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Single Locus (single + locus)
Selected AbstractsPERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIESEVOLUTION, Issue 6 2000ScottV. Abstract Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (,) to T and the effect of uncertainty in , on estimates of population divergence (,) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on , decrease when the range over which ancestral population size , is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time. [source] Isolation and characterization of microsatellite loci from Quercus mongolica var. crispulaMOLECULAR ECOLOGY RESOURCES, Issue 3 2006KENTARO MISHIMA Abstract Microsatellites were isolated and characterized for the Japanese oak species, Quercus mongolica var. crispula, distributed in temperate deciduous forests of Japan. Eleven of the 48 primer pairs designed successfully amplified unambiguous and polymorphic single loci among 67 Q. mongolica var. crispula individuals within a plot in southwestern Japan. The observed and expected heterozygosities of the 11 microsatellite markers ranged from 0.522 to 0.896 and from 0.536 to 0.882, respectively. These polymorphic microsatellite markers are useful for estimating pollen-mediated gene flow in Q. mongolica var. crispula. [source] Genetic diversity within and among Atlantic cod (Gadus morhua) farmed in marine cages: a proof-of-concept study for the identification of escapeesANIMAL GENETICS, Issue 5 2010K. A. Glover Summary This study presents a molecular genetic characterization of Atlantic cod reared in commercial marine farms. Samples consisted of approximately 47 fish collected from nine cages located on four farms throughout Norway. In addition, 28 farmed escapees were recaptured in the sea (443 fish in total). Nine microsatellite loci and the Pan I gene were analysed, revealing a total of 181 alleles. Each sample contained 43,63% of total allelic variation. Comparing variation with published data for wild cod indicates that lower genetic variation exists within single cages than in wild populations. Significant linkage disequilibrium was observed amongst pairs of loci in all samples, suggesting a low number of contributing parental fish. Global FST was 0.049, and the highest pairwise FST value (pooled loci) was 0.085. For single loci, the Pan I gene was the most diagnostic, displaying a global FST of 0.203. Simulations amongst the samples collected on farms revealed an overall correct self-assignment percentage of 75%, demonstrating a high probability of identifying individuals to their farm of origin. Identification of the 28 escapees revealed a single cage as the most likely source of origin for half of the escapees, whilst the remaining fish were assigned to a mixture of samples, suggesting more than one source of escapees. [source] A MAGE/NDN-like gene in zebrafishDEVELOPMENTAL DYNAMICS, Issue 3 2003Jocelyn M. Bischof Abstract The human necdin/MAGE gene family has over 50 members, but most of the proteins encoded by these genes are of unknown function. We have now identified a single locus in Danio rerio that encodes a putative protein with significant coding sequence similarity to the mammalian NDN/MAGE genes. Analysis of the complete Fugu ribripes genome sequence also suggests that there is only a single MAGE-like gene in teleost fish. mage is expressed in the larval and adult brain, specifically the retina, the medial region of the telencephalon, periventricular gray zone of the optic tectum, and most highly in the cerebellar corpus. The discovery of a zebrafish NDN/MAGE gene expressed the developing brain facilitates studies of the MAGE homology domain in vertebrate development. Developmental Dynamics, 2003. © 2003 Wiley-Liss, Inc. [source] Familial dyslexia: neurocognitive and genetic correlation in a large Finnish familyDEVELOPMENTAL MEDICINE & CHILD NEUROLOGY, Issue 9 2002Jaana Nopola-Hemmi MD Neuropsychological findings of individuals with dyslexia (n=24) from a large, three-generation Finnish family are presented. We have previously performed whole genome linkage scanning in this family and found that dyslexia in this kindred segregates with a single locus in the pericentromeric area of chromosome 3. Those included in the analyses were carefully evaluated for general cognitive ability, reading and spelling skills, and reading-related neurocognitive skills. The neurocognitive type of dyslexia segregating in this family consisted of deficits in phonological awareness, verbal short-term memory, and rapid