Important Genetic Variation Research Articles

Association of the estrogen receptor gene Pvu II restriction polymorphism with expected progeny differences for reproductive and performance traits in swine herds in Brazil

Estrogen has an important function in swine reproduction and growth. A Pvu II restriction enzyme polymorphism has been proven to be an important genetic variation in the estrogen receptor gene (ESR) and may be considered as a candidate gene for use in pig production but there is no data regarding the prevalence of this polymorphism in the Brazilian pig population. We used DNA samples from the following three purebred pig breeds: Large White (336 females and 26 males), Landrace (304 females and 27 males) and Pietrain (125 females and 11 males). The ESR genotyping was performed using PCR-RFLP. For each breed, genotypes for the ESR gene were compared independently for expected progeny differences (EPD) in litter size (LS), average daily weight gain (DWG) (g/day) and back fat thickness (BT) as measured in mm by ultrasound. In the Large White breed, but not the other breeds, the ESR genotype was significantly (p < 0.05) associated to LS, DWG and BT. Large Whites genotyped as AA or AB had higher EPD values for the LS and BT traits compared to BB Large Whites, while AA Large Whites had higher DWG EPD values than BB Large Whites. Our results for the Large White population showed that the A allele has a beneficial effect on LS, DWG and BT expected progeny differences.

Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies

Strategies for the identification of functional genetic variation underlying phenotypic traits of ecological and evolutionary importance have received considerable attention in the literature recently. This paper aims to bring together and compare the relative strengths and limitations of various potentially useful research strategies for dissecting functionally important genetic variation in a wide range of organisms. We briefly explore the relative strengths and limitations of traditional and emerging approaches and evaluate their potential use in free-living populations. While it is likely that much of the progress in functional genetic analyses will rely on progress in traditional model species, it is clear that with prudent choices of methods and appropriate sampling designs, much headway can be also made in a diverse range of species. We suggest that combining research approaches targeting different functional and biological levels can potentially increase understanding the genetic basis of ecological and evolutionary processes both in model and non-model organisms.

The Reliable Identification of Disease-Gene Associations

A recent Cancer Epidemiology, Biomarkers & Prevention editorial proposed guidelines for prioritizing publication of genetic association studies in cancer ([1][1]). In their Introduction, they indicate that the journal will “… increasingly prioritize the publication of reports that are more

Genetic heterogeneity of the dengue vector Aedes aegypti in Martinique.

In Martinique, Aedes aegypti, the vector of dengue viruses has been the target of insecticide control for more than 35 years. Despite significant control efforts, dengue has become a major disease of public health concern. We conducted a population genetic analysis based on isoenzyme variations combined with an estimation of infection rate to a dengue virus among 26 Ae. aegypti samples. Aedes aegypti samples could be differentiated for their susceptibility to dengue infection (infection rates ranging from 42.8% to 98.6%) and showed important genetic variation (significant F(ST) values).

Ecological Genetics of Mpi and Gpi Polymorphisms in the Acorn Barnacle and the Spatial Scale of Neutral and Non-neutral Variation

Different allozyme genotypes at the mannose phosphate isomerase (Mpi) locus in the northern acorn barnacle (Semibalanus balanoides) show a strong association with distinct intertidal microhabitats. In estuaries along the Maine Coast, the FF homozygote has higher fitness in exposed, high-tide level microhabitats while the SS homozygote has higher fitness under algal cover or at low-tide microhabitats. These patterns are consistent with a Levene (1953) model of balancing selection. In these same samples, polymorphisms at the glucose phosphate isomerase locus (Gpi) and mitochondrial DNA (mtDNA) show no fitness differences among microhabitats, providing intra-genomic controls supporting selection at or near Mpi. Here we report a similar analysis of genotype-by-microhabitat associations at sites in Narragansett Bay, Rhode Island, close to the southern range limit of S. balanoides. Genotype zonation at Mpi between high- and low-tide microhabitats is significantly different between Maine and Narragansett Bay due to opposite zonation patterns for the SF and FF genotypes. Enzyme activity data are consistent with this "reverse" zonation. At Gpi, there is significant microhabitat zonation in Narragansett Bay, while this locus behaves as a neutral marker in Maine. Mt DNA shows no significant microhabitat zonation in either Rhode Island or Maine. The Mpi data suggest that Levene-type selection for alternative genotypes in alternative habitats may operate at scales of both 10's of meters and 100's of kilometers. The Gpi data show how an apparently neutral locus can exhibit non-neutral variation under different environmental conditions. We argue that both Mpi and Gpi provide important genetic variation for adaptation to environmental heterogeneity that is recruited under distinct conditions of stress and carbohydrate substrate availability.

