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PubMedDate not supplied

Identification and analysis of genetic variation among rose cultivars using random amplified polymorphic DNA.

Identified germplasm is an important component for efficient and effective management of plant genetic resources. Traditionally, cultivars or species identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and analysis of genetic variation within 34 rose cultivars through random amplified polymorphic DNA (RAPD) markers. Analysis was made by using twenty five decamer primers. Out of twenty five, ten primers were selected and used for identification and analysis of genetic relationships among 34 rose cultivars. A total of 162 distinct DNA fragments ranging from 0.1 to 3.4 kb was amplified by using 10 selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 34 rose cultivars form 9 clusters. The first cluster consists of eight hybrid cultivars, three clusters having five cultivars each, one cluster having four cultivars, two clusters having three cultivars each and two clusters having one cultivar each. The genetic distance was very close within the cultivars. Thus, these RAPD markers have the potential for identification of clusters and characterization of genetic variation within the cultivars. This is also helpful in rose breeding programs and provides a major input into conservation biology.

Base Sequence↗
PubMed2005

Shifts of Bordetella pertussis variants in Sweden from 1970 to 2003, during three periods marked by different vaccination programs.

The Swedish population of Bordetella pertussis strains was characterized from 1,247 isolates covering a whole-cell vaccine program up to 1979, a 17-year period without vaccination (1979 to 1996), and a period after the introduction of general vaccination among newborns with acellular pertussis vaccines (1997 to 2003). Strains were characterized by serotyping and genotyping of pertactin and ptxA and by means of pulsed-field gel electrophoresis (PFGE). With emphasis on vaccine-related markers, the vast majority of circulating strains were of nonvaccine type. There were shifts of serotype connected with shifts of vaccination program. Serotype Fim3 was most frequent during the periods with general vaccination schedules, whereas serotype Fim2 was predominant during the 17-year vaccine-free period. Pertactin 1 was predominant during the pertussis whole-cell (Pw) vaccine period but was thereafter replaced by prn2 and has not reappeared after the introduction of acellular pertussis (Pa) vaccines. ptxA (1) was predominant over all three decades. There was a significant difference in the distribution of serotypes between vaccinated and unvaccinated individuals, but not for pertactin. A few PFGE profiles were predominant over the years: BpSR25 (serotype Fim3 prn1/7) and BpSR18 (serotype Fim3 prn2) during the Pw period, BpSR1 (serotype Fim2 prn2) during the 17 years without general vaccination, and BpSR11 (serotype Fim3 prn2) after the reintroduction of general vaccination in 1996. Despite differences between the pertactin and toxin types of Pa vaccines and circulating strains, there is no evidence that there is a threat, i.e., the vaccination program so far has been effective against whooping cough, and there seems to be no impact on the effectiveness of the vaccination program from the bacterial polymorphism.

Bacterial Outer Membrane Proteins↗
PubMed2004

[Allozyme variability of provenance populations of Robinia pseudoacacia from Middle Europe].

Using starch gel and polyacrylamide gel electrophoresis, 11 enzyme systems of two-year-old seedlings from 18 provences of Robinia pseudoacacia distributing in the middle Europe and America were investigated. There were 14 polymorphic loci with a proportion of 70.0% in twenty loci. Twelve polymorphic loci in 7 enzyme systems were calculated. In the 12 polymorphic loci, the mean and effective numbers of alleles per locus were 2.733 and 1.794, as well as the mean observed and expected heterozygosities were 0.368 and 0.400, respectively. Fixation index in most of the loci was slightly higher than zero with a mean value of 0.080. The most population genetic parameters (A, Ae, Ho, He) at the Fe-b and Lap-a loci correlated closely with the mean number of the twelve loci, and such relation was not evident among other loci which may be more important. The genetic distance among the 8 provenances in Germany changed between 0.09 and 0.26, while in contrast, that of the 6 provenances in Hungary were very small and most of them were below 0.11. The genetic distance among the provenances in Germany, Hungary and Slovakia varied from 0.09 to 0.24. Among the 2 provenances in America and provenances in Europe, the genetic distance changed from 0.09 to 0.23, which was not higher than the differences among that of the Europe provenances. Genetic parameters and heredity diversities of the 8 provenances in Hungary and Slovakia were higher than those of the Germany provenances. The differentiation coefficient of the two countries changed from 2.92% to 9.97%, indicting that the genetic difference among the provenances in Hungary and Slovakia was smaller than in Germany provenances. Interpopulational differentiation coefficient in Germany provenances was higher compared with that in Hungary and Slovakia provenances. We took a country as one unit of provenance population, and then the differentiation coefficient of the genetic parameters of the four populations, changing between 3.870% and 5.139%, was rather small. This indicated that it was not evident for the interpopulational geographic differentiations of Robinia pseudoacacia. Therefore, it is suggested that Robinia pseudoacacia has higher genetic diversity and the breeding programs might have been concentrated on intrapopulational variation.

