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At least 1,207 records · Page 67Linked to original sources
PubMed2005

SNP detection and genetic mapping of porcine genes encoding enzymes in hepatic metabolic pathways and evaluation of linkage with carcass traits.

We have previously identified and mapped porcine expressed sequence tags (ESTs) derived from genes that are preferentially expressed in liver. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in porcine genes encoding enzymes in hepatic metabolic pathways and use the SNPs for mapping. Furthermore, these genes, which are involved in utilization and partitioning of nutrients, were examined for their effects on carcass and meat quality traits by linkage analyses. In total, 100 ESTs were screened for SNPs by single strand conformation polymorphism analyses across a diverse panel of animals with a 36% success rate. Twelve of 36 polymorphic loci segregated in a three-generation Duroc x Berlin Miniature Pig (F2) resource population, the DUMI resource population, and were genetically mapped. Interval mapping of the corresponding chromosomes was performed to verify mapping of the genes within quantitative trait loci (QTL) regions detected in this resource population. QTL with genome-wide significance were detected in the vicinity of GNMT, ESTL147 and HGD. These loci therefore are positional candidate genes.

Animals↗
PubMed2001

Case-control studies of association in structured or admixed populations.

Case-control tests for association are an important tool for mapping complex-trait genes. But population structure can invalidate this approach, leading to apparent associations at markers that are unlinked to disease loci. Family-based tests of association can avoid this problem, but such studies are often more expensive and in some cases--particularly for late-onset diseases--are impractical. In this review article we describe a series of approaches published over the past 2 years which use multilocus genotype data to enable valid case-control tests of association, even in the presence of population structure. These tests can be classified into two categories. "Genomic control" methods use the independent marker loci to adjust the distribution of a standard test statistic, while "structured association" methods infer the details of population structure en route to testing for association. We discuss the statistical issues involved in the different approaches and present results from simulations comparing the relative performance of the methods under a range of models.

Alleles↗
PubMed2000

Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection.

Linkage disequilibrium (LD) mapping of disease genes is complicated by population- and chromosome-region-specific factors. We have analysed demographic factors by contrasting intermarker LD results obtained in a large cosmopolitan population (UK), a large genetic isolate (Sardinia) and a subisolate (village of Gavoi) for two regions of the X chromosome. A dramatic increase of LD was found in the subisolate. Demographic history of populations therefore influences LD. Chromosome-region-specific effects, namely the pattern and frequency of homologous recombination, were next delineated by the analysis of chromosome 6p21, including the HLA region. Patterns of global LD in this region were very similar in the UK and Sardinian populations despite their entirely distinct demographies, and correlate well with the pattern of recombinations. Nevertheless, haplotypes extend across recombination hot spots indicative of selection of certain haplotypes. Subisolate aside, chromosome-region-specific differences in LD patterns appear to be more important than the differences in intermarker LD between distinct populations.

Chromosomes, Human, Pair 6↗
PubMed2005

Selection at work in self-incompatible Arabidopsis lyrata: mating patterns in a natural population.

Identification and characterization of the self-incompatibility genes in Brassicaceae species now allow typing of self-incompatibility haplotypes in natural populations. In this study we sampled and mapped all 88 individuals in a small population of Arabidopsis lyrata from Iceland. The self-incompatibility haplotypes at the SRK gene were typed for all the plants and some of their progeny and used to investigate the realized mating patterns in the population. The observed frequencies of haplotypes were found to change considerably from the parent generation to the offspring generation around their deterministic equilibria as determined from the known dominance relations among haplotypes. We provide direct evidence that the incompatibility system discriminates against matings among adjacent individuals. Multiple paternity is very common, causing mate availability among progeny of a single mother to be much larger than expected for single paternity.

Arabidopsis↗
PubMedDate not supplied

[Prospects for using multimarker dihaploid lines for mapping the barley genome].

Model population of spring barley Oregon Wolfe Pack dihaploid lines, derived from F1 of cross between dominant marker stock and recessive line, was studied on presence of morphological markers. For detection of DNA variability RAPD-analysis of these genotypes was carried out. Polymorphic fragment correlating with morphological trait was detected using primer P89.

Genetic Markers↗
PubMed1998

Least squares interval mapping of quantitative trait loci under the infinitesimal genetic model in outbred populations.