Hybrid populations selectively filter gene introgression between species.

Hybrids have long been recognized as a potential pathway for gene flow between species that can have important consequences for evolution and conservation biology. However, few studies have demonstrated that genes from one species can introgress or invade another species over a broad geographic area. Using 35 genetically mapped restriction fragment length polymorphism (RFLP) markers of two species of cottonwoods (Populus fremontii x P. angustifolia) and their hybrids (n = 550 trees), we showed that the majority of the genome is prohibited from introgressing from one species into the other. However, this barrier was not absolute; Fremont cpDNA and mtDNA were found throughout the geographic range of narrowleaf cottonwood, and 20% of the nuclear markers of Fremont cottonwood introgressed varying distances (some over 100 km) into the recipient species' range. Rates of nuclear introgression were variable, but two nuclear markers introgressed as fast as the haploid, cytoplasmically inherited chloroplast and mitochondrial markers. Our genome-wide analysis provides evidence for positive, negative, and neutral effects of introgression. For example, we predict that DNA fragments that introgress through several generations of backcrossing will be small, because small fragments are less likely to contain deleterious genes. These results argue that recombination will be important, that introgression can be very selective, and that evolutionary forces within the hybrid population to effectively "filter" gene flow between species. A strong filter may make introgression adaptive, prevent genetic assimilation, lead to relaxed isolating mechanisms, and contribute to the stability of hybrid zones. Thus, rather than hybridization being a negative factor as is commonly argued, natural hybridization between native species may provide important genetic variation that impacts both ecological and evolutionary processes. Finally, we propose two hypotheses that contrast the likelihood of contemporary versus ancient introgression in this system.

HYBRID POPULATIONS SELECTIVELY FILTER GENE INTROGRESSION BETWEEN SPECIES

Hybrids have long been recognized as a potential pathway for gene flow between species that can have important consequences for evolution and conservation biology. However, few studies have demonstrated that genes from one species can introgress or invade another species over a broad geographic area. Using 35 genetically mapped restriction fragment length polymorphism (RFLP) markers of two species of cottonwoods (Populus fremontii x P. angustifolia) and their hybrids (n = 550 trees), we showed that the majority of the genome is prohibited from introgressing from one species into the other. However, this barrier was not absolute; Fremont cpDNA and mtDNA were found throughout the geographic range of narrowleaf cottonwood, and 20% of the nuclear markers of Fremont cottonwood introgressed varying distances (some over 100 km) into the recipient species' range. Rates of nuclear introgression were variable, but two nuclear markers introgressed as fast as the haploid, cytoplasmically inherited chloroplast and mitochondrial markers. Our genome-wide analysis provides evidence for positive, negative, and neutral effects of introgression. For example, we predict that DNA fragments that introgress through several generations of backcrossing will be small, because small fragments are less likely to contain deleterious genes. These results argue that recombination will be important, that introgression can be very selective, and that evolutionary forces within the hybrid population to effectively “filter” gene flow between species. A strong filter may make introgression adaptive, prevent genetic assimilation, lead to relaxed isolating mechanisms, and contribute to the stability of hybrid zones. Thus, rather than hybridization being a negative factor as is commonly argued, natural hybridization between native species may provide important genetic variation that impacts both ecological and evolutionary processes. Finally, we propose two hypotheses that contrast the likelihood of contemporary versus ancient introgression in this system.Corresponding Editor: S. Tonsor