Genetic Variation↗
PubMed2005

Exploiting genotypic variation in plant nutrient accumulation to alleviate micronutrient deficiency in populations.

More than 2 billion people consume diets that are less diverse than 30 years ago, leading to deficiencies in micronutrients, especially iron (Fe), zinc (Zn), selenium (Se), iodine (I), and also vitamin A. A strategy that exploits genetic variability to breed staple crops with enhanced ability to fortify themselves with micronutrients (genetic biofortification) offers a sustainable, cost-effective alternative to conventional supplementation and fortification programs. This is more likely to reach those most in need, has the added advantages of requiring no change in current consumer behaviour to be effective, and is transportable to a range of countries. Research by our group, along with studies elsewhere, has demonstrated conclusively that substantial genotypic variation exists in nutrient (e.g. Fe, Zn) and nutrient promotor (e.g. inulin) concentrations in wheat and other staple foods. A rapid screening technique has been developed for lutein content of wheat and triticale, and also for pro-vitamin A carotenoids in bread wheat. This will allow cost-effective screening of a wider range of genotypes that may reveal greater genotypic variation in these traits. Moreover, deeper understanding of genetic control mechanisms and development of molecular markers will facilitate breeding programs. We suggest that a combined strategy utilising plant breeding for higher micronutrient density; maximising the effects of nutritional promoters (e.g. inulin, vitamin C) by promoting favourable dietary combinations, as well as by plant breeding; and agronomic biofortification (e.g. adding iodide or iodate as fertiliser; applying selenate to cereal crops by spraying or adding to fertiliser) is likely to be the most effective way to improve the nutrition of populations. Furthermore, the importance of detecting and exploiting beneficial interactions is illustrated by our discovery that in Fe-deficient chickens, circulating Fe concentrations can be restored to normal levels by lutein supplementation. Further bioavailability/bioefficacy trials with animals and humans are needed, using varying dietary concentrations of Fe, Zn, carotenoids, inulin, Se and I to elucidate other important interactions in order to optimise delivery in biofortification programs.

Carotenoids↗
PubMedDate not supplied

Assessment of genetic diversity among 16 promising cultivars of ginger using cytological and molecular markers.

Ginger (Zingiber officinale Roscoe) is an economically important plant, valued all over the world. The existing variation among 16 promising cultivars as observed through differential rhizome yield (181.9 to 477.3 g) was proved to have a genetic basis using different genetic markers such as karyotype, 4C nuclear DNA content and random amplified polymorphic DNA (RAPD). The karyotypic analysis revealed a differential distribution of A, B, C, D and E type of chromosomes among different cultivars as represented by different karyotype formulas. A significant variation of 4C DNA content was recorded in ginger at an intraspecific level with values ranging from 17.1 to 24.3 pg. RAPD analysis revealed a differential polymorphism of DNA showing a number of polymorphic bands ranging from 26 to 70 among 16 cultivars. The RAPD primers OPC02, OPA02, OPD20 and OPN06 showing strong resolving power were able to distinguish all 16 cultivars. The extent of genetic diversity among these cultivars was computed through parameters of gene diversity, sum of allele numbers per locus and Shannon's information indices. Cluster analysis, Nei's genetic similarity and genetic distances, distribution of cultivars into special distance classes and principal coordinate analysis and the analysis of molecular variance suggested a conspicuous genetic diversity among different cultivars studied. The genetic variation thus detected among promising cultivars of ginger has significance for ginger improvement programs.

