Alleles Of Different Loci Research Articles

Detecting directional and non-directional epistasis in bi-parental populations using genomic data.

Epistasis, commonly defined as interaction effects between alleles of different loci, is an important genetic component of the variation of phenotypic traits in natural and breeding populations. In addition to its impact on variance, epistasis can also affect the expected performance of a population and is then referred to as directional epistasis. Before the advent of genomic data, the existence of epistasis (both directional and non-directional) was investigated based on complex and expensive mating schemes involving several generations evaluated for a trait of interest. In this study, we propose a methodology to detect the presence of epistasis based on simple inbred biparental populations, both genotyped and phenotyped, ideally along with their parents. Thanks to genomic data, parental proportions as well as shared parental proportions between inbred individuals can be estimated. They allow the evaluation of epistasis through a test of the expected performance for directional epistasis or the variance of genetic values. This methodology was applied to two large multiparental populations, i.e. the American maize and soybean nested association mapping populations, evaluated for different traits. Results showed significant epistasis, especially for the test of directional epistasis, e.g. the increase in anthesis to silking interval observed in most maize inbred progenies or the decrease in grain yield observed in several soybean inbred progenies. In general, the effects detected suggested that shuffling allelic associations of both elite parents had a detrimental effect on the performance of their progeny. This methodology is implemented in the EpiTest R-package and can be applied to any bi/multiparental inbred population evaluated for a trait of interest.

Sex initiates adaptive evolution by recombination between beneficial loci.

Current theory proposes that sex can increase genetic variation and produce high fitness genotypes if genetic associations between alleles at different loci are non-random. In case beneficial and deleterious alleles at different loci are in linkage disequilibrium, sex may i) recombine beneficial alleles of different loci, ii) liberate beneficial alleles from genetic backgrounds of low fitness, or iii) recombine deleterious mutations for more effective elimination. In our study, we found that the first mechanism dominated the initial phase of adaptive evolution in Brachionus calyciflorus rotifers during a natural selection experiment. We used populations that had been locally adapted to two environments previously, creating a linkage disequilibrium between beneficial and deleterious alleles at different loci in a combined environment. We observed the highest fitness increase when several beneficial alleles of different loci could be recombined, while the other mechanisms were ineffective. Our study thus provides evidence for the hypothesis that sex can speed up adaptation by recombination between beneficial alleles of different loci, in particular during early stages of adaptive evolution in our system. We also suggest that the benefits of sex might change over time and state of adaptive progress.

Identification and distribution of alleles of hybrid necrosis gene Ne2 in soft wheat cultivars (Triticum aestivum L.)

Aim. To determine the correspondence of different alleles of locus Xbarc55-2В to alleles of gene Ne2, different in their strength, and to investigate the distribution of alleles of locus Xbarc55-2В and the corresponding alleles of gene Ne2 from wheat cultivars of Ukrainian and Russian selection. Methods. Polymerase chain reaction, electrophoresis in PAAG, statistical methods. Results. The alleles of locus Xbarc55-2В, bound to the hybrid necrosis gene Ne2, were used to identify the genotypes of 290 soft wheat cultivars of different geographic origin. The correspondence of different alleles of locus Xbarc55-2В to alleles of gene Ne2, different in their strength, was defi ned: 142 bp – ne2, 136 bp – Ne2 w/m , 132 bp – Ne2 ms , 126 bp – Ne2 s . The distribution of the identifi ed alleles of gene Ne2 among the wheat cultivars of Ukrainian and Russian selection was demonstrated. Conclusions. The advantage of some alleles for cultivars of different regions was determined, which may testify to their selection and adaptation value.

