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PubMed2006

Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers.

Population-based methods for the genetic mapping of adaptive traits and the analysis of natural selection require that the population structure and demographic history of a species are taken into account. We characterized geographic patterns of genetic variation in the model plant Arabidopsis thaliana by genotyping 115 genome-wide single nucleotide polymorphism (SNP) markers in 351 accessions from the whole species range using a matrix-assisted laser desorption/ionization time-of-flight assay, and by sequencing of nine unlinked short genomic regions in a subset of 64 accessions. The observed frequency distribution of SNPs is not consistent with a constant-size neutral model of sequence polymorphism due to an excess of rare polymorphisms. There is evidence for a significant population structure as indicated by differences in genetic diversity between geographic regions. Accessions from Central Asia have a low level of polymorphism and an increased level of genome-wide linkage disequilibrium (LD) relative to accessions from the Iberian Peninsula and Central Europe. Cluster analysis with the structure program grouped Eurasian accessions into K = 6 clusters. Accessions from the Iberian Peninsula and from Central Asia constitute distinct populations, whereas Central and Eastern European accessions represent admixed populations in which genomes were reshuffled by historical recombination events. These patterns likely result from a rapid postglacial recolonization of Eurasia from glacial refugial populations. Our analyses suggest that mapping populations for association or LD mapping should be chosen from regional rather than a species-wide sample or identified genetically as sets of individuals with similar average genetic distances.

Arabidopsis↗
PubMed2006

Identification and analysis of gene families from the duplicated genome of soybean using EST sequences.

BACKGROUND: Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. Soybean has a large (1115 Mbp) genome that has yet to be fully sequenced. However it does have the 6th largest EST collection comprised of ESTs from a variety of soybean genotypes. Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. We used the ESTminer suite of programs to identify potential soybean gene transcripts from a single genetic background allowing us to observe functional classifications between gene families as well as structural differences between genes and gene paralogs within families. The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. RESULTS: We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean (Glycine max L. Merr.) using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. CONCLUSION: The predominance of single nucleotide insertion/deletions and substitution events between genes within families (individual genes and gene paralogs) is consistent with a model of gene amplification followed by single base random mutational events expected under the classical model of duplicated gene evolution. Molecular functions of small and large gene families appear to be non-randomly distributed possibly indicating a difference in retention of duplicates or local expansion.

Evolution, Molecular↗
PubMed2002

Factor analysis of cluster-specific gene expression levels from cDNA microarrays.

The ever-increasing use of cDNA microarrays in medical research will require the development of new algorithms designed specifically for desktop analysis of potentially large genetic data sets. This paper describes the CLUSFAVOR algorithm (CLUSter and Factor Analysis Using Varimax Orthogonal Rotation) for performing cluster and factor analysis of gene expression data obtained from cDNA microarrays. A unique feature of the CLUSFAVOR algorithm is that a user can perform cluster analysis, view dendograms, and run factor analysis on cluster-specific genes selected interactively within a single executable program. CLUSFAVOR also performs a varimax orthogonal rotation on the extracted factors to increase parsimony in the loadings, revealing unique expression profiles for genes and expressed sequence tags (ESTs) for which pathway and function information is unknown. Microarray data used by the program must be stored and input from a disk file. Optional output contains matrices for the input data, standardized data, distance matrices, factor loadings, eigenvalues, eigenvectors, and percentage of total variation for genes within a cluster. Color cluster image displays containing gene expression levels, dendograms for arrays and genes, and factor loadings are displayed for the entire group of genes and arrays analyzed as well as selected genes within a cluster. Cluster images are also exported to JPG and linked to HTML files for viewing.

Algorithms↗
PubMed1982

Enzyme polymorphism in Ascaris suum (Nematoda).

The potential of multilocus electrophoretic studies for providing insight into the population biology of parasitic organisms was studied using the swine parasite Ascaris suum suum. Thirty-eight loci encoding enzymatic or nonenzymatic proteins have been resolved in extracts of adult worms by starch-gel electrophoresis. A preliminary study of variation in Ascaris from eastern Iowa revealed an average heterozygosity of 6.6%. Allele frequencies at six polymorphic loci were similar in males and females and genotypic frequencies were in accord with those expected in a single, randomly mating population; however, the significant linkage disequilibrium between Pep-2 and Es-3 suggested that there may be some genetic substructuring within Ascaris from Iowa. Genetic comparisons of Ascaris from Iowa with Ascaris from New Jersey and Maryland indicated slight differences between eastern and midwestern populations, as well as between the east coast localities. Larger samples from more locations are needed before any statistical significance can be attached to these differences; however, qualitative comparisons suggest that the differentiation is a biological reality. Knowledge of the population biology of this and other parasites may contribute to planning effective control programs.

