Unlinked Markers Research Articles

QTL affecting morphometric traits and stress response in the gilthead seabream ( Sparus aurata)

The gilthead seabream ( Sparus aurata) is an important aquaculture species that has only been subject to an incipient selective breeding programme. This study, which examined the genetic architecture of seabream morphology and stress response to confinement, takes a step toward the use of marker assisted selection in this species. Major loci affecting these traits were mapped, using data from 460 offspring derived from seven paternal and 73 maternal half-sib families. Fish were killed following a four-hour confinement experiment to induce stress, after which 15 morphometric measurements were collected and blood was sampled for DNA extraction and plasma cortisol level determination. Heritabilities for the morphometric traits were moderate to high (0.24–0.58), with genetic and phenotypic correlations between the traits generally very high. However, the heritability of plasma cortisol level was not significantly different from zero. A population-specific genetic linkage map was built for 56 microsatellite markers, comprising 16 linkage groups (LG) and ten unlinked markers. Half-sib and variance components QTL analyses detected a single genome-wide significant QTL (SaimbcF7b), a single unlinked marker explaining 13–23% of the phenotypic variance in the majority of the morphometric traits. Several other putative QTL were identified for morphometric traits (on LG 4a, 7, 9, 18, A, C, F and I), along with two other QTL (LG10 and B) that were suggestive for stress response. Fitting body weight as a covariate for the morphometric traits resulted in three genome-wide significant QTL affecting aspects of body shape independent of overall body size. For stress response we only identified suggestive evidence for QTL. These findings contribute to understanding the genetic regulation of important economic traits in seabream.

Wide Disparity in Genetic Admixture Among Mexican Americans from San Antonio, TX

We studied 706 participants of the San Antonio Family Diabetes Study (SAFDS) and 586 male samples from the San Antonio Center for Biomarkers of Risk of Prostate Cancer (SABOR) and used 64 ancestry informative markers to compare admixture proportions between both groups. Existence of population substructure was demonstrated by the excess association of unlinked markers. In the SAFDS sample, ancestral proportions were estimated at 50.2 ± 0.6% European, 46.4 ± 0.6% Native American, and 3.1 ± 0.2% West African. For the SABOR sample, the proportions were 58.9 ± 0.7%, 38.2 ± 0.7%, and 2.9 ± 0.2%, respectively. Additionally, in the SAFDS subjects a highly significant negative correlation was found between individual Native American ancestry and skin reflectance (R(2) = 0.07, P= 0.00006). The correlation was stronger in males than in females but clearly showed that ancestry only accounts for a small percentage of the variation in skin color and, conversely, that skin reflectance is not a robust surrogate for genetic admixture. Furthermore, a substantial difference in substructure is present in the two cohorts of Mexican American subjects from the San Antonio area in Texas, which emphasizes that genetic admixture estimates should be accounted for in association studies, even for geographically related subjects.

A general method to assess the utility of the X-chromosomal markers in kinship testing

In studies involving pedigree reconstruction and kinship estimation, it is acknowledged that some pedigrees have the same algebraic expressions for the joint genotypic probabilities and are, therefore, indistinguishable when considering only genetic information, no matter what the mode of transmission considered. Indeed, although standard forensic practice considers solely unlinked autosomal markers, the existence of pedigrees with the referred theoretical property (that are then said to belong to the same kinship class) is possible when considering any kind of genetic transmission. The research on genetic relatedness has always been linked to the root concept of identity-by-descent (IBD). However, although the basic theoretical core for autosomal transmission has been long formalised, a general method allowing the decision if two pedigrees linking two non-inbred individuals are distinguishable using unlinked autosomal markers along with the respective IBD partitions (and consequently the algebraic expressions for the joint genotypic probabilities) was only recently published.In this work X-chromosomal transmission will be at stake, considering that the analytical framework for X-chromosomal markers has been recently established and the importance of X-chromosome markers for these questions has been steadily growing, particularly in forensics, as a tool both to complement the information given by autosomes in complex kinship testing cases and to differentiate pedigrees belonging to the same autosomal kinship class. Therefore, here it will be presented a formal and mathematically well supported framework where a general counting rule is given, allowing a secure and expeditious decision on the usefulness of typing (unlinked) X-chromosomal markers on pairwise kinship testing involving two non-inbred individuals. Moreover the counting rule now presented allows the derivation of algebraic expressions for the joint genotypic probabilities associated with any pedigree.