naming. Severe dyslexia also seemed to be connected with a general language difficulty and was most common in the eldest generation. [source] ALLELIC DIVERGENCE PRECEDES AND PROMOTES GENE DUPLICATIONEVOLUTION, Issue 5 2006Stephen R. Proulx Abstract One of the striking observations from recent whole-genome comparisons is that changes in the number of specialized genes in existing gene families, as opposed to novel taxon-specific gene families, are responsible for the majority of the difference in genome composition between major taxa. Previous models of duplicate gene evolution focused primarily on the role that neutral processes can play in evolutionary divergence after the duplicates are already fixed in the population. By instead including the entire cycle of duplication and divergence, we show that specialized functions are most likely to evolve through strong selection acting on segregating alleles at a single locus, even before the duplicate arises. We show that the fitness relationships that allow divergent alleles to evolve at a single locus largely overlap with the conditions that allow divergence of previously duplicated genes. Thus, a solution to the paradox of the origin of organismal complexity via the expansion of gene families exists in the form of the deterministic spread of novel duplicates via natural selection. [source] COALESCENCE IN A METAPOPULATION WITH RECURRENT LOCAL EXTINCTION AND RECOLONIZATIONEVOLUTION, Issue 5 2003John R. Pannell Abstract Many species exist as metapopulations in balance between local population extinction and recolonization. The effect of these processes on average population differentiation, within-deme diversity, and specieswide diversity has been considered previously. In this paper, coalescent simulations of Slatkin's propagule-pool and migrant-pool models are used to characterize the distribution of neutral genetic diversity within demes (,s), diversity in the metapopulation a whole (TTT), the ratio FST= (,t,,S)/,T, Tajima's D statistic, and several ratios of gene-tree branch lengths. Using these distributions, power to detect differences in key metapopulation parameter values is determined under contrasting sampling regimes. The results indicate that it will be difficult to use sequence data from a single locus to detect a history of extinctions and recolonizations in a metapopulation because of high genealogical variance, the loss of diversity due to reductions in effective population size, and the fact that a genealogy of lineages from different demes under Slatkin's model differs from a neutral coalescent only in its time scale. Genetic indices of gene-tree shape that capture the effects of extinction/recolonization on both external branches and the length of the genealogy as a whole will provide the best indication of metapopulation dynamics if several lineages are sampled from several different demes. [source] PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIESEVOLUTION, Issue 6 2000ScottV. Abstract Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (,) to T and the effect of uncertainty in , on estimates of population divergence (,) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on , decrease when the range over which ancestral population size , is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time. [source] A FORMAL ASSESSMENT OF GENE FLOW AND SELECTION IN THE FIRE ANT SOLENOPSIS INVICTAEVOLUTION, Issue 2 2000Michael A. D. Goodisman Abstract., Recent studies of the introduced fire ant Solenopsis invicta suggest that introduced polygyne (with multiple queens per nest) populations are strongly influenced by male-mediated gene flow from neighboring monogyne (single queen per nest) populations and selection acting on a single locus, general protein-9 (Gp-9). This investigation formally tests this hypothesis and determines if these processes can account for the genotypic structure of polygyne S. invicta. To increase the statistical power of this test, we considered the genotypes of polygyne queens and workers at both Gp-9 and the closely linked, selectively neutral locus Pgm-3. We then constructed and analyzed a novel mathematical model to delimit the effects of monogyne male gene flow and selection on the joint genotypes at the Pgm-3/Gp-9 superlocus. Using this framework, a hierarchical maximum-likelihood method was developed to estimate the best-fitting gene flow and selection parameters based on the fit of our model to data from both the current study and an earlier one of the same population. In each case, selection on polygyne queens and workers alone, with no monogyne male gene flow, provides the most parsimonious explanation for the observed genotype frequencies. The apparent discrepancy between this result and the empirical evidence for monogyne male gene flow indicates that undocumented factors, such as other forms of selection in polygyne males or workers, are operating in introduced polygyne S. invicta. [source] Update on peptidylarginine deiminases and deimination in skin physiology and severe human diseasesINTERNATIONAL JOURNAL OF COSMETIC SCIENCE, Issue 3 2007M.