Animals↗
PubMed2001

Population pharmacokinetic analysis resulting in a tool for dose individualization of busulphan in bone marrow transplantation recipients.

The aims of the present study were (1) to investigate and quantify the pharmacokinetics, including inter-occasion variability and covariate relationships, of busulphan in BMT patients and (2) to develop a user-friendly initial dosing and therapeutic drug monitoring (TDM) strategy for the treatment of those patients with busulphan. The pharmacokinetics of busulphan was studied in 64 adults and 12 children who received busulphan (1 mg/kg) four times daily for 4 days. A one-compartment model with first order absorption and a lag time was sufficient in describing the concentration-time profile. Oral clearance (CL/F) was found to be correlated to weight (+1.2%/kg), ALT (-13%/microcat/l) and concomitant phenytoin treatment (+21%). CL/F and the volume of distribution (V/F) were estimated to 9.23 l/h and 39.3 l, respectively, in a typical individual. Inter-occasion variability (9.4%) in CL/F was estimated to be less than inter-individual variability (28%), a prerequisite for the value of TDM. Bayesian CL/F estimates based on three samples were in good accordance with those based on all samples. The final population model was implemented into the program Excel. The resulting flexible and easy to use dosing program might be used for both initial and, requiring only three plasma samples, maintenance dose individualization of busulphan therapy.

Administration, Oral↗
PubMed2006

Estimating relatedness between individuals in general populations with a focus on their use in conservation programs.

Relatedness estimators are widely used in genetic studies, but effects of population structure on performance of estimators, criteria to evaluate estimators, and benefits of using such estimators in conservation programs have to date received little attention. In this article we present new estimators, based on the relationship between coancestry and molecular similarity between individuals, and compare them with existing estimators using Monte Carlo simulation of populations, either panmictic or structured. Estimators were evaluated using statistical criteria and a diversity criterion that minimized relatedness. Results show that ranking of estimators depends on the population structure. An existing estimator based on two-gene and four-gene coefficients of identity performs best in panmictic populations, whereas a new estimator based on coancestry performs best in structured populations. The number of marker alleles and loci did not affect ranking of estimators. Statistical criteria were insufficient to evaluate estimators for their use in conservation programs. The regression coefficient of pedigree relatedness on estimated relatedness (beta2) was substantially lower than unity for all estimators, causing overestimation of the diversity conserved. A simple correction to achieve beta2 = 1 improves both existing and new estimators. Using relatedness estimates with correction considerably increased diversity in structured populations, but did not do so or even decreased diversity in panmictic populations.

Alleles↗
PubMed2003

Fast identification and statistical evaluation of segmental homologies in comparative maps.

MOTIVATION: Chromosomal segments that share common ancestry, either through genomic duplication or species divergence, are said to be segmental homologs of one another. Their identification allows researchers to leverage knowledge of model organisms for use in other systems and is of value for studies of genome evolution. However, identification and statistical evaluation of segmental homologies can be a challenge when the segments are highly diverged. RESULTS: We describe a flexible dynamic programming algorithm for the identification of segments having multiple homologous features. We model the probability of observing putative segmental homologies by chance and incorporate our findings into the parameterization of the algorithm and the statistical evaluation of its output. Combined, these findings allow segmental homologies to be identified in comparisons within and between genomic maps in a rigorous, rapid, and automated fashion.

Algorithms↗
PubMed2002

Identification of 127 amino acid substitution variants in screening 37 DNA repair genes in humans.