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Model-based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P<0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r(2)≥0.1). Of the syntenic marker pairs separated by distances<10cM, 11-20cM, 21-50cM, and>50cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P≤0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r(2)>0.035 was found to distinguish mean r(2) values of linkage distance groups statistically from the mean r(2) values of unlinked markers; LD was found to extend to 10cM over the entire minicore collection by this criterion. However, there were large differences in r(2) values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.

Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm

Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinations and helps understanding the genetic basis of complex traits. Many factors affect LD and, therefore, it must be determined empirically in the germplasm under investigation to examine the prospects of successful genome-wide association mapping. The objectives of our study were to (1) examine the extent of LD with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in 1,537 commercial maize inbred lines belonging to four heterotic pools, (2) compare the LD patterns determined by these two marker types, (3) evaluate the number of SNP markers needed to perform genome-wide association analyses, and (4) investigate temporal trends of LD. Mean values of the squared correlation coefficient ([Formula: see text]) were almost identical for unlinked, linked, and adjacent SSR marker pairs. In contrast, [Formula: see text] values were lowest for the unlinked SNP loci and highest for the SNPs within amplicons. LD decay varied across the different heterotic pools and the individual chromosomes. The SSR markers employed in the present study are not adequate for association analysis, because of insufficient marker density for the germplasm evaluated. Based on the decay of LD in the various heterotic pools, we would need between 4,000 and 65,000 SNP markers to detect with a reasonable power associations with rather large quantitative trait loci (QTL). A much higher marker density is required to identify QTL with smaller effects. However, not only the total number of markers but also their distribution among and along the chromosomes are primordial for undertaking powerful association analyses.

A single nucleotide polymorphism (SNP) assay for population stratification test between eastern Asians in association studies

Population subdivision or recent admixture of populations can lead to spurious associations between the certain phenotypes and unlinked candidate loci in case-control and cohort studies of association. False positive associations due to population stratification can be controlled by genotyping a few dozen unlinked genetic markers. Lots of researches have reported SNP markers with high ethnic differentiation among African and European populations, but very few SNP panels can test stratification among Asians, especially in eastern Asians. Therefore, we developed the first SNP assay to test stratification between Chinese and Japanese populations living in East Asia. The ancestry informative SNP markers (AIMs) were selected from HapMap Affymetrix 500K data and evaluated on 113 unrelated subjects recruited from Xi’an City, located Northwest of China. This SNP based assay has proven very reliable, and made it possible to perform population stratification analyses with Sequenom MassARRAY SNP genotyping technology. The SNP assay showed excellent promise as a highly potential application to test population stratification in case-control studies of association in Eastern Asians. Key words: Chinese, Japanese, population stratification, ancestry informative markers (AIMs).

Barcoding type specimens helps to identify synonyms and an unnamed new species in Eumunida Smith, 1883 (Decapoda : Eumunididae)

The primary purpose of DNA-barcoding projects is to generate an efficient expertise and identification tool. This is an important challenge to the taxonomy of the 21st century, as the demand increases and the expert capacity does not. However, identifying specimens using DNA-barcodes requires a preliminary analysis to relate molecular clusters to available scientific names. Through a case study of the genus Eumunida (Decapoda : Eumunididae), we illustrate how naming molecule-based units, and thus providing an accurate DNA-based identification tool, is facilitated by sequencing type specimens. Using both morphological and unlinked molecular markers (COI and 28S genes), we analysed 230 specimens from 12 geographic areas, covering two-thirds of the known diversity of the genus, including type specimens of 13 species. Most hypotheses of species delimitation are validated, as they correspond to molecular units linked to only one taxonomic name (and vice versa). However, a putative cryptic species is also revealed and three entities previously named as distinct species may in fact belong to a single one, and thus need to be synonymised. Our analyses, which integrate the current naming rules, enhance the α-taxonomy of the genus and provide an effective identification tool based on DNA-barcodes. They illustrate the ability of DNA-barcodes, especially when type specimens are included, to pinpoint where a taxonomic revision is needed.

