A genetic study on the relationship between total finger ridge count and its variability

The relationship between mean total finger ridge count (TFRC) and its variability is examined using 43 male and 34 female samples from the State of Andhra Pradesh, India, using the approach of Jantz (1977) to verify the major gene effect. The mean TFRC is found to be inversely and significantly related to its variability barring standard deviation (SD). The F ratios are highly significant and the variation of TFRC due to coefficient of variation (CV) is around 39 per cent. The values of correlations, regressions, F ratios etc., of the present study fully support the hypothesis of major gene effect on TFRC.     

Segregation analysis reveals a major gene effect in compact and cancellous bone mineral density in 2 populations

Involvement of genetic factors in determining bone mineral density (BMD) is doubtless. However, the exact nature of the genes governing BMD variation and sources for genetic determination of BMD of different parts of bone (compact and cancellous) have not been completely studied. The results of the complex segregation analyses performed in our previous study (Livshits et al. 1996) on a Turkmenian sample strongly support the hypothesis that a single Mendelian locus has a large effect on BMD. The parameter estimates for both types of bone tissue were so similar that we could assume a common gene effect for BMD variation of cancellous and compact bone. The objectives of the present study are to test again the possibility of major gene control of BMD in a different ethnic sample of pedigrees, namely, the Chuvasha. In addition, we report here the results of a bivariate segregation analysis of compact and cancellous BMD performed in both the Turkemenian and the Chuvasha samples of pedigrees. The results of the present study closely resemble the results obtained on the Turkmenian pedigrees. Likewise, the major finding of the present study is that there is a significant major gene effect on both compact and cancellous BMD; polygenic hypotheses were clearly rejected. Moreover, the results of the bivariate segregation analysis in both the Chuvasha and Turkmenian samples were similar. They lead to acceptance of the hypothesis that there is a single major locus with pleiotropy to both compact and cancellous bone.     

Detection of major gene for Gilles de la Tourette syndrome

The families of 250 consecutive, unselected patients with Tourette syndrome (TS) were analyzed. If the parents had either motor or vocal tics, but not both, there was an increased risk of both TS and tics in the offspring. The mode of inheritance of the combined tic-Tourette trait was evaluated in both nuclear families and extended pedigrees. Complex segregation analysis was carried out allowing for possible contributions from both a major autosomal locus and multifactorial inheritance of variation in the background of each genotype. The most likely mode of inheritance was a major semidominant gene, Ts, with low heritability of the multifactorial background variation. This was true regardless of assumptions about the prevalence of the disorder. The hypothesis of strict multifactorial inheritance could not be rejected with nuclear family data alone. However, the hypothesis of no major gene effect was rejected using data on 3 generations for any estimate of lifetime risk less than 12 per 1,000 in the general population. A pure recessive major gene effect was also rejected. With a gene frequency of approximately .5%, the penetrance was estimated to be about 94% in abnormal Ts/Ts homozygotes, 50% in Ts/ts heterozygotes, and less than 0.3% in normal ts/ts homozygotes. More than two of every three cases are heterozygotes, and nearly all other cases are phenocopies or new mutations. This is the first demonstration by segregation analysis of a major gene in a human neuropsychiatric disorder with a frequency approaching 1% of the population.     

Mode of inheritance of hand osteoarthritis in ethnically homogeneous pedigrees

The aim of the present study was to investigate the extent and mode of inheritance of hand osteoarthritis (OA) using a large sample of ethnically homogeneous pedigrees. Two types of segregation analysis (SA) models were examined. Type I models used the data adjusted for potential significant covariates, particularly age and sex, prior to genetic analysis. Type 11 models incorporated effects of the potential covariates into major gene penetrance functions, permitting an account of the genotype covariate-specific effect on study variables. The results of this study strongly supported the hypothesis of a major gene effect and additional multifactorial component. The best-fitting model was the Mendelian one with an additive type of inheritance. The estimates obtained using the standard three-factor variance decomposition analysis suggest that age (72.8%) and major gene (14.5%) are the main sources of interindividual differences in the development of hand OA. The contribution of the putative major gene on age- and sex-adjusted OA phenotype variation was 55% in the present study.     