Genetic marker and phenotypic data for a quantitative trait were simulated on 20 paternal half-sib families with 100 progeny to investigate properties of within-family-regression interval mapping of a postulated single quantitative trait locus (QTL) in a marker interval under the infinitesimal genetic model, which has been the basis of the application of quantitative genetics to genetic improvement programs, and to investigate use of the infinitesimal model as null hypothesis in testing for presence of a major QTL. Genetic effects on the marked chromosome were generated based on a major gene model, which simulated a central biallelic QTL, or based on 101 biallelic QTL of equal effect, which approximated the infinitesimal model. The marked chromosome contained 0, 3.3%, 13.3%, or 33.3% of genetic variance and heritability was 0.25 or 0.70. Under the polygenic model with 3.3% of genetic variance on the marked chromosome, which corresponds to the infinitesimal model for the bovine, significant QTL effects were found for individual families. Correlations between estimates of QTL effects and true chromosome substitution effects were 0.29 and 0.47 for heritabilities of 0.25 and 0.70 but up to 0.85 with 33.3% of polygenic variance on the marked chromosome. These results illustrate the potential of marker-assisted selection even under the infinitesimal genetic model. Power of tests for presence of QTL was substantially reduced when the polygenic model with 3.3% of genetic variance on the chromosome was used as a null hypothesis. The ability to determine whether genetic variance on a chromosome was contributed by a single QTL of major effect or a large number of QTL with minor effects, corresponding to the infinitesimal model, was limited.

Chromosome Mapping↗
PubMed2000

Mathematical/computational challenges in creating deformable and probabilistic atlases of the human brain.

Striking variations in brain structure, especially in the gyral patterns of the human cortex, present fundamental challenges in human brain mapping. Probabilistic brain atlases, which encode information on structural and functional variability in large human populations, are powerful research tools with broad applications. Knowledge-based imaging algorithms can also leverage atlased information on anatomic variation. Applications include automated image labeling, pathology detection in individuals or groups, and investigating how regional anatomy is altered in disease, and with age, gender, handedness and other clinical or genetic factors. In this report, we illustrate some of the mathematical challenges involved in constructing population-based brain atlases. A disease-specific atlas is constructed to represent the human brain in Alzheimer's disease (AD). Specialized strategies are developed for population-based averaging of anatomy. Sets of high-dimensional elastic mappings, based on the principles of continuum mechanics, reconfigure the anatomy of a large number of subjects in an anatomic image database. These mappings generate a local encoding of anatomic variability and are used to create a crisp anatomical image template with highly resolved structures in their mean spatial location. Specialized approaches are also developed to average cortical topography. Since cortical patterns are altered in a variety of diseases, gyral pattern matching is used to encode the magnitude and principal directions of local cortical variation. In the resulting cortical templates, subtle features emerge. Regional asymmetries appear that are not apparent in individual anatomies. Population-based maps of cortical variation reveal a mosaic of variability patterns that segregate sharply according to functional specialization and cytoarchitectonic boundaries.

Aged↗
PubMed2003

Efficient fine mapping of the naked caryopsis gene ( nud) by HEGS (High Efficiency Genome Scanning)/AFLP in barley.

The hulled or naked caryopsis character of barley ( Hordeum vulgare L.) is an important trait for edibility and to follow its domestication process. A single recessive gene, nud, controls the naked caryopsis character, and is located on the long arm of chromosome 7H. To develop a fine map around the nud locus efficiently, the HEGS (High Efficiency Genome Scanning) electrophoresis system was combined with amplified fragment length polymorphism (AFLP). From bulked segregant analysis of 1,894 primer combinations, 12 AFLP fragments were selected as linked markers. For mapping, an F(2 )population of 151 individuals derived from a cross between Kobinkatagi (naked type) and Triumph (hulled type) was used. Seven AFLP markers were localized near the nud region. A fine map was developed with one-order higher resolution than before, along with the seven anchor markers. Among the seven linked AFLP markers (KT1-7), KT1, KT2 and KT6 were co-dominant, and the former two were detected for their single-nucleotide polymorphisms (SNPs) in the same length of fragments after electrophoresis with the non-denaturing gels of HEGS. The nud locus has co-segregated with KT3 and KT7, and was flanked by KT2 and KT4, at the 0.3-cM proximal and the 1.2-cM distal side, respectively. Four of these AFLP markers were converted into sequence-characterized amplified region (SCAR) markers, one of which was a dominant marker co-segregating with the nud gene.

Chromosome Mapping↗
PubMed1998

High genetic susceptibility to ethanol withdrawal predicts low ethanol consumption.