-C. Méchin Synopsis Deimination (or citrullination) is a recently described post-translational modification, but its consequences are not yet well understood. It is catalysed by peptidylarginine deiminases (PADs). These enzymes transform arginyl residues involved in a peptidyl link into citrullyl residues in a calcium-dependent manner. Several PAD substrates have already been identified like filaggrin and keratins K1 and K10 in the epidermis, trichohyalin in hair follicles, but also ubiquitous proteins like histones. PADs act in a large panel of physiological functions as cellular differentiation or gene regulation. It has been suggested that deimination plays a role in many major diseases such as rheumatoid arthritis, multiple sclerosis, Alzheimer's disease and psoriasis. Five human genes (PADIs), encoding five highly conserved paralogous enzymes (PAD1-4 and 6), have been characterized. These genes are clustered in a single locus, at 1p35-36 in man. Only PAD1-3 are expressed in human epidermis. PADs seem to be controlled at transcriptional, translational and activity levels and they present particular substrate specificities. In this review, we shall discuss these main biochemical, genetic and functional aspects of PADs together with their pathophysiological implications. Résumé La désimination (ou citrullination) est une modification post-traductionnelle catalysée par les peptidyl-arginine désiminases (PADs), décrite depuis peu et dont les conséquences sont encore mal comprises. Ces enzymes transforment, de façon dépendante du calcium, les résidus arginyl engagés dans un lien peptidique en résidus citrullyl. Plusieurs substrats ont été identifiés: la filaggrine et les cytokératines K1 et K10 de l'épiderme, la trichohyaline dans le follicule pileux mais aussi des protéines ubiquistes comme les histones. Les PADs interviennent dans de nombreuses fonctions physiologiques telles que la différenciation cellulaire ou la régulation génique. La désimination pourrait jouer un rôle dans plusieurs maladies sévères et fréquentes comme la polyarthrite rhumatoïde, la sclérose en plaque, la maladie d'Alzheimer ou encore le psoriasis. Cinq gènes humains (PADIs) codant pour 5 enzymes paralogues conservées (PAD1-4 et 6) ont été caractérisés. Ils sont regroupés en un seul locus, en 1p35-36 chez l'homme. Seules les PAD1-3 sont exprimées dans l'épiderme humain. Les PADs semblent contrôlées aux niveaux transcriptionnel et traductionnel, ainsi qu'au niveau de leur activité. Elles présentent chacune leurs spécificités de substrats. Ces principaux aspects biochimiques, génétiques et fonctionnels des PADs tout comme leurs implications physiopathologiques seront discutés dans cette revue. [source] Recovery of normal autologous myelopoiesis after graft rejection following allogeneic bone marrow transplant for agnogenic myeloid metaplasiaINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 2 2006S. ALKINDI Summary Allogeneic hematopoietic transplantation is the only currently available therapy that has the potential to cure agnogenic myeloid metaplasia (AMM) or primary myelofibrosis (PMF). Amelioration of fibrosis and eradication of the abnormal clone is thought to occur through the repopulation of marrow by donor-derived hematopoiesis and graft- vs. -host reaction leading to graft vs. tumor effect. We report here a 50-year-old female with AMM/PMF, conditioned with busulfan and cyclophosphamide, who rejected a single locus (HLA-B) mismatched bone marrow transplant from her daughter, but recovered normal autologous hematopoiesis with disappearance of marrow fibrosis and extramedullary hematopoiesis. Variable number tandem repeats (VNTR) analysis showed a gradual loss of donor-derived hematopoietic cells with recovery of autologous hematopoiesis. This case therefore illustrates that eradication of AMM/PMF in this patient with myeloablative chemotherapy combined with a transient allogeneic effect was sufficient to suppress the abnormal stem cell clone