Commingling in the distributions of immunoglobulin levels

Commingling in the distributions of five immunoglobulins from a Canadian sample of 810 Caucasians and IgE from a US sample of 935 Caucasians was investigated. For both the Canadian and US samples significant commingling was found in the child's but not the adult's IgE distribution. Contrary to expectations based upon the major gene hypothesis for IgM, we found no evidence for commingling in the IgM distribution. Finally, the distributions of IgA, IgD and IgG all evidenced significant commingling that may be the result of a single gene effect or the operation of a discrete environmental effect.     

Genetic Polymorphism for Human Platelet Thermostable Phenol Sulfotransferase (Ts Pst) Activity

Platelet TS PST basal activity and thermal stability were measured in blood samples from 237 individuals in 50 nuclear families. Significant correlations were found among first degree relatives, confirming the previously reported familial aggregation of TS PST basal activity and thermal stability. Commingling analysis of basal TS PST activity provided evidence for multiple component distributions, and after transformation to remove skewness, segregation analysis supported a major gene hypothesis. For TS PST thermal stability, commingling analysis also provided evidence for multiple component distributions. However, segregation analyses were equivocal with regard to the presence of a major gene for thermal stability, since support for a major gene model depended on skewness. Bivariate commingling analysis, which examined thermal stability by simultaneously considering basal activity and activity after heating, suggested that genotypes, as defined by the inferred component distributions for TS PST activity, differ in thermal stability. A three-allele model is proposed as one hypothesis that may account for the combined results of basal activity and thermal stability. The results of this study indicate that a major gene polymorphism in conjunction with polygenic inheritance plays an important role in the regulation of both level of activity and thermal stability of this important drug-metabolizing enzyme in humans.     

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton‐producing and cotton‐consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome‐wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high‐density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single‐nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty‐eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high‐resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.     

重齿当归形态数量性状的分级研究

为明确重齿当归（Angelica biserrata）数量性状的分布规律,对6份种质资源的14个数量性状指标进行测定与分析。结果表明,6份种质资源的8个数量性状存在显著差异,在6个数量性状的差异不显著。14个数量性状的变异系数为6.47%~33.34%,最大的是叶面积,最小的是复叶回数。复叶回数不符合正态分布,叶序数近似于正态分布,其余数量性状均符合正态分布。叶宽、叶长、叶面积、叶周长间呈极显著正相关,相关系数为0.568~0.925,其余数量性状间的相关系数均低于0.560;主成分分析表明,10个数量性状在2个以上主成分中起主要决定作用。概率分级结果表明,去除复叶回数、叶周长、叶面积、叶长、叶序数等5个数量性状,8个数量性状被分为5个连续分布的分级,1个数量性状被分为3个连续分布的分级。     

Genetic regulation of plasma and red blood cell magnesium concentration in man. II. Segregation analysis.

A previous paper in this series reported that genetic factors play a major role in the familial transmission of plasma (P) and red blood cell (RBC) magnesium (Mg) concentrations. We report here the results of commingling analysis based on a random sample of unrelated individuals, and complex segregation analysis of a random sample of nuclear families. For RBC Mg, there is evidence for a mixture of two distributions, but not for three. For P Mg, there is no evidence for commingling. Complex segregation analysis under a mixed model yielded significant support for a major gene effect on RBC Mg, but not on P Mg. Parameter estimates indicated that the data are compatible with a rather common major gene (q = .23) for elevated RBC Mg, roughly 5% of the population being homozygotes for this gene, that the nonfamilial factors account for a small fraction of the total variance, and that the overlap of distributions of homozygotes is not large.     

Commingling in the distributions of fat-related measures in Punjabi families

The distribution of anthropometric measurements related to fatness levels is examined to determine if skewness alone accounts for the nonnormality of such measures. A mixture of two normal distributions or a single skewed distribution fit the data significantly better than a single normal in all cases. For maximum hip width, knee diameter, and weight, two skewed distributions give a better fit than one skewed distribution, rejecting the null hypothesis of a single distribution even when skewness is considered. There is evidence for three skewed component distributions for biceps skinfold. Abdomen circumference, upper arm circumference, triceps skinfold, and calf skinfold are best approximated by a one component log-normal distribution. Children and parents show slightly different patterns in skewness and kurtosis when considered separately, but differences between them do not account for the commingling found in the combined distributions.     