C57BL/6J (B6) inbred mice are well known to drink large amounts of alcohol (ethanol) voluntarily and to have only modest ethanol-induced withdrawal under fixed dose conditions. In contrast, DBA/2J (D2) mice are "teetotallers" and exhibit severe ethanol withdrawal. Speculation that an inverse genetic relationship existed between these two traits was substantiated by meta-analysis of existing data collected in multiple genetic models, including large panels of standard and recombinant inbred strains, their crosses, and selectively bred mouse lines. Despite methodological differences among laboratories in measurement of both preference drinking and withdrawal, a nearly universal finding was that genotypes consuming large amounts of 10% ethanol (calculated as g/kg/day) during two-bottle choice preference drinking were genetically predisposed to low withdrawal scores in independent studies after either acute or chronic ethanol treatment. Conversely, low-drinking genotypes had higher withdrawal severity scores. The genetic relationship appears to be strongest in populations derived from B6 and D2, where data from more genotypes (BXD RIs, B6D2F2s, BXD RI F1s, and B6D2F2-derived selectively bred lines) were available for analysis. Gene mapping studies in these populations identified four chromosome regions [on Chromosomes (Chrs) 1, 2, 4, and 15] where genes might potentially influence both traits. Among genotypes with greater genetic diversity (for example, a panel of standard inbred strains or selectively bred lines), the relationship was less pronounced. Thus, reduced susceptibility to the development of high alcohol use may be supported by increased genetic susceptibility to ethanol withdrawal symptoms.

Alcohol Drinking↗
PubMed2002

Molecular genecology of temperature response in Lolium perenne: 2. association of AFLP markers with ecogeography.

Improved winter hardiness is an important breeding objective in the forage grass Lolium perenne. This is a complex trait with several components, including the ability to survive and grow at low temperature, to acclimate to cold, tolerate wind, snow cover and ice encasement. Marker-assisted selection has the potential to increase the efficiency of breeding for improved cold tolerance. Here we describe a genecological approach to identifying molecular markers that are associated with adaptation to low winter temperatures. AFLP was used to assess the genetic diversity in 29 wild populations of ryegrass (Lolium perenne) representing a pan-European temperature cline in terms of their geographical origin. A further 18 populations from a temperature cline in Bulgaria were also analysed. In addition, two varieties and five populations representing parents of mapping families currently in use at IGER were included in the analysis. Principal coordinate (PCoA) and cluster analyses of the molecular marker data showed that the Bulgarian altitude cline populations could be distinguished clearly from the other populations. Two regression analyses were carried out; one to identify AFLP markers that correlated in frequency with low mean January temperature of the geographical origin of the population, and another to identify AFLP markers correlating in frequency with the cold tolerance phenotype of the populations, as determined by LT50 values in freezing tests. In the first analysis six AFLP markers showed significant type II trends with mean January temperature, and in the second analysis 28 bands had a significant univariate relationship with the LT50 value of the accessions. In steps 2 and 3 of the stepwise analysis a further 4 and 5 bands, respectively, improved the fit significantly. The results of the two types of regression analysis are discussed in relation to ecogeography and cold tolerance phenotype of the populations.

Ecology↗
PubMed2004

Genomic regions influencing resistance to the parasitic weed Striga hermonthica in two recombinant inbred populations of sorghum.

Molecular markers for resistance of sorghum to the hemi-parasitic weed Striga hermonthica were mapped in two recombinant inbred populations (RIP-1, and -2) of F(3:5) lines developed from the crosses IS9830 x E36-1 (1) and N13 x E36-1 (2). The resistant parental lines were IS9830 and N13; the former is characterized by a low stimulation of striga seed germination, the latter by "mechanical" resistance. The genetic maps of RIP-1 and RIP-2 spanned 1,498 cM and 1,599 cM, respectively, with 137 and 157 markers distributed over 11 linkage groups. To evaluate striga resistance, we divided each RIP into set 1 (116 lines tested in 1997) and set 2 (110 lines evaluated in 1998). Field trials were conducted in five environments per year in Mali and Kenya. Heritability estimates for area under the striga number progress curve (ASNPC) in sets 1 and 2 were respectively 0.66 and 0.74 in RIP-1 0.81 and 0.82 in RIP-2. Across sites, composite interval mapping detected 11 QTL (quantitative trait loci) and nine QTL in sets 1 and 2 of RIP-1, explaining 77% and 80% of the genetic variance for ASNPC, respectively. The most significant RIP-1 QTL corresponded to the major-gene locus lgs (low stimulation of striga seed germination) in linkage group I. In RIP-2, 11 QTL and nine QTL explained 79% and 82% of the genetic variance for ASNPC in sets 1 and 2, respectively. Five QTL were common to both sets of each RIP, wtih the resistance alleles deriving from IS9830 or N13. Since their effects were validated across environments, years and independent RIP samples, these QTL are excellent candidates for marker-assisted selection.