Variability of Osteocalcin Status in Chinese Holstein Cattle: Do Phylogeny, Vitamin D or Gene Polymorphisms Matter?

Osteocalcin (OC), a marker of bone turnover, displays patterns in relation to physiological and genetic factors. Here, we present an association study in a population of Chinese Holstein cattle (n = 24) with OC serum concentration as a phenotypic trait. We hypothesised that OC status is associated with phylogeny, vitamin D serum level and single nucleotide polymorphisms (SNPs). Mitochondrial DNA (mtDNA) was used as an unlinked marker to examine phylogeny and linkage to measured phenotypic traits of vitamin D and OC status. Following an association study with OC serum variability as the trait, genotyping of SNPs (n = 27) in OC-related genes was performed. Candidate SNPs were chosen in genes with an emphasis on the vitamin D and vitamin K pathways. Multivariant factor analysis revealed a correlation between vitamin D serum concentration and a SNP in the gene GC (rs43338565), which encodes a vitamin D-binding protein, as well as between a SNP in NFATc1 (rs42038422) and OC concentration. However, univariate analysis revealed that population structure, vitamin D serum levels and SNPs were not significant determinants of OC status in the studied group.

Linkage and linkage disequilibrium analysis of X-STRs in Italian families

Twenty X-chromosomal short tandem repeat (STR) loci were typed in 80 families of Italian descent, composed by mother and two or more sons, for a total of 93 meiosis. The analyzed X-STR panel included six clusters of closely linked markers (each spanning<3cM): DXS10135–DXS10148–DXS8378 (Xp22); DXS7132–DXS10074–DXS10079 (Xq12); DXS6801–DXS6809–DXS6789 (Xq21); DXS7424–DXS101 (Xq22); DXS10103–HPRTB–DXS10101 (Xq26); DXS8377–DXS10134–DXS7423–DXS10146 (Xq28).Recombination fractions between pairs of markers calculated by pedigree analysis were compared with those obtained from the second-generation Rutgers combined linkage-physical map of the human genome. The observed differences confirm that recombination is not homogeneous along the X chromosome and that the conventional subdivision of X-STRs in four groups of completely unlinked markers cannot be regarded as true.Significant linkage disequilibrium was found between markers DXS6801 and DXS6809 (p=0.017). The effect on likelihood calculations of inferring haplotype frequencies from allele distributions rather than haplotype count in the relevant population was evaluated.

Effect of balancing selection on spatial genetic structure within populations: theoretical investigations on the self-incompatibility locus and empirical studies in Arabidopsis halleri

The effect of selection on patterns of genetic structure within and between populations may be studied by contrasting observed patterns at the genes targeted by selection with those of unlinked neutral marker loci. Local directional selection on target genes will produce stronger population genetic structure than at neutral loci, whereas the reverse is expected for balancing selection. However, theoretical predictions on the intensity of this signal under precise models of balancing selection are still lacking. Using negative frequency-dependent selection acting on self-incompatibility systems in plants as a model of balancing selection, we investigated the effect of such selection on patterns of spatial genetic structure within a continuous population. Using numerical simulations, we tested the effect of the type of self-incompatibility system, the number of alleles at the self-incompatibility locus and the dominance interactions among them, the extent of gene dispersal, and the immigration rate on spatial genetic structure at the selected locus and at unlinked neutral loci. We confirm that frequency-dependent selection is expected to reduce the extent of spatial genetic structure as compared to neutral loci, particularly in situations with low number of alleles at the self-incompatibility locus, high frequency of codominant interactions among alleles, restricted gene dispersal and restricted immigration from outside populations. Hence the signature of selection on spatial genetic structure is expected to vary across species and populations, and we show that empirical data from the literature as well as data reported here on three natural populations of the herb Arabidopsis halleri confirm these theoretical results.

Learning Genetic Population Structures Using Minimization of Stochastic Complexity

Considerable research efforts have been devoted to probabilistic modeling of genetic population structures within the past decade. In particular, a wide spectrum of Bayesian models have been proposed for unlinked molecular marker data from diploid organisms. Here we derive a theoretical framework for learning genetic population structure of a haploid organism from bi-allelic markers for which potential patterns of dependence are a priori unknown and to be explicitly incorporated in the model. Our framework is based on the principle of minimizing stochastic complexity of an unsupervised classification under tree augmented factorization of the predictive data distribution. We discuss a fast implementation of the learning framework using deterministic algorithms.

Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon, Oncorhynchus kisutch

In quantitative genetics, multivariate statistical approaches are increasingly used to describe genetic correlations in natural populations, yet the exact genetic relationship between phenotype and genotype is often unknown. Quantitative trait locus (QTL) analyses can be used to describe the molecular basis of this relationship. In salmonids, growth and development are important fitness traits that are phenotypically correlated with each other and with other life-history traits, and an understanding of the molecular basis of these relationships is valuable for future evolutionary studies. Here, a QTL analysis using an outbred cross was initiated to determine the molecular basis of phenotypic correlations between such growth traits in coho salmon (Oncorhynchus kisutch), an important fish species distributed throughout the North Pacific Ocean. Fifty-three QTL for growth rate, length and weight at eight time periods were located on seven linkage groups (OKI03, OKI06, OKI18, OKI19, OKI23, OKI24 and an unnamed linkage group) or associated with five unlinked markers (Omm1159, Omm1367/i, Omy325UoG, OmyRGT55TUF and OtsG422UCD). One QTL for hatch timing was associated with the marker, Omm1241. All QTL were of minor effect, explaining no more than 20% of the observed variation in phenotypic value. Several instances of colocalization of QTL weight, length and growth rate were observed, suggesting a genetic basis for phenotypic correlations observed between these traits. This study lays the foundation for future QTL mapping efforts, for detailed examinations of the genetic basis of phenotypic correlations between growth traits, and for exploring the adaptive significance of growth traits in natural populations.

X-chromosome markers in kinship testing: A generalisation of the IBD approach identifying situations where their contribution is crucial

The standard practice of forensic kinship evaluation uses unlinked autosomal markers. However, X-chromosome markers have recently gained recognition as a powerful tool to complement the information provided by autosomes, particularly in complex cases. In this paper, the X-chromosome mode of transmission is addressed in the theoretical identity-by-descent framework. Formulas for the joint genotypic probabilities considering various pedigrees relating two inbred and/or non-inbred individuals are derived. Finally, the importance of X-chromosome markers is highlighted by the fact that, in addition to complementing the autosomal information, X-chromosome transmission allows differential weighting of certain hypotheses regarding pedigrees belonging to the same autosomal class, i.e., pedigrees that are indistinguishable by the use of unlinked autosomal markers. Illustrative examples of common kinship testing are shown.

General Derivation of the Sets of Pedigrees with the Same Kinship Coefficients

Quantification of kinships between two individuals using unlinked autosomal markers rests upon the identity-by-descent (IBD) probabilities among their four alleles at a locus because they determine the algebraic expressions of the joint genotypic probabilities. Nevertheless, some pedigrees share the same IBD probabilities and are therefore indistinguishable using those markers. Examples of these pedigrees were previously described, such as the case of half-siblings, grandparent-grandchild and avuncular, but a general analysis has not been attempted. The aim of this study is to present a systematic and mathematically supported framework where considering unlinked autosomal markers complete sets of indistinguishable pedigrees linking two non-inbred individuals are generally derived. In our work, complete sets of pedigrees with the same IBD partitions are formally established and mathematically treated, considering kinships linking any pair of non-inbred individuals, whether they are related just maternally or paternally, or both. Moreover, general expressions for IBD partitions, and consequently for joint genotypic probabilities, are derived considering a simple counting rule based on two ‘atom’ pedigrees: parent-child and full-siblings. Besides the theoretical formalization of the problem, the developed framework has potential applications in forensics as well as in breeding strategies design and in conservation studies.

Correcting for cryptic relatedness by a regression-based genomic control method

BackgroundGenomic control (GC) method is a useful tool to correct for the cryptic relatedness in population-based association studies. It was originally proposed for correcting for the variance inflation of Cochran-Armitage's additive trend test by using information from unlinked null markers, and was later generalized to be applicable to other tests with the additional requirement that the null markers are matched with the candidate marker in allele frequencies. However, matching allele frequencies limits the number of available null markers and thus limits the applicability of the GC method. On the other hand, errors in genotype/allele frequencies may cause further bias and variance inflation and thereby aggravate the effect of GC correction.ResultsIn this paper, we propose a regression-based GC method using null markers that are not necessarily matched in allele frequencies with the candidate marker. Variation of allele frequencies of the null markers is adjusted by a regression method.ConclusionThe proposed method can be readily applied to the Cochran-Armitage's trend tests other than the additive trend test, the Pearson's chi-square test and other robust efficiency tests. Simulation results show that the proposed method is effective in controlling type I error in the presence of population substructure.