The repair of damaged DNA requires the function of multiple proteins in generally damage-specific, nonredundant pathways. The relationship of DNA repair to cancer susceptibility is obvious in "cancer families," in which low frequency, high penetrance, loss-of-function variant alleles of genes with roles in the repair of damaged DNA have been associated with a high risk of disease. More important for the cancer incidence in the general population, many individuals exhibit reduced (60-75% of normal) repair capacity phenotypes that have been associated with several-fold increases in individual cancer risk. In a program to identify the molecular basis for the variation in repair capacity and the elevated cancer susceptibility, we have identified 127 amino acid substitution variants in resequencing 37 DNA repair genes in 36-164 unrelated individuals. Over 50% of the substitutions are exchanges of amino acid residues with dissimilar physical or chemical properties, at sites at which the common residue is identical in the human and mouse proteins. Five additional sequence changes resulting in proteins with altered termination of translation and one amino acid insertion variant were detected. The variant allele frequencies average 0.047, with individual variant allele frequencies ranging from <0.01 to 0.43. Homozygous variant individuals and individuals with multiple amino acid substitutions in a gene were observed. Most individuals exhibited variation in multiple genes in a repair pathway. Ten variant alleles accounted for 52% of the genetic variation among individuals, but a striking 23% of the total variation is associated with 108 variants with allele frequencies of less than 5%. Screening generally healthy individuals generates a catalogue of common variants that is a resource for molecular epidemiology studies endeavoring to use a genotype to phenotype paradigm to estimate the role of genetic variation and individual susceptibility in disease risk from environmental and lifestyle exposures in the general population of the United States.

Amino Acid Substitution↗
PubMed2004

Establishing the rDNA IGS structure of Cannabis sativa.

The rDNA intergenic spacer (IGS) structure of Cannabis sativa was established and can be used for classification and identification of this species. In this study, DNA fragments of rDNA IGS were amplified by PCR from Cannabis sativa plant extracts and a 1387 bp fragment was obtained. DNA sequence analysis revealed six different repeat motifs. In the middle of the IGS sequence, there were three sequence motifs, and the same three sections of DNA were then repeated with minor variation in sequence. The terminal region of the IGS was composed of another three different repeat units; multiple copies of these terminal repeat motifs were present in no discernible order. Within six repeat motifs, point variations were observed in five. The DNA sequence of the locus was compared with all the plant sequences registered in GenBank by the Fasta program of GCG software with the result that this DNA fragment was significantly different from any other DNA sequence recorded to date. The most similar sequence was that of Hops (Humulus lupulus), but with a similarity of only 88.9% over 579 bp. These specific and complex variations of IGS may be related to the species and geographic distributions.

Base Sequence↗
PubMed2001

[Necessary sites: identical duplication of living organisms].

The paper deals with the concept of the identity of living organisms, a concept used up until now very ambiguously. The discussion rests on the combination of two concepts, one proposed by Munzer (1993) and another derived from the considerations of Riedl (1975). The first is the proposal that the identity of living organisms depends on the properties of their elementary constituents, such as cells and tissues, and that these properties, in turn, depend on those of their DNA and RNA. It follows that the identity of a living organism remains constant or changes during life according to whether its DNA and RNA content also remains constant or changes. The second is the consideration that, during duplication of a cell population, the informational content of the population does not increase if the duplicated cells are identical (increase only of redundant DNA). On the other hand the informational content of the cell population increases if the duplicated cells are the result of a variation-selection process (increase of essential DNA). The changes of DNA and RNA content, occurring in the germinal cells during phylogenesis and in the somatic cells of the evolutionary systems during ontogenesis, lead, therefore, to the generation of new identities. Living organisms are suggested to reflect two types of identity, that of the deterministic and that of the evolutionary systems. Since the informational content of the deterministic systems (the essential DNA content) remains approximately constant during life, their identity also remains constant. The changes in the number of elementary constituents and cell volumes during the processes of hypertrophy and atrophy are accompanied only by changes in the amount of DNA (the redundant DNA). On the other hand the informational content of the evolutionary systems (the essential DNA), such as the brain-mind system, the immunological system and some receptor systems, undergo a marked increase during the ontogenic development: this leads to changes of identity of these systems. For example, in the immunological system the process of mutation and recombination of the DNA of the immunological cells leads to the generation of new proteins in the amount about 10,000 times larger than that produced through the decodification of the genome. Also the construction of the neural network, and of a number of synapses much larger than that of the neuronal cells, requires the generation of an amount of new information much larger than that contained in the genome. In short, the attribution of a double identity to living organisms reflects the simultaneous presence of systems developing either within strictly programmed limits or without programs and limits, say as closed or open projects. The difference between the two types of systems explains the different effects in the case of the transplants. The identity of the recipient of transplants is not altered in the case of transplants of a deterministic system but is so in case of transplants of evolutionary systems. There is now a widespread fear of the possibility of human cloning. It is argued that this fear is unjustified because a cloning process can never succeed in duplicating those parts which are essential for the characters of humans, namely those concerned with the properties of the evolutionary systems.