VARIATION IN REACTION NORMS AMONG POPULATIONS OF THE GRASS BOUTELOUA RIGIDISETA

Recent research has emphasized the importance of investigating the reaction norms of quantitative traits to understand evolution in natural environments. In this study, genetic differences in reaction norms among eight populations of the grass Bouteloua rigidiseta were examined using clonal replicates of genotypes planted in a common garden with two levels of competition (single B. rigidiseta without competition and single B. rigidiseta surrounded by four Erioneuron pilosum). The populations were found to be genetically differentiated for a variety of traits. Differences in reaction norms of size-specific fecundity (spikelet clusters per tiller number) were detected among the populations: some showed little response to competition; in others size-specific fecundity was much greater in the absence of competition. This divergence in reaction norms among these populations may be the result of past selection (including the cost of plasticity), or genetic drift.     

Population structure in the barn swallow,Hirundo rustica: a comparison between neutral DNA markers and quantitative traits

Local adaptation to variable environments can generate clinal variation in morphological traits. Alternatively, similar patterns of clinal variation may be generated simply as a result of genetic drift/migration balance. Teasing apart these different processes is a continuing focus in evolutionary ecology. We compare genetic differentiation at molecular loci and quantitative traits to analyse the effect of these different processes in a morphological latitudinal cline of the barn swallow, Hirundo rustica, breeding across Europe. The results obtained show no structuring at neutral microsatellite loci, which contrasts with positive structuring at five quantitative morphometric traits. This supports the hypothesis that the observed morphometric cline in barn swallows is the result of selection acting in a spatially heterogeneous environment. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 306–314.     

The search for causal traits of speciation: Divergent female mate preferences target male courtship song,not pheromones,in Drosophila athabasca species complex

Understanding speciation requires the identification of traits that cause reproductive isolation. This remains a major challenge since it is difficult to determine which of the many divergent traits actually caused speciation. To overcome this difficulty, we studied the sexual cue traits and behaviors associated with rapid speciation between EA and WN sympatric behavioral races of Drosophila athabasca that diverged only 16,000–20,000 years ago. First, we found that sexual isolation was essentially complete and driven primarily by divergent female mating preferences. To determine the target of female mate choice, we found that, unlike cuticular hydrocarbons (CHCs), male courtship song is highly divergent between EA and WN in both allopatry and sympatry and is not affected by latitudinal variation. We then used pheromone rub‐off experiments to show no effect of CHCs on divergent female mate choice. In contrast, both male song differences and male mating success in hybrids exhibited a large X‐effect and playback song experiments confirmed that male courtship song is indeed the target of sexual isolation. These results show that a single secondary sexual trait is a major driver of speciation and suggest that we may be overestimating the number of traits involved in speciation when we study older taxa.     

Simple inheritance of key traits distinguishing maize and teosinte

The segregation of key traits distinguishing maize and teosinte was analyzed in three F₂ and three backcross populations derived from crosses of the modern maize inbred T232 withZea mays ssp.parviglumis. These traits were (i) paired vs. single female spikelets; (ii) two-ranked vs. many-ranked ears; (iii) non-indurated vs. indurated glumes; (iv) inclination of the kernels toward the rachis, and (v) distichous vs. polystichous central staminate spike. All traits showed a simple mode of inheritance except for paired female spikes, which appeared to be controlled by two genes. The loci controlling these major changes were mapped with RFLP markers to four chromosomal regions. These results support the suggestion that maize became differentiated from teosinte with as few as five major gene changes.This paper is dedicated to the memory of Professor Jean Pernes     

Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families

Typical linkage and quantitative trait locus (QTL) analyses in forest trees have been conducted in single pedigrees with sex-averaged linkage maps. The results of a QTL analysis for wood quality and growth traits of coastal Douglas-fir using eight full-sib families, each consisting of 40 progeny, replicated on four sites are presented. The resulting map of segregating genetic markers consisted of 120 amplified fragment length polymorphism (AFLP) loci distributed across 19 linkage groups. The wood quality traits represent the widest suite of traits yet examined for QTL analysis in a tree species in a single study. Wood fiber traits showed the lowest number of QTLs (3) with relatively small effect (ca. 4%); wood density traits also showed just three QTLs but with slightly larger effect; wood chemistry traits showed more QTLs (7), while ring density traits showed many QTLs with large numbers of QTLs (78) and interesting patterns of temporal variation. Growth traits gave just five QTLs but of major effect (10–16%). Trees, with their long generation times, provide a rich resource for studies of temporal variation of QTL expression.     