Spatial Scale, Genetic Structure, and Speciation of Hawaiian Endemic Yeasts 1

Two Hawaiian endemic yeast species, Metschnikowia hawaiiensis and Metschnikowia hamakuensis , were examined by means of multilocus characterization. In spite of their narrow range of distribution, restricted to the island of Hawai‘i, both species were found to be polymorphic at several loci. Alleles of different loci were distributed independently within local populations, confirming that sexual reproduction prevails among these facultatively asexual organisms. No alleles were shared across species, confirming their reproductive isolation. Although the sample size for the northern species, M. hamakuensis , is much less ( N = 7) than that for its southern relative, M. hawaiiensis ( N = 161), their genetic diversity is comparable. Genetic differentiation was detected in M. hawaiiensis populations at both regional (ca. 30–40 km) and local (ca. 1 km) scales. A single isolate recovered in a separate locality exhibited considerable allelic divergence from others, indicating that genetic isolation can occur over relatively short distances and suggesting a first step towards cessation of gene flow, which is required for speciation.

FEATURES OF ASSOCIATIVE LINKS BETWEEN NONHOMOLOGOUS ALLELES OF THE GENE-ENZYME SYSTEMS IN DIFFERENT RAPANA GROUPS OF BLACK SEA

Rapa whelk (Rapana venosa, Valenciennes, 1846) has a great influence on the operation of such an isolated marine ecosystem, as the Black Sea. However, many aspects of its vital functioning, including the genetic and biochemical mechanisms of Rapana high adaptive capacity, practically unknown. Therefore, the aim of this work was to find among Rapana genotypes stable combinations (pairings, association) of different alleles of a gene-enzyme systems, the totality of which can be regarded as adaptive gene complexes. The shellfish from waters of the three north-western parts of the Black Sea (Odessa Bay, Tarhankut and island Zmeiniy) were investigated. There were analyzed 169 individuals of a species R. venosa. The homogenates for electrophoretic separation were prepared from gland of Leiblein of molluscs; the identification of allozymes were performed in PAA-gels. The following enzymes were studied: alkaline phosphatase, NADH oxidase, esterase, alcohol dehydrogenase and glutathione peroxidase. The eight loci, including two for next enzimes - alkaline phosphatase, esterase and NADH oxidase were chosen for the testing of genotypes; the alcohol dehydrogenase and glutathione peroxidase were presented by one locus for each enzime. In conducting the genetic analysis based on the hypothesis about the two allel structure of the investigated loci. The presence of conjugation between alleles of different loci, controlling different enzyme systems, determined by the coefficient of association and Russell-Rao coefficient of linkage disequilibrium. It revealed that between certain alleles of enzymes' loci formed temporary association. Specific association of alleles in a population can be kept for several years; this fact may indicate their adaptive value. The example of such combination is a long association between alleles of alkaline phosphatase Alp-126 and the alcohol dehydrogenase Adh03. Number of associated alleles of the gene-enzyme systems to a certain Rapana group due to the general state of the animals in the waters: the largest number of complexes between alleles of gene-enzymes systems were observed in a set of Odessa Bay Rapana individuals (grouping in good condition), the lowest - in Tarkhankut waters (grouping in the doldrums). It is suggested that the role of the alleles in the adaptation of associations: negomologinih found temporary combinations of alleles can act as a source of adaptive gene complexes. It is suggested that the role of the alleles associations is important for the adaptation : detected temporary combination of non-homologous alleles can act as a source of adaptive complexes

Mixed linear model approaches in mapping QTLs with epistatic effects by a simulation study

AbstractEpistasis refers to the phenotypic effects of interactions between alleles of different loci. Statistical detection of such interactions remains to be the subject of presented studies. A method based on mixed linear model was developed for mapping QTLs with digenic epistasis. Reliable estimates of QTL additive and epistasis effects can be obtained by the maximum-likelihood estimate methods. Likelihood ratio andtstatistics were combined for testing hypotheses about QTL effects (additive and epistasis effects). Monte Carlo simulations were conducted for evaluating the unbiasedness, accuracy and power for parameter estimation in QTL mapping. The results indicated that the mixed-model approaches could provide unbiased estimates for effects of QTLs. Additionally, the mixed-model approaches also showed high accuracy in mapping QTLs with epistasis effects. The information obtained in this study will be useful for manipulating the QTLs for plant breeding by marker assisted selection.

Allele frequencies of 15 autosomal STR loci in the Caymanian population.