Population studies of polymorphisms of the serotonin transporter protein gene

The range of allele frequency variation in humans for any locus that may have functionally important genetic variation needs to be documented. Therefore, we tested two polymorphisms at the serotonin transporter protein locus (SLC6A4) in samples from seven specific populations from five continental regions. We studied the promoter polymorphism which is reported to have functional significance and to be associated with anxiety- and depression-related phenotypes [Lesch et al., 1996: Science 274:1527-1531], and the intron 2 VNTR polymorphism [Lesch et al., 1994: J Neural Transm 95:157-162]. Allele frequencies for both systems show significant global variation, and consequently so do haplotype frequencies. Linkage disequilibrium varied among the populations, being absent in some and highly significant in others. These differences further document a large potential for population stratification in association studies of either of these SLC6A4 polymorphisms.

Genetic Characterization of the nef Gene from Human Immunodeficiency Virus Type 1 Group M Strains Representing Genetic Subtypes A, B, C, E, F, G, and H

Most efforts to characterize sequence variation of HIV isolates has been directed toward the structural envelope gene. Few studies have evaluated the sequence variability of auxiliary genes such as nef. In this study 41 new HIV-1 strains, representing the majority of the described envelope subtypes of HIV-1 (A to H), were genetically characterized in the nef region. Phylogenetic analysis showed that 34 strains could be classified in the same subtype in nef and env, and 7 (19%) of the 41 new viruses were recombinants. For two of the seven strains, recombination occurred upstream of the nef gene, whereas for five of the seven strains recombination occurred within the nef gene with a crossover close to the 5' end of the LTR (long terminal repeat). The low intersubtype distance between subtype B and D in the nef gene confirms previous observations in the pol, env, and gag genes, which suggest a common ancestor for these subtypes. The majority of all the previously described functional domains in the nef gene were relatively conserved among the different subtypes, with only minor differences being observed. The myristoylation signal among the different subtypes, with only minor differences being observed. The myristoylation signal was less conserved for subtype C, with one or more amino acid changes being observed at positions 3, 4, and 5. The highly conserved acidic region (positions 62 to 65), critical for the enhancement of viral synthesis with an increased virus growth rate, was less conserved among the subtype G strains from our study. At least three epitopic regions of the nef gene have been defined and each can be recognized by CTLs under a variety of HLA restrictions; all were also relatively well conserved between the different genetic subtypes. Despite the relatively important genetic variation in nef sequences obtained among the different genetic subtypes, functional domains and CTL epitopes were relatively well conserved. In vitro and/or in vivo studies are necessary to study the relevance of the observed differences.

Variability in dehydrodiferulic acid composition of durum wheat (Triticum durum Desf.) and distribution in milling fractions

The dehydrodiferulic acid content of different common and durum wheat grains and milling fractions was determined by an HPLC procedure. The 8-O-4′, 5–8′ benzofuran, 5–8′ and 5-5′ dehydrodimers were identified in all samples studied and occurred in decreasing relative amounts, respectively. Durum wheats were twice as concentrated in dimers as common wheats. An important genetic variation for dehydrodiferulic acid content was shown within durum wheat grains, whereas the agronomic conditions had no effect. There was 10 to 20 times more dehydrodiferulic acids in external layers (aleurone, bran) than in the starchy endosperm of durum wheat grains. The content and composition in dimers of the inner endosperm did not vary according to genotypes and cultivation conditions. The ratio of dehydrodimers to monomers of ferulic acid which represented an index of dimerisation, was 1·6 times higher in the external layers of the grain than in the endosperm. No relation was found, however, between the degree of ferulic acid dimerisation and the milling behaviour of durum wheat grains.

Evaluation of genetic variation in nutritive value of Gliricidia sepium in feeding trials and by an in vitro gas production technique

Gliricidia sepium (Jacq.) Steud. is widely used as a high-protein supplementary food for ruminants in many parts of the tropics. Native to Central America and Mexico, it has become widely naturalized elsewhere but the introduced populations are mostly of unknown origin and uncertain quality. Studies of the genetic resources from the native range, under a research programme at OFI, have shown great variation between populations in yield (Dunsdon and Simons, 1996). The objective of the research described here was to investigate whether there is also important genetic variation in fodder quality, to inform decisions on future distribution of ‘superior’ germplasm of G. sepium under the OFI programme.