Area Under Curve↗
PubMed1998

Effects of glutamate-induced excitotoxicity on calretinin-expressing neuron populations in the area postrema of the rat.

We mapped the distribution of calretinin-immunoreactive neuron populations in a circumventricular organ of the rat, the area postrema, and investigated their sensitivity to excitotoxic stimuli mediated by subcutaneously administered monosodium glutamate. We were specifically interested to ascertain whether the presence of calretinin can, per se, confer an in vivo intrinsic resistance for area postrema neurons to glutamate excitotoxicity. We found that dense populations of calretinin-positive neurons displayed a subregional compartmentation in coronal sections of the area postrema along its rostrocaudal axis. We demonstrated that calretinin-positive neurons differ in their sensitivities to monosodium glutamate depending on their position within the area postrema. Neurons in the caudal area postrema were the most sensitive ones, while those in the rostral area postrema were spared of degeneration. We conclude that calretinin-positive neurons in the area postrema are not uniformly protected against glutamate excitotoxicity. It is possible that differences in the local concentrations of monosodium glutamate due to regional heterogeneities in density and permeability of the capillary bed rather than neuronal expression of calretinin account for the observed effects.

Animals↗
PubMed2000

The decay of linkage disequilibrium under random union of gametes: how to calculate Bennett's principal components.

How rapidly does an arbitrary pattern of statistical association among a set of loci decay under meiosis and random union of gametes? This problem is non-trivial, even in the case of an infinitely large population where selection and other forces are absent. J. H. Bennett (1954, Ann. Hum. Genet. 18, 311-317) found that, for an arbitrary number of loci with an arbitrary linkage map, it is possible to define measures of linkage disequilibrium that decay geometrically with time. He found a recursive method for deriving expressions for these variables in terms of "allelic moments" (the factorial moments about the origin of the "allelic indicators"), and expressions for the allelic moments in terms of his new variables. However, Bennett no where stated his recursive algorithm explicitly, nor did he give a general formula for his measures of linkage disequilibrium, for an arbitrary number of loci. Recursive definitions of Bennett's variables were obtained by Lyubich. However, the expressions generated by these recursions are not the same as those found by Bennett. (They do not express Bennett's variables as functions of the allelic moments.) Lyubich's derivations employ genetic algebras. Here, I present a method for obtaining explicit expressions for Bennett's variables in terms of the allelic moments. I show that the transformation from the allelic moments to Bennett's variables and the inverse transformation always have the form that Bennett claimed. (This transformation and its inverse have essentially the same form.) I present general recursions for calculating the coefficients in the forward transformation and the coefficients in the inverse transformation. My derivations involve combinatorial arguments and ordinary algebra only. The special case of unlinked loci is briefly discussed.

Algorithms↗
PubMed1999

Prospects for whole-genome linkage disequilibrium mapping of common disease genes.

Recently, attention has focused on the use of whole-genome linkage disequilibrium (LD) studies to map common disease genes. Such studies would employ a dense map of single nucleotide polymorphisms (SNPs) to detect association between a marker and disease. Construction of SNP maps is currently underway. An essential issue yet to be settled is the required marker density of such maps. Here, I use population simulations to estimate the extent of LD surrounding common gene variants in the general human population as well as in isolated populations. Two main conclusions emerge from these investigations. First, a useful level of LD is unlikely to extend beyond an average distance of roughly 3 kb in the general population, which implies that approximately 500,000 SNPs will be required for whole-genome studies. Second, the extent of LD is similar in isolated populations unless the founding bottleneck is very narrow or the frequency of the variant is low (<5%).

Chromosome Mapping↗
PubMed1987

Human papillomavirus types 6 and 11 mRNAs from genital condylomata acuminata.