Segregation analysis of fat mass and other body composition measures derived from underwater weighing.

Segregation patterns of three body composition measures which were derived from underwater weighing were evaluated in a random sample of 176 French-Canadian families. Two of the variables can be considered as primary partitions of weight (fat mass [FM] and fat-free mass [FFM]), while the remaining variable (percent body fat [%BF]) is a derived index combining the measures of both fat and fat-free weight. This study represents the first report investigating major gene effects for these measures. Segregation analyses revealed that a major locus hypothesis could not be rejected for two of the three phenotypes. The single exception was FFM, for which nearly 60% of the variance was accounted for by a non-Mendelian major effect, which may reflect environmentally based commingling or may be in part a function of gene-environment interactions or correlations. In contrast to the results for FFM, the results for each of FM and %BF were similar and suggested a major locus which accounted for 45% of the variance, with an additional 22%-26% due to a multifactorial component. Given the similarity of the major gene characteristics for these two phenotypes, the possibility that the same gene underlies both measures warrants investigation. A reasonable hypothesis is to consider genes that may influence nutrient partitioning, as the family of candidate genes to receive the major attention.     

Population differentiation in floral and life history traits ofOxalis corniculata L. (Oxalidaceae) with style length polymorphism

A quantitative genetic analysis was conducted on the amounts and distribution of variation of 20 floral, reproductive and life history traits of a self-compatible perennial,Oxalis cornlculata L. (Oxalidaceae). This species comprises two floral morphs, homostyled and long-styled, with different breeding systems. The hierarchical design of the experiments on three homostyled and three long-styled populations allowed partitioning of variation into four levels of organization using nested ANOVAs. Seven of the 20 traits examined were differentiated between homostyled and long-styled populations. Significant genetic variance components were detected in the major traits (114 of the 120 traits) examined for six populations. Average values of variance components among families within a population across 20 traits for homostyled populations were higher than those of long-styled populations. These responses likely reflect the consequences of different levels of selfing and/or mixed mating on genetic variation in the two floral morphs ofO. corniculata. Pearson product-moment correlations for family means of seven traits selected were also calculated. Two groups of trait combinations (i.e., between floral traits, and between reproductive and life history traits) showed significant family mean correlation coefficients. The origins of these varlation patterns found in different populations ofO. corniculata are discussed in terms of the underlying selective regimes operating in each population.     

Genetic control of yield related stalk traits in sugarcane

A major focus of sugarcane variety improvement programs is to increase sugar yield, which can be accomplished by either increasing the sugar content of the cane or by increasing cane yield, as the correlation between these traits is low. We used a cross between an Australian sugarcane variety Q165, and a Saccharum officinarum accession, IJ76-514, to dissect the inheritance of yield-related traits in the complex polyploid sugarcane. A population of 227 individuals was grown in a replicated field trial and evaluated over 3 years for stalk weight, stalk diameter, stalk number, stalk length and total biomass. Over 1,000 AFLP and SSR markers were scored across the population and used to identify quantitative trait loci (QTL). In total, 27 regions were found that were significant at the 5% threshold using permutation tests with at least one trait; individually, they explained from 4 to 10% of the phenotypic variation and up to 46% were consistent across years. With the inclusion of digeneic interactions, from 28 to 60% of the variation was explained for these traits. The 27 genomic regions were located on 22 linkage groups (LGs) in six of the eight homology groups (HGs) indicating that a number of alleles or quantitative trait alleles (QTA) at each QTL contribute to the trait; from one to three alleles had an effect on the traits for each QTL identified. Alleles of a candidate gene, TEOSINTE BRANCHED 1 (TB1), the major gene controlling branching in maize, were mapped in this population using either an SSR or SNP markers. Two alleles showed some association with stalk number, but unlike maize, TB1 is not a major gene controlling branching in sugarcane but only has a minor and variable effect.     

Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping

Kernel size‐related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10^?6) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10^?3) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable‐effect SNPs and the co‐localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co‐localized SNPs, of which zma‐miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma‐miR164e resulted in the down‐regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker‐assisted selection (MAS) for high‐yield breeding in maize.     