Mapping genes for growth rate and fatness in a Large White x Meishan F2 pig population

DNA-based markers and genetic maps of major livestock species have been developed in the last few years. These, together with experimental populations and appropriate statistical methods, provide the tools to dissect causes of economically important genetic variation in livestock. A cross between genetically diverse lines is a powerful experimental design for such a study. In an F2 or backcross population from such a cross, markers are likely to be highly informative and the genes that control the differences between the lines will be segregating. We have been developing such a resource population based on a cross between the British Large White and Chinese Meishan pigs. These breeds differ for many traits, with the Meishan being inferior for growth rate and fatness, but superior for reproduction traits. Here we report the mapping of major genetic effects on growth rate and fatness in our cross.

Mapping genes for growth rate and fatness in a Large White x Meishan F2pig population

DNA-based markers and genetic maps of major livestock species have been developed in the last few years. These, together with experimental populations and appropriate statistical methods, provide the tools to dissect causes of economically important genetic variation in livestock. A cross between genetically diverse lines is a powerful experimental design for such a study. In an F2or backcross population from such a cross, markers are likely to be highly informative and the genes that control the differences between the lines will be segregating. We have been developing such a resource population based on a cross between the British Large White and Chinese Meishan pigs. These breeds differ for many traits, with the Meishan being inferior for growth rate and fatness, but superior for reproduction traits. Here we report the mapping of major genetic effects on growth rate and fatness in our cross.

Genetic Structure of Endangered Clapper Rail (Rallus longirostris) Populations in Southern California.

We assessed the genetic structure of two subspecies of endangered Clapper Rails (Rallus longirostris) in Southern California using DNA fingerprinting to uncover variation in minisatellite DNA. Minisatellite DNA variation in the Salton Sea population of the R. I. yumanensis subspecies was at a level typical of outbred avian species (average proportion of fragments shared, or S, was 0.33). Variation was extremely low (S from 0.63 to 0.77), however, within four coastal, salt-marsh populations of the subspecies R. I. levipes located along a transect extending about 260 km northwest from the Mexican border. Between-population similarity (Sij ) was also high for the four levipes populations, although individuals of the small, isolated population at Mugu Lagoon consistently clustered separately in phenograms constructed using neighbor-joining or other algorithms. Individuals of yumanensis always clustered as a sister group to all levipes individuals. The minisatellite data were contrasted with the extremely low mtDNA and RAPD variation we found in both subspecies. We propose that variation in these less-mutable markers was lost in a bottleneck that occurred at least 1000 years ago, thus allowing sufficient time for recovery of variation in the rapidly mutating (μ∼ 0.001/gamete/generation) minisatellites (t = 1/μ, or 1000 generations). A second, more-recent bottleneck, or series of bottlenecks within a metapopulation structure, likely resulted in the depauparate variation seen in levipes today. We suggest that translocations from large to small levipes populations could restore important genetic variation to the small populations and would not compromise genetic boundaries. Estructura genética de las poblaciones de Rallus longirostris en peligro de extinción en el sur de California.

Photosynthetic performance in wild emmer wheat, Triticum dicoccoides: ecological and genetic predictability

In a twin study, we have shown that wild emmer wheat, Triticum dicoccoides, the progenitor of all cultivated wheats, harbours important genetic variation (Vg) in photosynthetic characteristics. This Vg resides within and between populations and ecogeographical regions in Israel, which is the center of origin and diversity of wild emmer wheat. Here we analyzed, by univariate and multivariate methods, the significant differentiation of variation in photosynthetic characteristics of 107 genotypes from 27 populations of wild emmer in Israel, distributed in three ecogeographical regions including central, xeric (northern cold and eastern warm) marginal, and mesic (western) marginal populations. The highest photosynthetic efficiency was displayed by populations of the xeric marginal region, but most variation for photosynthetic capacity occurs between accessions within ecogeographical regions and populations. Genotypes and populations of T. dicoccoides having high photosynthetic capacity can be identified by climatic factors and isozyme markers. The identification by genetic markers, if substantiated by testcrosses, can facilitate the maximization of conservation, in situ or ex situ, and utilization of these photosynthetic genetic resources for improvement of hexaploid wheat (T. aestivum).