DNA, Plant↗
PubMed2001

The generation and persistence of genetic variation in foot-and-mouth disease virus.

Genetic variation in foot-and-mouth disease virus (FMDV) is of interest for at least two reasons. First, changes to the genes encoding capsid proteins results in antigenic variation, and affects vaccine efficiency and effectiveness of vaccination programs; second, genetic changes can lead to important insights into the transport of virus between countries, regions, herds, and even possibly individuals. Current estimates of RNA virus mutation rates suggest that an average of about one base mis-incorporation is likely to occur each time a single FMDV genome replicates. This should result in the introduction of every possible 1-step mutation from the progenitor genotype into the viraemia of a single infected animal many times a day. In the absence of purifying selection, a single infected animal should therefore generate a genetically very diverse population of virus.Viral-capsid sequences obtained from infected animals sampled over long-term FMDV epidemics suggest that these genetic changes accrue in a remarkably linear 'clock-like' fashion and at rates of around 1% change per year. While such a rate is generally regarded as quite high, it is actually somewhat lower than one might expect based on the rate at which viral diversity could be generated within a single animal. The difference might be explained in a variety of possible ways: (1) the mutation rate has been overestimated; (2) purifying selection is stronger than predicted; (3) only a restricted subset of excreted virus is actually infectious; (4) infected animals only excrete virus from a small partitioned subset of amplified virus, and that most of the generated viral diversity is unable to exit the animal; or (5) only a small fraction of all infected animals participate in the actual disease-transmission process.

Animals↗
PubMedDate not supplied

Identification and genetic variation among Hibiscus species (Malvaceae) using RAPD markers.

Germplasm identification and characterization is an important link between the conservation and utilization of plant genetic resources. Traditionally, species or cultivars identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and determination of genetic variation within the two species of Hibiscus and 16 varieties of Hibiscus rosa-sinensis L. through random amplified polymorphic (RAPD) markers. Primer screening was made by using the DNA of variety "Prolific". Genetic analysis was made by using ten selected decamer primers. A total of 79 distinct DNA fragments ranging from 0.3 to 2.5 kb were amplified by using ten selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 16 varieties and two species formed one cluster. The first major cluster consisted of three varieties and a second major cluster consisted of two species and 13 varieties. The genetic distance was very close within the varieties and also among the species. Thus, these RAPD markers have the potential for identification of species/varieties and characterization of genetic variation within the varieties. This is also helpful in Hibiscus breeding programs and provides a major input into conservation biology.

Base Sequence↗
PubMedDate not supplied

Newborn screening and genetic testing.

New screening techniques and diagnostic tests for genetic diseases available for newborn screening can provide information about many diseases long before they are clinically detected. However, this information creates complex questions and ethical dilemmas regarding which newborns should be tested, when testing should occur, availability and costs of tests, and how families should be counseled. There is no national policy regarding newborn screening, which leads to great variation among states' newborn screening programs. This article reviews newborn genetic testing and provides a blueprint for clinicians to improve practice by incorporating into their care knowledge of new developments in newborn testing and screening.

Genetic Counseling↗
PubMed2003

Persistence of vaccine-derived polioviruses among immunodeficient persons with vaccine-associated paralytic poliomyelitis.

To estimate long-term poliovaccine virus persistence among immunodeficient patients with vaccine-associated paralytic poliomyelitis (iVAPP), cases reported in the United States during 1975-1997 were reviewed, with subsequent follow-up and virological testing. Six (16.2%) of 37 subjects excreted poliovaccine viruses for > or =6 months. Partial genomic sequencing of their available poliovirus isolates showed considerable divergence from the prototype Sabin strain in all cases. Poliovirus persistence declined over time since the last oral poliovaccine dose: at 6 months, 19.4%; 1 year, 14.3%; 5 years, 4%; and 10 years, 0% (P<.05) of patients. Despite the high prevalence of poliovaccine virus persistence among patients with iVAPP, this group appears to be an unlikely source of poliovirus reintroduction in developed countries because of the rarity and high fatality rate of iVAPP and the possible spontaneous clearance of polioviruses. These results are important for developing "endgame" strategies for the Global Poliomyelitis Eradication Program.