associated with AMM/PMF with subsequent cure. [source] Contrasting effects of heterozygosity on survival and hookworm resistance in California sea lion pupsMOLECULAR ECOLOGY, Issue 7 2006KARINA ACEVEDO-WHITEHOUSE Abstract Low genetic heterozygosity is associated with loss of fitness in many natural populations. However, it remains unclear whether the mechanism is related to general (i.e. inbreeding) or local effects, in particular from a subset of loci lying close to genes under balancing selection. Here we analyse involving heterozygosity,fitness correlations on neonatal survival of California sea lions and on susceptibility to hookworm (Uncinaria spp.) infection, the single most important cause of pup mortality. We show that regardless of differences in hookworm burden, homozygosity is a key predictor of hookworm-related lesions, with no single locus contributing disproportionately. Conversely, the subsequent occurrence of anaemia due to blood loss in infected pups is overwhelmingly associated with homozygosity at one particular locus, all other loci showing no pattern. Our results suggest contrasting genetic mechanisms underlying two pathologies related to the same pathogen. First, relatively inbred pups are less able to expel hookworms and prevent their attachment to the intestinal mucosa, possibly due to a weakened immune response. In contrast, infected pups that are homozygous for a gene near to microsatellite Hg4.2 are strongly predisposed to anaemia. As yet, this gene is unknown, but could plausibly be involved in the blood-coagulation cascade. Taken together, these results suggest that pathogenic burden alone may not be the main factor regulating pathogen-related mortality in natural populations. Our study could have important implications for the conservation of small, isolated or threatened populations, particularly when they are at a risk of facing pathogenic challenges. [source] A simulated annealing approach to define the genetic structure of populationsMOLECULAR ECOLOGY, Issue 12 2002I. Dupanloup Abstract We present a new approach for defining groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by-product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims to maximize the proportion of total genetic variance due to differences between groups of populations (spatial analysis of molecular variance; samova). Monte Carlo simulations were used to study the performance of our approach and, for comparison, the behaviour of the Monmonier algorithm, a procedure commonly used to identify zones of sharp genetic changes in a geographical area. Simulations showed that the samova algorithm indeed finds maximally differentiated groups, which do not always correspond to the simulated group structure in the presence of isolation by distance, especially when data from a single locus are available. In this case, the Monmonier algorithm seems slightly better at finding predefined genetic barriers, but can often lead to the definition of groups of populations not differentiated genetically. The samova algorithm was then applied to a set of European roe deer populations examined for their mitochondrial DNA (mtDNA) HVRI diversity. The inferred genetic structure seemed to confirm the hypothesis that some Italian populations were recently reintroduced from a Balkanic stock, as well as the differentiation of groups of populations possibly due to the postglacial recolonization of Europe or the action of a specific barrier to gene flow. [source] Characterization of microsatellite markers for the endemic sand dune lizard, Sceloporus arenicolusMOLECULAR ECOLOGY RESOURCES, Issue 2 2007L. M. CHAN Abstract Here we characterize and report on the genetic variability of eight microsatellite loci for the endemic sand dune lizard, Sceloporus arenicolus, that amplified consistently for individuals throughout the species' range. The number of alleles per locus was high (mean = 13.25) and observed heterozygosities ranged from 0.354 to 0.808. With the exception of a single locus, the loci did not deviate from Hardy,Weinberg expectations. This set of markers is currently being used to examine population structure and landscape genetics in S. arenicolus, a habitat specialist with a restricted range and patchy distribution. [source] Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microtiMOLECULAR MICROBIOLOGY, Issue 3 2002Alexander S. Pym Summary Although large human populations have been safely immunized against tuberculosis with two live vaccines, Mycobacterium bovis BCG or Mycobacterium microti, the