Allele frequency distributions in the Caymanian population were determined using the AmpFlSTR® Identifiler® PCR amplification kit. Little evidence of departure from Hardy-Weinberg equilibrium or the association of alleles of different loci was detected. Comparison with relevant population groups supports the Caymanian population having a distinct allelic distribution. The 15 Identifiler® loci provide combined power of discrimination and exclusion values of 0.999999999999999995 and 0.9999992, respectively, proving suitable for the forensic and paternity testing requirements of the Cayman Islands.

Allele frequency data of 15 autosomal STR loci in four major population groups of South Africa

Allele frequency distributions for 15 tetrameric short tandem repeat (STR) loci were determined using the AmpFlSTR® Identifiler Plus™ PCR amplification kit. There was little evidence of departures from Hardy-Weinberg equilibrium or association of alleles of different loci in the population samples. The probability of identity values for the different populations range from 1/3.3 × 10(17) (White) to 1/1.88 × 10(18) (Coloured). The combined probability of paternal exclusion for the different population groups ranges from 0.9995858 (Coloured) to 0.9997874 (Indian).

Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx

Microsatellite markers are commonly used for examining population structure, especially inbreeding, outbreeding and gene flow. An array of microsatellite loci, preferably with multiallelic presentation, is preferable for ensuring accurate results. However, artifact peaks or stutters in the electrophoretograms significantly hamper the reliable interpretation of genotypes. We interpreted electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx. All the alleles of different loci exhibited good peak resolutions and hence were clearly identified. Moreover, none of the stutter peaks impaired the recognition or differentiation between homozygote and heterozygote. Our findings suggest that correct identification of alleles in the presence of co-amplified nonspecific fragments is important for reliable interpretation of microsatellite data.

Low genetic structure in an epiphytic Orchidaceae (Oncidium hookeri) in the Atlantic rainforest of South-eastern Brazil.

Oncidium hookeri is a neotropical species of epiphytic Orchidaceae found in the Brazilian Atlantic rainforest at the top of the Mantiqueira Range of mountains. The genetic variation of O. hookeri was studied to assess the distribution of genetic variability within and among six populations localized in Atlantic rainforest remnants. Gene flow among populations and the occurrence of recent bottlenecks were investigated in order to infer the degree of isolation of these populations. Thirteen polymorphic loci were used for allozyme electrophoresis. The data were analysed by means of standard statistical approaches, to estimate gene diversity and the genetic structure of the populations. The mean gene diversity and allelic richness were H(e) = 0.099 and A = 1.75, respectively. F-statistics revealed high heterozygote deficiencies in all populations (F(IS) = 0.43-0.82). Several rare alleles were found in all the populations, and three populations presented private alleles. Low genetic differentiation among O. hookeri populations was detected (F(ST) = 0.029); natural selection may be involved in PGM locus differentiation among populations. The genetic differentiation between paired populations was low, bearing no correlation with geographic distance (Mantel test: r = -0.34, P = 0.72). Only two populations showed signs of recent bottlenecks. The heterozygote deficiency found seems to be caused by pollinator behaviour; the low frequencies of several alleles of different loci can be maintained due to clonal propagation. Despite the stochastic nature of the wind-dispersal of seeds to long distances, this process may promote an effective gene flow among populations, thus avoiding genetic differentiation.

Identification and confirmation of three neutral alleles conferring wide compatibility in inter-subspecific hybrids of rice (Oryza sativa L.) using near-isogenic lines