Animals↗
PubMed1998

Hepatitis C virus transmission dynamics in injection drug users.

Hepatitis C virus (HCV) presents several challenges to the development of prevention programs. HCV infection is persistent in up to 80% of cases, and viremic individuals may transmit infection to others. With 65-90% of injection drug users anti-HCV positive, a large reservoir of infection exists in most drug-injector populations. Studying the genetic variability of HCV infections could permit researchers to reconstruct chains of viral transmission in IDUs. However, the relationship of HCV to HIV epidemiology remains unclear and may depend on whether the proportions of infectious persons in the population are similar for both viruses.

DNA, Viral↗
PubMed2000

Consequences of selection for milk yield from a geneticist's viewpoint.

The annual genetic trend for milk yield of Holsteins in the United States has accelerated with time and had means of 37 kg during the 1960s, 79 kg during the 1970s, 102 kg during the 1980s, and 116 kg from 1990 to 1996. Selection programs of the dairy cattle breeding firms in the United States have become more selective and effective with time, and selection goals continue to place major emphasis on yield traits, which clearly impact profitability of dairying. Traits other than yield are also included in selection goals of the industry. Type traits, especially those related to udder conformation, body size, and angularity have been included in selection programs and have altered the appearance and physiological functions of Holstein cows. Selection programs have continued to increase the body size of Holsteins despite mounting evidence that smaller cows have advantages for survival and efficiency. Favorable emphasis on cows that appear sharper might result in cows that are more prone to metabolic problems. The high intensity of current selection in the United States has brought about a rapid increase in genetic relationships among animals. Increased relationships will inevitably result in undesirable levels of inbreeding in the commercial cow population unless dairy producers turn to crossbreeding.

Animals↗
PubMed2004

Biology, ecology and control of the Penthaleus species complex (Acari: Penthaleidae).

Blue oat mites, Penthaleus spp. (Acari: Penthaleidae), are major agricultural pests in southern Australia and other parts of the world, attacking various pasture, vegetable and crop plants. Management of these mites has been complicated by the recent discovery of three cryptic pest species of Penthaleus, whereas prior research had assumed a single species. The taxonomy, population genetics, ecology, biology and control of the Penthaleus spp. complex are reviewed. Adult Penthaleus have a dark blue-black body approximately 1 mm in length, and eight red-orange legs. Within Australia, they are winter pests completing two or three generations a season, depending on conditions. The summer is passed as diapausing eggs, when long-distance dispersal is thought to occur. The Penthaleus spp. reproduce by thelytokous parthenogenesis, with populations comprising clones that differ ecologically. The three pest Penthaleus spp. differ markedly in their distributions, plant hosts, timing of diapause egg production and response to pesticides, highlighting the need to develop control strategies that consider each species separately. Chemicals are the main weapons used in current control programs, however research continues into alternative more sustainable management options. Host plant resistance, crop rotations, conservation of natural enemies, and improved timing of pesticide application would improve the management of these pests. The most cost-effective and environmentally acceptable means of control will result from the integration of these practices combined with the development of a simple field-based kit to distinguish the different mite species.

Agriculture↗
PubMed2002

DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family.

SUMMARY: DetectIng Variability in Evolutionary Rates among GEnes (DIVERGE) is a software system to study functional divergence of a protein family by detecting site-specific change in evolutionary rate using a multiple alignment of amino acid sequences for a given phylogenetic tree. The program first conducts a statistical test for site-specific rate shifts along the tree, and predicting candidate amino acid residues responsible for functional divergence based on posterior analysis. These results can then be mapped on the 3D protein structure if available. AVAILABILITY: DIVERGE is available free of charge from http://xgu1.zool.iastate.edu/. Distribution packages for both Linux and Microsoft Windows operating systems are available, including manual and example files.

Amino Acid Sequence↗
PubMed2024

Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand?

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.