Feces↗
PubMed2003

Characterization of microsatellites in wild and sweet cherry (Prunus avium L.)--markers for individual identification and reproductive processes.

Nuclear microsatellites were characterized in Prunus avium and validated as markers for individual and cultivar identification, as well as for studies of pollen- and seed-mediated gene flow. We used 20 primer pairs from a simple sequence repeat (SSR) library of Prunus persica and identified 7 loci harboring polymorphic microsatellite sequences in P. avium. In a natural population of 75 wild cherry trees, the number of alleles per locus ranged from 4 to 9 and expected heterozygosity from 0.39 to 0.77. The variability of the SSR markers allowed an unambiguous identification of individual trees and potential root suckers. Additionally, we analyzed 13 sweet cherry cultivars and differentiated 12 of them. An exclusion probability of 0.984 was calculated, which indicates that the seven loci are suitable markers for paternity analysis. The woody endocarp was successfully used for resolution of all microsatellite loci and exhibited the same multilocus genotype as the mother tree, as shown in a single seed progeny. Hence, SSR fingerprinting of the purely maternal endocarp was also successful in this Prunus species, allowing the identification of the mother tree of the dispersed seeds. The linkage of microsatellite loci with PCR-amplified alleles of the self-incompatibility locus was tested in two full-sib families of sweet cherry cultivars. From low recombination frequencies, we inferred that two loci are linked with the S locus. The present study provides markers that will significantly facilitate studies of spatial genetic variation and gene flow in wild cherry, as well as breeding programs in sweet cherry.

Genetic Linkage↗
PubMed2004

Association between variation in the human KCNJ10 potassium ion channel gene and seizure susceptibility.

PURPOSE: Our research program uses genetic linkage and association analysis to identify human seizure sensitivity and resistance alleles. Quantitative trait loci mapping in mice led to identification of genetic variation in the potassium ion channel gene Kcnj10, implicating it as a putative seizure susceptibility gene. The purpose of this work was to translate these animal model data to a human genetic association study. METHODS: We used single stranded conformation polymorphism (SSCP) electrophoresis, DNA sequencing and database searching (NCBI) to identify variation in the human KCNJ10 gene. Restriction fragment length polymorphism (RFLP) analysis, SSCP and Pyrosequencing were used to genotype a single nucleotide polymorphism (SNP, dbSNP rs#1130183) in KCNJ10 in epilepsy patients (n = 407) and unrelated controls (n = 284). The epilepsy group was comprised of patients with refractory mesial temporal lobe epilepsy (n = 153), childhood absence (n = 84), juvenile myoclonic (n = 111) and idiopathic generalized epilepsy not otherwise specified (IGE-NOS, n = 59) and all were of European ancestry. RESULTS: SNP rs#1130183 (C > T) alters amino acid 271 (of 379) from an arginine to a cysteine (R271C). The C allele (Arg) is common with conversion to the T allele (Cys) occurring twice as often in controls compared to epilepsy patients. Contingency analysis documented a statistically significant association between seizure resistance and allele frequency, Mantel-Haenszel chi square = 5.65, d.f. = 1, P = 0.017, odds ratio 0.52, 95% CI 0.33-0.82. CONCLUSION: The T allele of SNP rs#1130183 is associated with seizure resistance when common forms of focal and generalized epilepsy are analyzed as a group. These data suggest that this missense variation in KCNJ10 (or a nearby variation) is related to general seizure susceptibility in humans.

Chi-Square Distribution↗
PubMed2006

Recent advances in array comparative genomic hybridization technologies and their applications in human genetics.

Array comparative genomic hybridization (array CGH) is a method used to detect segmental DNA copy number alterations. Recently, advances in this technology have enabled high-resolution examination for identifying genetic alterations and copy number variations on a genome-wide scale. This review describes the current genomic array platforms and CGH methodologies, highlights their applications for studying cancer genetics, constitutional disease and human variation, and discusses visualization and analytical software programs for computational interpretation of array CGH data.

Gene Dosage↗
PubMed2006

Genome-wide investigation on the genetic variations of rice disease resistance genes.