The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population

Amylose content (AC), gel consistency (GC) and gelatinazation temperature (GT) are three important traits that influence the cooking and eating quality of rice. The objective of this study was to characterize the genetic components, including main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs), that are involved in the control of these three traits. A population of doubled haploid (DH) lines derived from a cross between two indica varieties Zhenshan 97 and H94 was used, and data were collected from a field experiment conducted in two different environments. A genetic linkage map consisting of 218 simple sequence repeat (SSR) loci was constructed, and QTL analysis performed using qtlmapper 1.6 resolved the genetic components into main-effect QTLs, epistatic QTLs and QEs. The analysis detected a total of 12 main-effect QTLs for the three traits, with a QTL corresponding to the Wx locus showing a major effect on AC and GC, and a QTL corresponding to the Alk locus having a major effect on GT. Ten digenic interactions involving 19 loci were detected for the three traits, and six main-effect QTLs and two pairs of epistatic QTLs were involved in QEs. While the main-effect QTLs, especially the ones corresponding to known major loci, apparently played predominant roles in the genetic basis of the traits, under certain conditions epistatic effects and QEs also played important roles in controlling the traits. The implications of the findings for rice quality improvement are discussed.     

Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection

Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterflies Heliconius erato and H. melpomene, which are distantly related Müllerian mimics which show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping‐by‐sequencing also revealed weaker population structure in H. melpomene, suggesting the hybrid zones may have evolved differently in each species, which may also contribute to the patterns of phenotypic divergence in this system. Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role.     

Conservation of genetic diversity in old‐growth forest communities of the southeastern United States

Question: How do studies of the distribution of genetic diversity of species with different life forms contribute to the development of conservation strategies? Location: Old‐growth forests of the southeastern United States. Methods: Reviews of the plant allozyme literature are used to identify differences in genetic diversity and structure among species with different life forms, distributions and breeding systems. The general results are illustrated by case studies of four plant species characteristic of two widespread old‐growth forest communities of the southeastern United States: the Pinus palustris – Aristida stricta (Longleaf pine – wiregrass) savanna of the Coastal Plain and the Quercus – Carya – Pinus (Oak‐hickory‐pine) forest of the Piedmont. Genetic variation patterns of single‐gene and quantitative traits are also reviewed. Results: Dominant forest trees, represented by Pinus palustris(longleaf pine) and Quercus rubra (Northern red oak), maintain most of their genetic diversity within their populations whereas a higher proportion of the genetic diversity of herbaceous understorey species such as Sarracenia leucophylla and Trillium reliquum is distributed among their populations. The herbaceous species also tend to have more population‐to‐population variation in genetic diversity. Higher genetic differentiation among populations is seen for quantitative traits than for allozyme traits, indicating that interpopulation variation in quantitative traits is influenced by natural selection. Conclusion: Developing effective conservation strategies for one or a few species may not prove adequate for species with other combinations of traits. Given suitable empirical studies, it should be possible to design efficient conservation programs that maintain natural levels of genetic diversity within species of conservation interest.     

Segregation Analysis on Genetic System of Quantitative Traits in Plants

Based on the traditional polygene inheritance model of quantitative traits, the author suggests the major gene and polygene mixed inheritance model. The model was considered as a general one, while the pure major gene and pure polygene inheritance model was a specific case of the general model. Based on the proposed theory, the author established the segregation analysis procedure to study the genetic system of quantitative traits of plants. At present, this procedure can be used to evaluate the genetic effect of individual major genes (up to two to three major genes), the collective genetic effect of polygene, and their heritability value. This paper introduces how to establish the procedure, its main achievements, and its applications. An example is given to illustrate the steps, methods, and effectiveness of the procedure. Translated from Hereditas, 2005, 27(1) (in Chinese)     

No correlation between multi‐locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour

Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome‐wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the morphs which may lead to subpopulation structuring and tested for correlations between three fitness‐related traits and heterozygosity, both genome wide and at each locus separately. Despite their assortative mating pattern, the buzzard morphs were found to be genetically undifferentiated. Multilocus heterozygosity was only found to be correlated with a single fitness‐related trait, infection with the blood parasite, Leucocytozoon buteonis, and this was via interactions with vole abundance and age. One locus also showed a significant relationship with blood parasite infection and ectoparasite infestation. The vicinity of this locus contains two genes, one of which is potentially implicated in the immune system of birds. We conclude that genome‐wide heterozygosity is unlikely to be a major determinant of parasite burden and body condition in the polymorphic common buzzard.