Animals↗
PubMedDate not supplied

Synthetic amphiploids in breeding--genetic and evolutionary studies in wheat.

Synthetic amphiploids play an important role in breeding programs of wheat and in the genetic and evolutionary studies of the wheat group. One of the most obvious uses of amphiploidy has been the development of hexaploid and octaploid Triticale. The utilization of synthetic amphiploids as a means of introducing commercially important features of related species into cultivated wheat is now well documented. The projects to produce hybrid wheat are based on the manipulation of cytoplasms and restorers by means of artificially obtained amphiploids. The amphiploidization of interspecific hybrids by treatment with colchicine results in homozygosity. Therefore, a direct use of synthetic amphiploids for genetic studies has been limited to some extent. More often they were used indirectly, viz. as the initial step in the production of single chromosome addition and substitution lines. Such lines were used for detailed and highly informative genetic analyses and also as sources of alien variation for wheat breeding. Crosses between some of the synthetic amphiploids resembling natural species and the cultivated wheats have been successfully used in the evolutionary studies of wheats.

Biological Evolution↗
PubMed2006

[Evaluation of the state of the gene pool of natural populations of vertebrate animals inhabiting the fragmented landscape of Moscow and Moscow district (with special reference to brown frogs)].

A system of urban ecological genetic monitoring has been developed for the first time in Russia and in the world. As a model, two species of brown frogs, Rana arvalis Nilss. and R. temporaria L. (16 populations, seven isozyme loci) were used. An evaluation of the gene pool state in urban frog populations has shown that the diversity in the Moscow frog populations was lower than that in natural populations (up to 80 and 50% in respectively R. anvalis and R. temporaria). Mean heterozygosities per locus were higher in large natural populations than in small urban isolates: in R. arvalis, these values were 0.16 and 0.06; in R. temporaria, 0.34 and 0.18, respectively. The number of polymorphic loci was also higher in natural populations than in the urban ones: 4 versus 2 in R. arvalis and 5 versus 4 in R. temporaria. Using superoxiddismutase as an example, fixation of different alleles of the same locus in different small isolates was shown. The gene pool condition of all but one urban populations of brown frog was evaluated as unsatisfactory, and that of the R. arvalis populations, as critical. These changes of the gene pool are explained mainly by gene drift accompanied by inbreeding, which was caused by human-induced fragmentation of the range and a decrease in population size of the species. The results of this study was employed in the development of the Moscow governmental program on restoration of the gene pools of vanishing animal species on specially protected natural urban territories. The series of works on long-term monitoring and assessment of the state of natural populations of model species in anthropogenic landscapes of Moscow and Moscow district has laid a foundation for a new branch of science, gene urbanology.

Alleles↗
PubMed2004

mecA Locus diversity in methicillin-resistant Staphylococcus aureus isolates in Brisbane, Australia, and the development of a novel diagnostic procedure for the Western Samoan phage pattern clone.

An emerging public health phenomenon is the increasing incidence of methicillin-resistant Staphylococcus aureus (MRSA) infections that are acquired outside of health care facilities. One lineage of community-acquired MRSA (CA-MRSA) is known as the Western Samoan phage pattern (WSPP) clone. The central aim of this study was to develop an efficient genotyping procedure for the identification of WSPP isolates. The approach taken was to make use of the highly variable region downstream of mecA in combination with a single nucleotide polymorphism (SNP) defined by the S. aureus multilocus sequence typing (MLST) database. The premise was that a combinatorial genotyping method that interrogated both a highly variable region and the genomic backbone would deliver a high degree of informative power relative to the number of genetic polymorphisms interrogated. Thirty-five MRSA isolates were used for this study, and their gene contents and order downstream of mecA were determined. The CA-MRSA isolates were found to contain a truncated mecA downstream region consisting of mecA-HVR-IS431 mec-dcs-Ins117, and a PCR-based method for identifying this structure was developed. The hospital-acquired isolates were found to contain eight different mecA downstream regions, three of which were novel. The Minimum SNPs computer software program was used to mine the S. aureus MLST database, and the arcC 272G polymorph was identified as 82% discriminatory for ST-30. A real-time PCR assay was developed to interrogate this SNP. We found that the assay for the truncated mecA downstream region in combination with the interrogation of arcC position 272 provided an unambiguous identification of WSPP isolates.

Bacterial Proteins↗