Wide-compatibility varieties (WCVs) are a special class of rice germplasm that is able to produce fertile hybrids when crossed to both indica and japonica subspecies. Previous studies determined 'Dular' and 02428 as two WCVs and identified a number of QTLs as having large effects on fertility of inter-subspecific hybrids. In this study, we developed five near-isogenic lines (NILs) for three of the QTLs, f5, f6 and S5, by backcrossing and marker-assisted selection, using "Dular" and 02428 as the donors and "Zhenshan 97" as the recipient. Three of the NILs each carried one introgressed allele, and two NILs each carried two introgressed alleles in combinations. The NILs were testcrossed to an indica tester "Nanjing 11" and a japonica tester "Balilla". The results showed that the f5 allele from "Dular"(f5-Du) is a neutral allele conferring wide compatibility, with a large effect on both pollen and spikelet fertility, and the f6 allele from "Dular" (f6-Du) is a neutral allele for spikelet fertility with smaller effect. The S5 allele from 02428 (S5-08) was confirmed to be a neutral allele for spikelet fertility. It is likely that f6 and S5 are the same locus as deduced by their genomic locations and effects. The results also showed that even in combination, two neutral alleles of different loci were not able to produce normal fertility hybrids in typical indica-japonica crosses. The implications of the findings in rice breeding programs are discussed.

Simulation Experiments for Observation of Different Genetic Parameters

The change of genetics variance in various simulated population were examined trough 25 generations. The population size were 1000, 2000, 4000, 8000 and 16000. The number of genes were1, 2, 3, 4 and 5. Two allels per gene were applied. It was assumed that base population was randomly mated. Also it was assumed that a pair of allel genes was independent, there was no epistasis, linkage between alleles of different loci, dominance and overlapping generations. In the selection was kept the 93% of females and 0.186% of males. The size of populations was close to constant through generations.The size of populations and the number of loci were effects that how many generation is necessary to get genetical maximum. The change of the genetical mean of the population and the genetical variance were well subscribed cube and logistical curve. We can use to estimate these genetical parameters with the previous functons.

Statistical modeling of interlocus interactions in a complex disease: rejection of the multiplicative model of epistasis in type 1 diabetes.

In general, common diseases do not follow a Mendelian inheritance pattern. To identify disease mechanisms and etiology, their genetic dissection may be assisted by evaluation of linkage in mouse models of human disease. Statistical modeling of multiple-locus linkage data from the nonobese diabetic (NOD) mouse model of type 1 diabetes has previously provided evidence for epistasis between alleles of several Idd (insulin-dependent diabetes) loci. The construction of NOD congenic strains containing selected segments of the diabetes-resistant strain genome allows analysis of the joint effects of alleles of different loci in isolation, without the complication of other segregating Idd loci. In this article, we analyze data from congenic strains carrying two chromosome intervals (a double congenic strain) for two pairs of loci: Idd3 and Idd10 and Idd3 and Idd5. The joint action of both pairs is consistent with models of additivity on either the log odds of the penetrance, or the liability scale, rather than with the previously proposed multiplicative model of epistasis. For Idd3 and Idd5 we would also not reject a model of additivity on the penetrance scale, which might indicate a disease model mediated by more than one pathway leading to beta-cell destruction and development of diabetes. However, there has been confusion between different definitions of interaction or epistasis as used in the biological, statistical, epidemiological, and quantitative and human genetics fields. The degree to which statistical analyses can elucidate underlying biologic mechanisms may be limited and may require prior knowledge of the underlying etiology.

HLA class II factors associated with Plasmodium falciparum merozoite surface antigen allele families.

In Plasmodium falciparum malaria, certain human leukocyte antigens (HLA) and the parasite's merozoite surface antigens 1 and 2 (MSA-1, MSA-2) have been shown to influence the course of the infection. This report is on associations of distinct HLA factors with the occurrence of particular MSA families in a group of patients with either severe or mild P. falciparum malaria in Gabon. Different distributions of HLA-DPB1 alleles were found in the 2 groups. DR *04 alleles were observed more frequently among patients with severe malaria. Several alleles of different loci were associated with distinct MSA allele families. In addition, carriers of the amino acid methionine at position 11 of the DPA1 allele were more often infected by MSA-1 K1 parasites and less frequently by MSA-1 RO33 parasites. Furthermore, associations of HLA factors with polyclonal infections were found.