Cortisone-Induced Cleft Palate in the Mouse. a Search for the Genetic Control of the Embryonic Response Trait

The cause of the difference in the mean tolerance (ED₅₀ ) to cortisone-induced cleft palate between the embryos of the A/J and C57BL/6J strains appears to be due to a small number of genes. A single major gene effect and a polygenic model, in the sense of many equal and additive genes, have been ruled out. The embryonic tolerance of C57BL/6J is greater than and dominant to that of A/J; two or three loci, possibly with independent effects, appear to explain the variability. A component of the variation in embryonic response may be associated with or linked to the major histocompatibility locus (H-2). No evidence was found to support the hypothesis of X-chromosome linked susceptibility to cortisone-induced cleft palate.     

Genome-Wide Association Studies Identifies Seven Major Regions Responsible for Iron Deficiency Chlorosis in Soybean (Glycine max)

Iron deficiency chlorosis (IDC) is a yield limiting problem in soybean (Glycine max (L.) Merr) production regions with calcareous soils. Genome-wide association study (GWAS) was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection.     

Complex segregation analysis of body height,weight and BMI in pedigree data from Middle Dalmatia,Croatia

It has recently been reported that the mode of inheritance of body height, weight and BMI in five ethnically and geographically different populations can be described in terms of a major gene (MG) model. Here, using the pedigree sample from the island populations of Middle Dalmatia, Croatia (1,312 observed individuals in 462 pedigrees), the evidence is presented that supports the above findings. By applying the usual transmission probability tests, the hypothesis has been accepted that a significant part of the variation of each one of those three basic morphological traits can be attributed to the effect of a putative large-effect gene. The effect of a putative MG is responsible for 39-50% of age and sex adjusted trait's variation and for 34-48% of the total (non age-adjusted) variation of height, weight and BMI.     

Social class,admixture, and skin color variation in Mexican-Americans and Anglo-Americans living in San Antonio,Texas

Social class may act in different ways as a barrier to gene flow in urban populations, depending on ethnicity. We test the hypothesis that biological variation is affected by social class subdivision using skin reflectance data collected for 393 Anglo-American and 930 Mexican-American adults in the major urban population of San Antonio, Texas. Two socioeconomic groups were sampled for the Anglo-American population: a middle-income transitional group and a high-income suburban group. In addition, we sampled a third socioeconomic group for Mexican-Americans: a low income barrio. Sex and age effects on skin color are minimal. Social class has no effect on skin color variation for Anglo-Americans, whereas there is a highly significant effect on social class subdivision for Mexican-Americans. Admixture estimates were derived from skin reflectance data and show that the proportion of native American ancestry decreases as social class increases.     

The Rift Valley complex as a barrier to gene flow for Anopheles gambiae in Kenya

Recent studies of Anopheles gambiae, the principal mosquito vector of malaria in Africa, suggested that the eastern Rift Valley and its surrounding areas act as a barrier to gene flow. To quantify the unique effect of these areas on gene flow, we measured genetic variation within and between populations from each side of the Rift. Low differentiation was measured between populations on each side of the Rift (mean FST < 0.008, mean RST < 0.002). However, high differentiation was measured across the Rift (mean FST = 0.104; mean RST = 0.032). Genetic diversity within populations was lower in eastern populations, suggesting that the effective population sizes (Ne) of these populations were lower than those of western populations. We partitioned the overall differentiation across the Rift into three factors: variation in Ne between populations contributed 7-20%; distance contributed 10-30%, and the remainder, corresponding to the unique effect of the Rift was 50-80%. The Rift's effect was highly significant based on FST. The greater sensitivity of FST in measuring differentiation indicated that drift and not mutation generated the differences between populations. Restricted gene exchange across several hundred kilometers on the face of intense human transportation implies that active mosquito dispersal is the major form of migration, and that migration is a multistep process, where step length is relatively short.     