vole bacillus, the molecular basis for the avirulence of these vaccine strains remains unknown. Comparative genomics has identified a series of chromosomal deletions common to both virulent and avirulent species but only a single locus, RD1, that has been deleted from M. bovis BCG and M. microti. Restoration of RD1, by gene knock-in, resulted in a marked change in colonial morphology towards that of virulent tubercle bacilli. Three RD1-encoded proteins were localized in the cell wall, and two of them, the immunodominant T-cell antigens ESAT-6 and CFP-10, were also found in culture supernatants. The BCG::RD1 and M. microti::RD1 knock-ins grew more vigorously than controls in immunodeficient mice, inducing extensive splenomegaly and granuloma formation. Increased persistence and partial reversal of attenuation were observed when immunocompetent mice were infected with the BCG::RD1 knock-in, whereas BCG controls were cleared. Knocking-in five other RD loci did not affect the virulence of BCG. This study describes a genetic lesion that contributes to safety and opens new avenues for vaccine development. [source] Genetics of spinosad resistance in a multi-resistant field-selected population of Plutella xylostellaPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 8 2004Ali H Sayyed Abstract Resistance to the bacteria-derived insecticides spinosad (Conserve), abamectin (Vertimec), Bacillus thuringiensis var kurstaki (Btk) (Dipel), B thuringiensis var aizawai (Bta) (Xentari), B thuringiensis crystal endotoxins Cry1Ac and Cry1Ca, and to the synthetic insecticide fipronil was estimated in a freshly-collected field population (CH1 strain) of Plutella xylostella (L) from the Cameron Highlands, Malaysia. Laboratory bioassays at G1 indicated significant levels of resistance to spinosad, abamectin, Cry1Ac, Btk, Cry1Ca, fipronil and Bta when compared with a laboratory insecticide-susceptible population. Logit regression analysis of F1 reciprocal crosses indicated that resistance to spinosad in the CH1 population was inherited as a co-dominant trait. At the highest dose of spinosad tested, resistance was close to completely recessive, while at the lowest dose it was incompletely dominant. A direct test of monogenic inheritance based on a back-cross of F1 progeny with CH1 suggested that resistance to spinosad was controlled by a single locus. Copyright © 2004 Society of Chemical Industry [source] Viability and bar expression are negatively correlated in Oregon Wolfe Barley Dominant hybridsPLANT BIOTECHNOLOGY JOURNAL, Issue 3 2007Phil Bregitzer Summary The expression level of bar, which encodes phosphinothricin acetyltransferase (PAT), was correlated with the inviability of barley hybrids between 20 Golden Promise-derived transgenic lines (Ds-bar lines) and a specialized genetic marker stock, Oregon Wolfe Barley Dominant (OWBD). Each Ds-bar line was homozygous for a modified maize Ds element that encoded bar and that had been delivered via transposition to a unique location. All Ds-bar lines were viable and morphologically similar. Only four of the 20 hybrid populations were viable. The remaining populations died prior to producing seed. Phenotypic, enzyme-linked immunosorbent assay and quantitative reverse transcriptase-polymerase chain reaction analyses of these lines, and of lines from unrelated transformation events that also expressed bar, showed that viability was negatively correlated with bar expression. Analysis of crosses of a high- bar -expressing line with the OWB mapping population showed that the sensitivity of OWBD to PAT segregated as a single locus on chromosome 6HL. No sensitivity to PAT could be detected in several other lines and cultivars. OWBD has been shown to be genetically divergent from other germplasm groups within cultivated barley; therefore, the observed sensitivity may be peculiar to OWBD and thus would not impact generally on the utility of bar as a selectable marker or source of herbicide resistance in barley. Nevertheless, these results demonstrate the extent of allelic variability present in Hordeum vulgare, and suggest an additional variable for consideration when devising protocols for the transformation of Hordeum cultivars or landraces that are not known to be tolerant to PAT. [source] Isolation and characterization of microsatellite markers from guineagrass (Panicum maximum) for genetic diversity estimate and cross-species amplificationPLANT BREEDING, Issue 1 2010A. Chandra With 1 figure and 1 table Abstract Guineagrass (Panicum maximum Jacq.) is one of