We have identified and mapped a number of RNA species of human papillomavirus types 6 and 11 from condylomata acuminata by the electron microscopic R-loop technique. Each of the early (E)- and late (L)-region open reading frames (ORFs) deduced from the DNA sequences was represented in one or more transcripts. In addition, RNA species that could encode the modulator of DNA replication and the repressor of transcription, functions recently identified in the genetically similar bovine papillomavirus type 1, were also detected. Some ORFs were 5' proximal in one or more transcripts, whereas others were not 5' proximal in any species, suggesting that internal initiation of translation might be required to gain access to these latter ORFs. Virtually all transcripts had their 5' ends located in the E region and were polyadenylated at one of two sites, i.e., at the end of the E region or at the end of the L region. The great majority of the RNAs were derived from the E region of the genome, with one species approximately 50 to 100 times more abundant than the others. For most of the RNAs, the 5' end mapped near nucleotide 700; minor populations had 5' ends near nucleotide 100 or 1200. By correlating our mapping data with the genomic DNA sequences as well as available RNA structures and cDNA sequences of several papillomaviruses, we predict a number of mRNA splice donor and acceptor sites and suggest that the papillomaviruses have sophisticated usage of ORFs through alternative promoters, mRNA splice sites, and polyadenylation sites.

Anus Neoplasms↗
PubMed2000

Identification and chromosomal localization of a transcriptionally active retrotransposon of Ty3-gypsy type in rice.

A DNA fragment representing a transcriptionally active retrotransposon of Ty3-gypsy type was isolated and characterized from rice (Oryza sativa L.). The fragment (named RIRE9) includes the coding sequences for the C-terminal part of the RNase H domain and the N-terminal part of the integrase domain in the polyprotein region. Northern blot hybridization indicated that this element was expressed in rice leaves and stems, suggesting that it is potentially active to transpose under normal growth conditions. Using dot-blot hybridization, the copy number of RIRE9 was estimated to be about 1600 copies per haploid rice genome. Five homologous copies of RIRE9 were assigned to five distinct positions of four chromosomes by restriction fragment length polymorphism (RFLP) mapping approach using an indica-japonica rice doubled-haploid (DH) population and its molecular linkage map.

Amino Acid Sequence↗
PubMed2003

A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum x Gossypium barbadense backcross population.

An interspecific Gossypium hirsutum x Gossypium barbadense backcross population of 75 BC1 plants was evaluated for 1014 markers. The map consists of 888 loci, including 465 AFLPs, 229 SSRs, 192 RFLPs, and 2 morphological markers, ordered in 37 linkage groups that represent most if not all of the 26 chromosomes, altogether spanning 4400 cM. Loci were not evenly distributed over linkage groups, and 18 of the 26 long groups had a single dense region. This paper proposes a partially revised list of the 13 pairs of homoeologous A/D chromosomes of the 2n = 4x = 52 tetraploid cotton genome. The major revisions, which involve the c3-c17, c4-c22, c5-D08, and c10-c20 homoeologous pairs, are based on the mapping of 68 SSR and RFLP loci with a known chromosome assignment, as well as on comparative alignments with previously published G. hirsutum x G. barbadense maps. The overall congruency in the locus orders and distances of common SSR and RFLP loci in these maps allows for an estimation of the consensus length that reaches a minimum of 5500 cM, and is encouraging for future efforts aimed at developing an integrated map of cultivated cotton. The present map also provides a firm framework for precision mapping of Mendelian components of quantitative traits in cotton

Chromosome Mapping↗
PubMed2003

Quantitative trait loci mapping of functional traits in the German Holstein cattle population.

A whole-genome scan to detect quantitative trait loci (QTL) for functional traits was performed in the German Holstein cattle population. For this purpose, 263 genetic markers across all autosomes and the pseudoautosomal region of the sex chromosomes were genotyped in 16 granddaughter-design families with 872 sons. The traits investigated were deregressed breedingvalues for maternal and direct effects on dystocia (DYSm, DYSd) and stillbirth (STIm, STId) as well as maternal and paternal effects on nonreturn rates of 90 d (NR90m, NR90p). Furthermore, deregressed breeding values for functional herd life (FHL) and daughter yield deviation for somatic cell count (SCC) were investigated. Weighted multimarker regression analyses across families and permutation tests were applied for the detection of QTL and the calculation of statistical significance. A ten percent genomewise significant QTL was localized for DYSm on chromosome 8 and for SCC on chromosome 18. A further 24 putative QTL exceeding the 5% chromosomewise threshold were detected. On chromosomes 7, 8, 10, 18, and X/Yps, coincidence of QTL for several traits was observed. Our results suggest that loci with influence on udder health may also contribute to genetic variance of longevity. Prior to implementation of these QTL in marker assisted selection programs for functional traits, information about direct and correlated effects of these QTL as well as fine mapping of their chromosomal positions is required.

Animals↗