Exploitation of plant disease resistance (R) gene in breeding programs has been proven to be the most efficient strategy for coping with the threat of pathogens. An understanding of R-gene variation is the basis for this strategy. Here we report a genome-wide investigation on the variation of NBS-LRR-encoding genes, the common type of R genes, between two sequenced rice genomes, Oryza sativa L. var. Nipponbare and 93-11. We show that the allelic nucleotide diversity in 65.0% of 397 least-divergent pairs is not high (0.344% on average), while the remaining 35% display a greater diversity (5.4% on average). The majority of conserved R genes is single-copy and/or located as a singleton. The clustered, particularly the complex-clustered, R-genes contribute greatly to the rich genetic variation. Surprisingly only 11.2% of R-genes have remarkably high ratios of non-synonymous to synonymous rates, which is much less than the 17.4% observed between Arabidopsis genomes. Noticeable "artificially selective sweeping" could be detected in a large proportion of the conserved R-genes, a scenario described in the "arms race" co-evolutionary model. Based on our study, a variation pattern of R-genes is proposed and confirmed by the analysis of R-genes from other rice lines, indicating that the observed variation pattern may be common in all rice lines.

Genes, Plant↗
PubMed2002

Spatial homogeneity and temporal heterogeneity of red drum (Sciaenops ocellatus) microsatellites: effective population sizes and management implications.

The red drum (Sciaenops ocellatus) is one of a number of species that occupy estuarine waters as juveniles and migrate to open ocean waters as adults. This species has experienced dramatic declines in population numbers over the past 2 decades, which has prompted increasing fishery restriction. In addition, hatchery augmentation has been initiated by several states to increase the abundance of juveniles in local areas. In South Carolina hatchery-reared fish have made significant (20%) contributions to the juvenile population on very local scales. As hatchery-reared fish are typically produced by a small number of individuals, the genetic consequences of augmentation programs are of concern. In this article we assess genetic variation at 5 microsatellite loci in S. ocellatus. The data indicate little geographic differentiation among samples collected along the Atlantic Coast of the United States, but substantial differences among year classes taken from South Carolina. The gene frequency differences among year classes were used to estimate the effective population size (Nc) of S. ocellatus in South Carolina and suggested that Ne was less than 300 from 1990 to 1993 and increased to about 1000 in 1994 and 1995. Whether this increase reflects the effectiveness of management regulations or simply a random fluctuation in S. ocellatus populations is not clear. The data suggest that a limited number of individuals produce the bulk of a given year class and support the sweepstakes hypothesis. Given the small Ne and estimates of the contribution of hatchery-reared fish to the wild stock, it is suggested that programs have the potential to increase, rather than decrease; Ne in the wild.

Journal Article↗
PubMed1987

Genetic relationships and additive genetic variation of productive and reproductive traits in Guernsey dairy cattle.

Data were first lactation production and reproduction records initiated from 1958 to 1981 in two experiment station Guernsey herds. Heritability estimates using paternal half sib groups were .24 +/- .12 for milk yield, .27 +/- .12 for fat yield, and .77 +/- .15 for fat percentage. Heritability estimates for reproductive traits ranged from .01 to .04 for number of services, service period, conception rate, and days open, but were higher for days in milk at first breeding (.12) and age at first calving (.13). Except for age at first calving, coefficients of additive genetic variation were larger for reproductive traits than for productive traits. Genetic correlations between measures of production and reproduction were moderate to large and antagonistic, except that the relationship between production and age at first calving was favorable. Breeding value estimates for milk yield and reproduction were negatively correlated for sires with above average breeding values for milk yield. Huge phenotypic variances for reproductive traits masked substantial additive genetic variation for these traits. When all things are considered it seems unwise to ignore reproductive performance in selection programs for dairy cattle.

Animals↗
PubMed1999

Population structure, speciation, and introgression in the Anopheles gambiae complex.