A Major Gene for Resting Metabolic Rate Unassociated with Body Composition: Results from the Québec Family Study

A major gene hypothesis for resting metabolic rate (RMR) was investigated using segregation analysis (POINTER) of data on families participating in Phase 2 of the Québec Family Study. Complete analyses were conducted on RMR adjusted for age, and also on RMR adjusted for age and other covariates, primarily fat mass (FM) and fat-free mass (FFM). Prior to adjustment for covariates, support for a major gene hypothesis was equivocal — i.e., there was evidence for either a major gene or a multifactorial component (i.e., polygenic and/or familial environment). The multifactorial model was preferred over the major gene model, although the latter did segregate according to Mendelian expectations. However, after the effects of FM and FFM were accounted for, a major gene effect was unambiguous and compelling. The putative locus accounted for 57% of the variance, affected 7% of the sample, and led to high values of RMR. The lack of a significant multifactorial effect suggested that the familial etiology of RMR adjusted for FM and FFM was likely to be entirely a function of the major locus. Comparing the RMR results from pre- and post-adjustment for FM and FFM suggests a plausible hypothesis. We know from earlier studies in this sample that there is a putative major gene for FM and a major non-Mendelian effect for FFM. The current study leads us to speculate that: (1) the gene(s) affecting body size and body composition also may have an effect on RMR, and further (2) removal of the effect of the major gene(s) for body size and composition allowed for detection of an additional major gene affecting only the RMR. Thus, RMR appears to be an oligogenic trait.     

Sibling-size variation in brown trout Salmo trutta in relation to egg size and stream size

Sibling-size variation (SSV), estimated as the coefficient of variation of egg size, was investigated for 13 populations of brown trout Salmo trutta . SSV was negatively correlated with mean egg size both at the population and individual levels. After correction for the effect of mean egg size, SSV was also negatively correlated with stream size. These results provide new information about how salmonid SSV can vary at different ecological scales (individual, population and region). The results are discussed in light of competing theories for explaining SSV: (1) the passive effect hypothesis, stating that egg size variation follows passively from selection on egg size and (2) the bet-hedging hypothesis, stating that high SSV is adaptive in unpredictable environments.     

Comparative analyses of codon and amino acid usage in symbiotic island and core genome in nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum

Genes involved in the symbiotic interactions between the nitrogen-fixing endosymbiont Bradyrhizobium japonicum, and its leguminous host are mostly clustered in a symbiotic island (SI), acquired by the bacterium through a process of horizontal transfer. A comparative analysis of the codon and amino acid usage in core and SI genes/proteins of B. japonicum has been carried out in the present study. The mutational bias, translational selection, and gene length are found to be the major sources of variation in synonymous codon usage in the core genome as well as in SI, the strength of translational selection being higher in core genes than in SI. In core proteins, hydrophobicity is the main source of variation in amino acid usage, expressivity and aromaticity being the second and third important sources. But in SI proteins, aromaticity is the chief source of variation, followed by expressivity and hydrophobicity. In SI proteins, both the mean molecular weight and mean aromaticity of individual proteins exhibit significant positive correlation with gene expressivity, which violate the cost-minimization hypothesis. Investigation of nucleotide substitution patterns in B. japonicum and Mesorhizobium loti orthologous genes reveals that both synonymous and non-synonymous sites of highly expressed genes are more conserved than their lowly expressed counterparts and this conservation is more pronounced in the genes present in core genome than in SI.     