Allotype-associated differences in concentrations of human IgG subclasses

The concentrations of seven immunoglobulin isotypes (IgA, IgE, IgM, IgG1, IgG2, IgG3, and IgG4) were measured in the sera of 207 Finnish blood donors, and they were allotyped with anti-Gm antibodies: anti-f, anti-a, anti-x, and anti-n. The above population could be divided into 12 phenotypes, and significant differences in isotype concentrations between different phenotypes were observed. They are best explained by postulating that the following alleles of different loci are associated with a high concentration of the product of the locus: a(x)-IgG1, n-IgG2, b-IgG3, and perhaps 4b-IgG4. The following concentration differences between the low and the high homozygotes were found: IgG1, 1.2-fold; IgG2, 1.5-fold; and IgG3, 2.6-fold. No significant allotype-associated differences in the concentrations of IgA, IgM, or IgE could be detected.

Isolation and characterization of omnipotent suppressors in the yeast Saccharomyces cerevisiae.

Approximately 290 omnipotent suppressors, which enhance translational misreading, were isolated in strains of the yeast Saccharomyces cerevisiae containing the psi+ extrachromosomal determinant. The suppressors could be assigned to 8 classes by their pattern of suppression of five nutritional markers. The suppressors were further distinguished by differences in growth on paromomycin medium, hypertonic medium, low temperatures (10 degrees), nonfermentable carbon sources, alpha-aminoadipic acid medium, and by their dominance and recessiveness. Genetic analysis of 12 representative suppressors resulted in the assignment of these suppressors to 6 different loci, including the three previously described loci SUP35 (chromosome IV), SUP45 (chromosome II) and SUP46 (chromosome II), as well as three new loci SUP42 (chromosome IV), SUP43 (chromosome XV) and SUP44 (chromosome VII). Suppressors belonging to the same locus had a wide range of different phenotypes. Differences between alleles of the same locus and similarities between alleles of different loci suggest that the omnipotent suppressors encode proteins that effect different functions and that altered forms of each of the proteins can effect the same function.

The Wilhelmine E. Key 1987 invitational lecture. Genetic changes associated with the evolution of adaptedness in cultivated plants and their wild progenitors.

The results of long-term studies of changes in adaptedness in a number of experimental populations of annual plants are summarized. Measurements made of quantitative traits showed that cumulative increases in reproductive capacity continued in these experimental populations for more than 50 generations. Highly significant allelic frequency changes also occurred for marker loci governing morphological variants, disease resistance, allozymes, and rDNA restriction fragments. Individual effects of the marker loci on quantitative traits were determined by extensive progeny testing of selfed families descended from single plants isolated from various generations of the experimental populations. Comparisons between homozygotes and heterozygotes of marker loci for quantitative trait expression revealed that all the marker loci studied had statistically significant additive effects on several to many quantitative traits; thus, each Mendelian locus, in addition to being a locus for its discrete descriptive effect, was also a locus for several quantitative traits. Consistent associations were found between superior reproductive capacity (e.g., larger numbers of kernels per plant) and the alleles of marker loci that increased in frequency over generations; no other quantitative traits measured were clearly and consistently associated with alleles that increased in frequency. Multilocus analyses based on canonical correlation, log linear, and cluster analysis procedures showed that highly significant associations developed in early generations among alleles of different loci in all the predominantly selfing populations studied. Dynamic changes featuring amalgamations of alleles into fewer clusters involving larger numbers of loci continued into the late generations. Patterns of ecogenetic differentiation that developed under predominant selfing were found to be fine-scaled overlays of environmental heterogeneity. The picture of evolutionary change that emerges is one in which the incorporation of increasing numbers of favorably interacting alleles into large synergistic complexes was accompanied in inbreeding populations by increases in adaptedness to the local environment and also by striking ecogenetic differentiation among local populations that occupy unlike habitats, including differentiation between cultivated plants and their wild progenitors. Selfing appears to promote the development and maintenance of adaptedness within populations and at the same time to facilitate the development of spatial differentiation by retarding gene flow between populations.(ABSTRACT TRUNCATED AT 400 WORDS)

A comment on the use of Nass's contingency test for random association of alleles at different loci.

A chi 2 test developed by Nass (1959) and recently used by Ahmad and Hedrick (1985) for the detection of non-random association between alleles of different loci is very sensitive to misclassification of genotypes.