A Study of Fructose Yield Components in Chicory

Abstract2557 chicory roots from 13 cultivars were analysed individually for root weight, root shape, total fructose, total glucose, potassium and amino‐N contents. Fructose yield is highly correlated with root weight and slightly with fructose content, both at the inter‐ and intra‐varietal levels. The comparison of total‐sample correlations to between‐ and within‐variation correlations suggests an important genetic variation within varieties.

Characteristics of a novel lentivirus derived from South African sheep with pulmonary adenocarcinoma (jaagsiekte)

A novel lentivirus was isolated from South African sheep with experimentally transmitted lung adenocarcinoma. Similar to visna virus and caprine arthritis encephalitis virus, this new strain induced cytopathic effects on ovine plexus choroid cultures. In contrast to a recent Israeli isolate from sheep with adenocarcinoma, the South African lentivirus could not transform fibroblast cultures. The antigenic relatedness between the new isolate and visna virus was assessed by immunoprecipitation of radiolabeled viral proteins, using monospecific antisera against visna virus proteins. The results indicate that the new virus contains four major structural proteins of sizes similar to those of visna virus (i.e., gp135, p30, p16, and pi 4) and have some common antigenic determinants (about 90% in the major core antigen p30). However, the nucleotidic sequences of the novel lentivirus were found to be only 16.5 to 27.4% homologous to visna virus and 8.3 to 15% homologous to caprine arthritis encephalitis virus, by means of liquid hybridization under stringent conditions. The genetic divergence indicated by this last result was confirmed by the dissimilar restriction endonuclease cleavage map of the new virus in comparison to those of visna virus and three caprine arthritis encephalitis virus strains. The demonstration of a third type of ovine lentivirus supports the concept of an important genetic variation among the lentiviruses infecting one animal species.

The early growth of artificially reared American lobsters

Twenty families of the lobster, Homarus americanus, were reared at 10°, 15° and 20°C with and without bilateral eye-stalk-ablation. At 20°C both eye-stalk-ablated and non-eye-stalk-ablated lobsters from each family were assigned to one of two dietary treatments: 1) frozen whole brine shrimp, or 2) a diet of cheap, local constituents. The means of growth traits improved while viability decreased with increasing temperature. The ablation technique shows promise since improved performance for growth was apparent in eye-stalk ablated lobsters, but mortality was greater. Important genetic variation of all traits was found in each of the environments tested. The genetic correlations between growth traits were reinforcing, but the correlations between growth and viability traits were mainly negative. Ease and reliability of measurement should be considered when choosing growth traits in any artifical selection program.

Possibilities for genetic manipulation of sex ratio in livestock.

Reports are reviewed in which genetic differences for sex ratio of offspring were found among breeds, breed crosses, strains, lines, line crosses, families or individuals. Although reports in which genetic variation could not be identified outnumber those in which it could, important genetic variation does exist in at least some populations. The direct or correlated response of sex ratio to selection is reviewed. Again, results are equivocal, but there is ample evidence that sex ratio will respond to selection in at least some populations of laboratory organisms. Segregation distortion in the mouse and in Drosophila is examined. Segregation distortion occurs when a heterozygous male mated to a homozygous female does not produce the two offspring types in equal proportions and the disparity cannot be accounted for by sampling or differential mortality. Although the most well-known systems have no effect (in the mouse) or only a moderate effect (in Drosophila) on sex ratio, systems in which sex ratio is subject to segregation distortion are known to exist in insects and could exist in mammals. Finally, the possibility is discussed that XX/XY chromosome chimaeric bulls, born co-twin to a heifer, might produce a preponderance of heifer progeny. A few reports suggest this might be the case, but other research is not in agreement.