. Thirdly, the best-fitting genetic model was chosen according to Akaike’s information criterion, a likelihood-ratio test, and tests for goodness of fit. Fourthly, the related genetic parameters, including gene effects, as well as the genetic variances of major genes and polygenes, were obtained from the estimates of component distributions. Finally, the individuals in segregating populations were classified into their major-gene genotypes according to their posterior probabilities. An example of the genetic analysis of plant height of a rice cross between Nanjing No. 6 and Guangcong was used to illustrate the above procedure. The method was especially appropriate to those crops with easy to obtain hybrid seeds. Received: 11 February 1998 / Accepted: 28 May 1998     

A regressive model analysis of congenital sensorineural deafness in German Dalmatian dogs

The objective of the present study was to analyze the mode of inheritance for congenital sensorineural deafness (CSD) in German Dalmatian dogs by consideration of association between phenotypic breed characteristics and CSD. Segregation analysis with regressive logistic models was employed to test for different mechanisms of genetic transmission. Data were obtained from all three Dalmatian kennel clubs associated with the German Association for Dog Breeding and Husbandry (VDH). CSD was tested by veterinary practitioners using standardized protocols for Brainstem Auditory-Evoked Response (BAER). The sample included 1899 Dalmatian dogs from 354 litters in 169 different kennels. BAER testing results were from the years 1986 to 1999. Pedigree information was available for up to seven generations. The segregation analysis showed that a mixed monogenic-polygenic model including eye color as covariate among all other tested models best explained the segregation of affected animals in the pedigrees. The recessive major gene segregated in dogs with blue and brown eye color as well as in dogs with and without pigmented coat patches. Models which took into account the occurrence of patches, percentage of puppies tested per litter, or inbreeding coefficient gave no better adjustment to the most general (saturated) model. A procedure for the simultaneous prediction of breeding values and the estimation of genotype probabilities for CSD is expected to improve breeding programs significantly.     

The role of major gene in clubfoot.

The roles of major gene and multifactorial inheritance in the etiology of clubfoot (talipes equinovarus) were studied using Caucasian clubfoot families ascertained in Indiana. The method of analysis used was complex segregation analysis under the mixed model, in which five genetic parameters were examined to test hypotheses on major gene by displacement (t), degree of dominance (d), gene frequency (q), transmission probability (tau2), and multifactorial inheritance by heritability (H). The analysis showed that the segregation pattern of clubfoot in these families is best explained by assuming the action of a major gene with additional contribution of multifactorial inheritance. The estimates of the parameters under the best-fitting model were d = .82, t = 4.69, q = .030, tau2 = .50, and H = .17.     

Inheritance of time to flowering in chickpea in a short-season temperate environment

Time to flowering is central in determining the adaptation and productivity of chickpea in short-season temperate environments. We studied the genetic control of this trait in three crosses, 272-2 x CDC Anna, 298T-9 x CDC Anna, and 298T-9 x CDC Frontier. From each cross, 180 F2 plants and parents were evaluated for time to flowering under greenhouse conditions. In summer 2004, multiple generations including P1, F1, P2, F2, and F2:3 (also called MG5) were evaluated for time to flowering under field conditions. The data on time to flowering in the F(2) populations were continuous in distribution but deviated from normal distribution. The F2:3 families derived from this showed a bimodal distribution for time to flowering, a typical case of major-gene inheritance model with duplicate recessive epistasis. A joint segregation analysis of MG5 also revealed that time to flowering in chickpea was controlled by two major genes along with other polygenes. Late flowering was dominant over early flowering for both major genes with digenic interaction between them, mainly an additive x additive type. This information can be used to formulate the most efficient breeding strategy for improvement of time to flowering in chickpea in short-season temperate environments.