the major forage grasses in tropical and semitropical regions, largely apomictic and predominantly exist as tetraploid. Non-availability of polymorphic molecular markers has been a major limitation in its characterization and improvement. We report isolation and characterization of microsatellites in P. maximum and cross-species results with other five Panicum species. Based on microsatellite-motifs, 15 functional and polymorphic simple sequence repeat (SSR) primer-pairs were designed, validated and employed in estimating genetic relationship among 34 guineagrass accessions. Thirteen primer-pairs amplified single locus and remaining two generated more than two loci with an average of 3.57 bands per locus amounts to 63 bands with 34 guineagrass accessions. Average expected heterozygosity (HE) of 0.35 (maximum 0.97) and observed heterozygosity (HO) of 0.37 (maximum 0.91) established the efficiency of developed markers for discriminating guineagrass accessions. Dice's similarity coefficients-based unweighted pair group with arithmetic average method-clustering supported with high bootstrap values (,40) indicated its significance and distinguished all accessions except IG97-93 and IG97-6. Utility of these new SSR loci in genetic diversity study of P. maximum and other cross,amplified species is discussed. [source] Inheritance of very high linoleic acid content and its relationship with nuclear male sterility in safflowerPLANT BREEDING, Issue 5 2008Y. A. S. Hamdan Abstract Safflower (Carthamus tinctorius L.) possesses the highest amount of linoleic acid among the 10 major vegetable oil crops of the world. Very high linoleic acid content is controlled by recessive alleles at a single locus Li. However, deviated segregations from the expected monogenic inheritance have been observed in crosses involving nuclear male-sterile (NMS) lines. The present research was undertaken to study the inheritance of very high linoleic acid content in safflower and its relationship with nuclear male sterility. F1, F2, F3, BC1F1 and BC1F2 seed generations were evaluated in a cross between CR-142 (a line with very high linoleic acid content, 88%) and CL1 (an NMS line with wild-type linoleic acid content, 74%). The genetics of linoleic acid content in male-sterile plants was determined by testcrossing with CR-142. The results confirmed monogenic inheritance. The analysis of the F3 and BC1F2 to CL1 seed generations demonstrated a repulsion-phase linkage between Li and Ms loci, the latter conferring the NMS trait. The recombination rate between Li and Ms was estimated to be 0.09. [source] Inheritance of resistance to broomrape (Orobanche cumana Wallr.) race F in a sunflower line derived from wild sunflower speciesPLANT BREEDING, Issue 1 2007L. Velasco Abstract Genetic resistance to broomrape (Orobanche cumana Wallr.) race F in sunflower line J1, derived from the wild perennial species Helianthusgrosseserratus Martens and Helianthus divaricatus L., has been reported to be controlled by dominant alleles at a single locus, Or6. However, deviations from this monogenic inheritance have been observed. The objective of the present study was to gain insight into the inheritance of resistance to broomrape race F in the sunflower line J1. F1, F2, F3 and BC generations from crosses between J1 and three susceptible lines, P21, NR5 and HA821 were evaluated. F1 hybrids showed both resistant (R) and moderately resistant (MR) plants, the latter having a maximum of five broomrape stalks per plant compared with >10 in the susceptible parents. This indicated incomplete dominance of the Or6 alleles. F2 plants were classified as R, MR or susceptible (more than five broomrape stalks per plant). Three different segregation ratios were observed: 3 : 1, 13 : 3 and 15 : 1 (R + MR : S), suggesting the presence of a second gene, Or7, whose expression was influenced by the environment. A digenic model was confirmed, based on the evaluation of F2:3 families. [source] Maize mutants affected at distinct stages of the arbuscular mycorrhizal symbiosisTHE PLANT JOURNAL, Issue 2 2006Uta Paszkowski Summary Maize mutants affected in the symbiotic interaction with the arbuscular mycorrhizal fungus Glomus mosseae have been found by a visual, macroscopic screen in a Mutator -tagged population of maize. Seven mutants have been identified, falling into three phenotypic classes. For each class one mutant has been characterized in more detail. The nope1 (noperception 1) mutant does not support appressoria formation of G. mosseae, suggesting the absence of