Mapping genetic loci for iron deficiency chlorosis in soybean

The objective of this study was to map genes controlling iron deficiency chlorosis in two intraspecific soybean [Glycine max (L.) Merrill] populations. Chlorosis symptoms were evaluated by visual scores and spectrometric chlorophyll determinations at the V4 stage (third trifoliolate leaf fully developed) in the field in 1993, and at V2 (first trifoliolate leaf fully developed) and V4 stages in 1994. A total of 89 RFLP and 10 SSR markers in the Pride B216 x A15 population, and 82 RFLP, 14 SSR and 1 morphological I (hilum color) markers in the Anoka x A7 population were used to map quantitative trait loci (QTL) affecting iron deficiency chlorosis. QTL with minor effects were detected on six linkage groups of the Pride B216 x A15 population, suggesting a typical polygene mechanism. In contrast, in the Anoka x A7 population, one QTL contributed an average of 72.7% of the visual score variation and 68.8% of the chlorophyll concentration variation and was mapped on linkage group N. Another QTL for visual score variation, and one for chlorophyll concentration variation were detected on linkage groups A1 and I, respectively. Due to the large LOD score and major genetic effect of the QTL on linkage group N, the quantitative data was reclassified into qualitative data fitting a one major gene model according to the means of the QTL genotypic classes. The major gene was mapped in the same interval of linkage group N using both visual scores and chlorophyll concentrations, thus verifying that one major gene is involved in segregation for iron chlorosis deficiency in the Anoka x A7 population. This study supported a previous hypothesis that two separate genetic mechanisms control iron deficiency in soybean.     

Genetic analysis of variation in the number of primary spermatocytes per cyst in Drosophila virilis

Two experiments were performed with the aim of clarifying the genetic basis of variation in the number of primary spermatocytes per cyst in the B12 strain of Drosophila virilis and identifying the chromosome responsible for the variation. First, crosses between B12, showing a mean cell number of 11.81, and strain TK with a mean of 7.91, were performed. From the results obtained, it was considered that there were two factors, i.e., a recessive gene and certain modifiers, which shifted the cell number toward a higher value in B12. Second, chromosomal analysis with a marker strain and the B12 strain revealed that the third chromosome of B12 was responsible for the major effect of changing the primary spermatocyte number, although this chromosome did not exert a sufficient effect alone, and furthermore that at least one of the modifiers located on the second chromosome.     

Independence of genetic variation between circadian rhythm and development time in the seed beetle, Callosobruchus chinensis

A positive genetic correlation between periods of circadian rhythm and developmental time supports the hypothesis that circadian clocks are implicated in the timing of development. Empirical evidence for this genetic correlation in insects has been documented in two fly species. In contrast, here we show that there is no evidence of genetic correlation between circadian rhythm and development time in the adzuki bean beetle, Callosobruchus chinensis. This species has variation that is explained by a major gene in the expression and period length of circadian rhythm between strains. In this study, we found genetic variation in development time between the strains. The development time was not covaried with either the incidence or the period length of circadian rhythm among the strains. Crosses between strains suggest that development time is controlled by a polygene. In the F₂ individuals from the crosses, the circadian rhythm is attributable to allelic variation in the major gene. Across the F₂ individuals, development time was not correlated with either the expression or the period length of circadian rhythm. Thus, we found no effects of major genes responsible for variation in the circadian rhythm on development time in C. chinensis. Our findings collectively give no support to the hypothesis that the circadian clock is involved in the regulation of development time in this species.     

几个水稻品种抽穗期主效基因与微效基因的定位研究

在构建２张ＲＦＬＰ图谱的基础上,定位分析了控制水稻抽穗期的主效基因和微效基因。在特三矮２号／Ｃ．Ｂ．群体中定位到２个主效基因和２个微效基因。该２个主基因分别位于第３、８染色体上,累加贡献率约达５０％,加性效应值分别为７天和６天,而分别位于第１、１２染色体的２个微效基因的贡献率仅分别为８．３％和９．６％,加性效应值仅为３天和４天。在外引２号／Ｃ．Ｂ．群体中定位了２个连锁于第６染色体的主效基因和１个位于第８染色体的微效基因,该２个主效基因的贡献率分别为３５．５％和２７．４％,来自外引２号的该２个基因其效应均为明显推迟抽穗,因而可推测它们为感光性基因,微效基因的贡献率仅为８．９％,基因效应值较小。     