Host-specific segregation of ribosomal nucleotide sequence diversity in the microsporidian Enterocytozoon bieneusi

Enterocytozoon bieneusi is a unicellular enteric fungal pathogen and the most common cause of human microsporidiosis. The frequent detection of this organism in animals, including companion animals, livestock and wildlife, has raised the question of the importance of animal reservoirs in the epidemiology of this pathogen. A partial sequence of the ribosomal internal transcribed spacer (ITS) has been widely used as a genetic marker for studying the molecular epidemiology of E. bieneusi. With the aim of comparing E. bieneusi ITS genotypes originating from different host species, and assess the potential for zoonotic transmission, E. bieneusi ITS sequences retrieved from GenBank were analyzed using two metrics of diversity, rarefaction and phylogenetic distance. In spite of the human ITS sample being geographically more diverse, ITS sequence diversity in animals exceeded that of humans. In both host groups much of the ITS diversity remains to be sampled. Using quantitative phylogenetic tests we found evidence for a partial but significant segregation of E. bieneusi ITS sequences according to host species. Host-specific segregation was confirmed by hierarchical analysis of molecular variation. To improve our understanding of the epidemiology of human microsporidiosis and strengthen the study of E. bieneusi populations, efforts to genotype additional E. bieneusi isolates from wildlife and companion animals should be prioritized and the geographic and species diversify of animal samples should be increased. Due to the possibility of genetic recombination in this species, additional unlinked genetic markers need to be developed and included in future studies.

THE VARIABLE GENOMIC ARCHITECTURE OF ISOLATION BETWEEN HYBRIDIZING SPECIES OF HOUSE MICE

Studies of the genetics of hybrid zones can provide insight into the genomic architecture of species boundaries. By examining patterns of introgression of multiple loci across a hybrid zone, it may be possible to identify regions of the genome that have experienced selection. Here, we present a comparison of introgression in two replicate transects through the house mouse hybrid zone through central Europe, using data from 41 single nucleotide markers. Using both genomic and geographic clines, we found many differences in patterns of introgression between the two transects, as well as some similarities. We found that many loci may have experienced the effects of selection at linked sites, including selection against hybrid genotypes, as well as positive selection in the form of genotypes introgressed into a foreign genetic background. We also found many positive associations of conspecific alleles among unlinked markers, which could be caused by epistatic interactions. Different patterns of introgression in the two transects highlight the challenge of using hybrid zones to identify genes underlying isolation and raise the possibility that the genetic basis of isolation between these species may be dependent on the local population genetic make-up or the local ecological setting.

Distinguishing kinship from genealogical likelihoods

Kinship analyses, besides paternity, are increasingly common in forensic genetics routine. The evaluation of the probability of a disputed kinship between individuals using unlinked autosomal markers employs a likelihood ratio format: the probability of the observations assuming the kinship is true against the probability of the same observations under the alternative hypothesis of a different degree of relationship (usually its absence). However, with very few exceptions (identity, first degree relatedness—paternity or maternity, full-brotherhood or unrelated), the algebraic expressions are not unique for a given kinship, the same probability value being obtained for various genealogical constellations. Then, in a likelihood ratio, what is compared are sets of possible kinship configurations, which are defined by identity-by-descent probabilities known as Jacquard's coefficients. Pedigrees with the same identity-by-descent probabilities are thus undistinguishable by unlinked autosomal markers. In the literature the most common reported undistinguishable kinships, by autosomal transmission, are avuncular, half-sibs and grandparent–grandchild. Therefore, when reporting the results of genetic information upon a specific kinship case a particular caution must be taken in order to avoid misconceptions and fallacious inferences.

The worm in the fruit of the mitochondrial DNA tree

The worm in the fruit of the mitochondrial DNA tree

The origins of lactase persistence in Europe.

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (−13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the −13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on −13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.