We review here what is known about the population structure and evolutionary dynamics of members of the Anopheles gambiae complex with emphasis on the situation in West Africa. First, the importance of the 2nd chromosome inversion polymorphism is demonstrated especially in adaptation to levels of aridity, a major environmental variable in Africa. This affects the distribution of karyotypes on both a macro- and micro-geographic scale as well as temporally. Such differentiation leads to karyotypes being differentially effective transmitters of malaria and differentially susceptible to indoor residual spraying of insecticides. Second, we review the evidence that cryptic taxa, especially in An. gambiae s.s., exist. This observation stems from both karyotype studies and molecular studies. It is abundantly clear that West African populations of An. gambiae s.s. are often not panmictic units, with premating factors evidently acting to maintain distinct genetic forms. Third, we review phylogenetic studies that have revealed the presence of introgression between the two most important vectors, An. gambiae and An. arabiensis. This is most evident for the 2nd chromosome inversions. This interpretation of phylogenetic data is consistent with a direct laboratory study indicating inversions in this chromosome are stably maintained in back-crossed populations. All of this information has led to the view that members of the An. gambiae complex are highly variable with an abundance of adaptive genetic variation. This presents a significant challenge to vector control programs designed to reduce malaria in sub-Saharan Africa.

Africa, Western↗
PubMed1994

Quantitative- and molecular-genetic effects on animal well-being: adaptive mechanisms.

Domestic farm animals play an important role in meeting some basic needs of humankind, especially food and clothing. The aspects of genetic improvement programs in livestock production pertinent to animal welfare and animal well-being are reviewed. A link is made between the evolutionary processes of adaptation and domestication and animal well-being. Animal behavior is a component of all these. Thus, the genetics of behavior may provide clues to the well-being of farm animal populations, and it will also be of relevance to public opinion issues of animal welfare. Many expressions of behavior by domestic livestock may be influenced by those processes that change gene as well as genotypic frequencies such as inbreeding, drift, and artificial selection. The environment in which the individual lives will also play a role, along with the interaction between genotype and environment. Selection for or against such behaviors as aggressiveness, docility, response to stress, and certain sexual behaviors in some livestock species has often been successful. This points to the existence of additive genetic variation for behavior, and scope for the inclusion of behavioral traits into selection programs, if these measures are shown to be related to welfare. Negative relationships between behaviors associated with well-being and traits of economic importance have been reported in most livestock species. However, estimates of genetic parameters, especially genetic correlations between objective measures of well-being and production traits, are scarce. There have been no comprehensive studies of the welfare of transgenic animals reported in the scientific literature. Increased use of biotechnology in animal agriculture, coupled with greater public scrutiny of livestock industries, may precipitate decisions concerning the interface of behavior and genetics that need to be addressed before scientists can conduct appropriate experimental evaluations.

Adaptation, Physiological↗
PubMed2002

Estimated genetic parameters for carcass traits of Brahman cattle.

Heritabilities and genetic and phenotypic correlations were estimated from feedlot and carcass data collected from Brahman calves (n = 504) in central Florida from 1996 to 2000. Data were analyzed using animal models in MTDFREML. Models included contemporary group (n = 44; groups of calves of the same sex, fed in the same pen, slaughtered on the same day) as a fixed effect and calf age in days at slaughter as a continuous variable. Estimated feedlot trait heritabilities were 0.64, 0.67, 0.47, and 0.26 for ADG, hip height at slaughter, slaughter weight, and shrink. The USDA yield grade estimated heritability was 0.71; heritabilities for component traits of yield grade, including hot carcass weight, adjusted 12th rib backfat thickness, loin muscle area, and percentage kidney, pelvic, and heart fat were 0.55, 0.63, 0.44, and 0.46, respectively. Heritability estimates for dressing percentage, marbling score, USDA quality grade, cutability, retail yield, and carcass hump height were 0.77, 0.44, 0.47, 0.71, 0.5, and 0.54, respectively. Estimated genetic correlations of adjusted 12th rib backfat thickness with ADG, slaughter weight, marbling score, percentage kidney, pelvic, and heart fat, and yield grade (0.49, 0.46, 0.56, 0.63, and 0.93, respectively) were generally larger than most literature estimates. Estimated genetic correlations of marbling score with ADG, percentage shrink, loin muscle area, percentage kidney, pelvic, and heart fat, USDA yield grade, cutability, retail yield, and carcass hump height were 0.28, 0.49, 0.44, 0.27, 0.45, -0.43, 0.27, and 0.43, respectively. Results indicate that sufficient genetic variation exists within the Brahman breed for design and implementation of effective selection programs for important carcass quality and yield traits.

Animals↗