Gene Network Polymorphism Is the Raw Material of Natural Selection: The Selfish Gene Network Hypothesis

Population genetics, the mathematical theory of modern evolutionary biology, defines evolution as the alteration of the frequency of distinct gene variants (alleles) differing in fitness over the time. The major problem with this view is that in gene and protein sequences we can find little evidence concerning the molecular basis of phenotypic variance, especially those that would confer adaptive benefit to the bearers. Some novel data, however, suggest that a large amount of genetic variation exists in the regulatory region of genes within populations. In addition, comparison of homologous DNA sequences of various species shows that evolution appears to depend more strongly on gene expression than on the genes themselves. Furthermore, it has been demonstrated in several systems that genes form functional networks, whose products exhibit interrelated expression profiles. Finally, it has been found that regulatory circuits of development behave as evolutionary units. These data demonstrate that our view of evolution calls for a new synthesis. In this article I propose a novel concept, termed the selfish gene network hypothesis, which is based on an overall consideration of the above findings. The major statements of this hypothesis are as follows. (1) Instead of individual genes, gene networks (GNs) are responsible for the determination of traits and behaviors. (2) The primary source of microevolution is the intraspecific polymorphism in GNs and not the allelic variation in either the coding or the regulatory sequences of individual genes. (3) GN polymorphism is generated by the variation in the regulatory regions of the component genes and not by the variance in their coding sequences. (4) Evolution proceeds through continuous restructuring of the composition of GNs rather than fixing of specific alleles or GN variants.     

Natural selection and the origin and maintenance of standard genetic marker systems

Natural selection has always been assumed to be the major force of evolution, but its presence has been difficult to demonstrate. A review of the evidence for selective differences among genotypes for most human genetic polymorphisms indicates there is little of a direct nature. Indirect theoretical evidence, however, seems to support a major role for natural selection, and it does not seem to support the hypothesis that most amino acid substitutions within the human species are neutral. Among small isolates, most of the gene frequency differences are most likely due to genetic drift or the founder effect, and the principal counterbalancing force is gene flow or migration. But genetic differences among the major human subdivisions do not seem to be due to the same interacting forces. One reason for the inability to detect selection has been an oversimplified view of its operation, which assigns genotypes a constant fitness in every generation. Many recent theoretical developments of more complicated kinds of selection may lead to a resolution of the problem and suggest better interpretations of the enormous amount of data on human genetic variation that is rapidly accumulating.     

Native breeds demonstrate high contributions to the molecular variation in northern European sheep

Population contribution to genetic diversity can be estimated using neutral variation. However, population expansion or hybridization of diverged ancestries may weaken correlation between neutral and non-neutral variation. Microsatellite variation was studied at 25 loci in 20 native and 12 modern or imported northern European sheep breeds. Breed contributions to total gene diversity, allelic richness and mean allele-sharing distance between individuals were measured. Indications of changes in population size and admixtures of divergent ancestries were investigated and the extent of inbreeding was estimated. The northern European sheep demonstrated signs of reduction in effective population size. Many old, small populations made a substantial positive contribution to total molecular variation, but populations with several divergent major ancestries did not contribute substantially to molecular variation, with the exception of the Norwegian Rygja sheep. However, several diverged major ancestries may cause it to contribute less to non-neutral variation than expected from the microsatellite data. Breed uniqueness and within-breed variability generally had opposite effects on breed contributions to molecular diversity. The degree of inbreeding did not reflect the breed contribution to total gene diversity or allelic richness, but inbred populations increased the mean allele-sharing distance between individuals. Our study indicates breed conservation to be especially important in maintaining allelic variation in northern European sheep and supports the evolutionary importance of peripheral populations.