a plant-encoded function necessary for early recognition prior to contact. The phenotype segregated as a monogenic recessive trait, indicating that a mutation in a single locus abolished compatibility of maize to G. mosseae. On a second mutant termed taci1 (taciturn 1), appressoria form at reduced frequency but their morphology is normal and leads to penetration of the rhizodermis. However, intraradically, the majority of hyphae are septate, resulting in terminated fungal spreading. This phenotype suggests that the mutation of taci1 has an effect on recognition and on cortex invasion. Segregation analysis indicates taci1 to carry a recessive mutation. In contrast, wild-type fungal morphology has been recorded in the Pram1 (Precocious arbuscular mycorrhiza 1) mutant, which displays enhanced and earlier fungal invasion. This trait segregates in a dominant fashion indicative of a gain-of-function mutation affecting the plant's control over restricting fungal colonization. [source] A Generalized Caprine-like Hypoplasia Syndrome is localized within a 6-cM interval on bovine chromosome 13 in the Montbéliarde breedANIMAL GENETICS, Issue 2 2008A. Duchesne Summary Caprine-like Generalized Hypoplasia Syndrome (or SHGC) is a new hereditary disorder described in the Montbéliarde breed. We report here the characterization of this new disease, based on the visual examination of animals affected by SHGC, and on physiological and biochemical studies undertaken on samples of both SHGC and normal animals. Biological samples for more than 150 affected calves and their parents have been collected over the past 4 years within the framework of the Bovine Genetic Disease Observatory. First, pedigree analyses showed that the mode of inheritance is most probably autosomal recessive. Then, a genome scan with 113 animals and 140 microsatellite markers revealed a single locus within a 35-cM region on bovine chromosome 13. Genotypes of 261 animals for 18 new microsatellite markers from the region confirmed the localization of the disorder to a 6-cM interval. Finally, based on the analysis of haplotypes in 463 Montbéliarde sires, we estimated the frequency of the SHGC mutated allele in the population and could propose a strategy for the systematic eradication of this disorder in the near future. [source] Binomial Mixture Model-based Association Tests under Genetic HeterogeneityANNALS OF HUMAN GENETICS, Issue 6 2009Hui Zhou Summary Most of the existing association tests for population-based case-control studies are based on comparing the mean genotype scores between the case and control groups, which may not be efficient under genetic heterogeneity. Given that most common diseases are genetically heterogeneous, caused by mutations in multiple loci, it may be beneficial to fully account for genetic heterogeneity in an association test. Here we first propose a binomial mixture model for such a purpose and develop a corresponding mixture likelihood ratio test (MLRT) for a single locus. We also consider two methods to combine single-locus-based MLRTs across multiple loci in linkage disequilibrium to boost power when causal SNPs are not genotyped. We show with a wide spectrum of numerical examples that under genetic heterogeneity the proposed tests are more powerful than some commonly used association tests. [source] Ancestral Inference in Population Genetics Models with Selection (with Discussion)AUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS, Issue 4 2003Matthew Stephens Summary A new algorithm is presented for exact simulation from the conditional distribution of the genealogical history of a sample, given the composition of the sample, for population genetics models with general diploid selection. The method applies to the usual diffusion approximation of evolution at a single locus, in a randomly mating population of constant size, for mutation models in which the distribution of the type of a mutant does not depend on the type of the progenitor allele; this includes any model with only two alleles. The new method is applied to ancestral inference for the two-allele case, both with genic selection and heterozygote advantage and disadvantage, where one of the alleles is assumed to have resulted from a unique mutation event. The paper describes how the method could be used for inference when data are also available at neutral markers linked to the locus under selection. It also informally describes and constructs the non-neutral Fleming,Viot measure-valued diffusion. [source] | ||||||||||||||||||||||||||||