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PubMed1997

WPC test based on randomization for analyzing quantitative traits on simulated pedigrees.

The weighted pairwise correlation (WPC) approach provides simple and flexible tests for genetic linkage which may be adapted to qualitative, quantitative or age-dependent traits. These tests also seem to have good power. However, when working with large pedigrees, a disease susceptibility gene not linked to the marker studied induces correlations of the trait values, leading to inflated type I errors for these tests. We propose here a new approach for inference based on the randomization of the alleles following the Mendelian laws and conditioning on the alleles of the founders. This approach is applied to the analysis of the quantitative traits in a set of simulated pedigrees. The alpha posteriori comparison of the findings to the true model indicates directions for future work.

Aging↗
PubMed2003

Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). 2. Characterisation of QTL involved in developmental and agronomic traits.

Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.

Chromosome Mapping↗
PubMed1995

Aedes aegypti: a quantitative trait locus (QTL) influencing filarial worm intensity is linked to QTL for susceptibility to other mosquito-borne pathogens.

Because intensity of infection was significantly increased in a substrain of Aedes aegypti selected for susceptibility to the filarial worm, Brugia malayi, experiments were designed to assess numbers of microfilariae (mf) ingested and midgut penetration by mf in this susceptible substrain as compared to a refractory substrain selected from the same parental stock. Refractory mosquitoes ingested significantly fewer mf than susceptible mosquitoes and significantly fewer numbers of mf penetrated through refractory midguts as compared to susceptible midguts. In 16.7% of the refractory midguts, no mf were able to penetrate the midgut and in three refractory mosquitoes over 250 mf were ingested, but no mf penetrated the midgut. These results indicate that permissiveness of the midgut for penetration by microfilariae can determine not only parasite intensity, but also prevalence of infection. The genetic basis for ingestion of mf and midgut penetration was assessed using restriction fragment length polymorphism markers and quantitative trait loci (QTL) mapping. This mapping identified a QTL on chromosome 2, idb[2,LF181] (idb, intensity determinant for Brugia), that seems to influence ingestion ability. This QTL is linked to a previously identified QTL for susceptibility to B. malayi, fsb[2,LF98], as well as to loci for susceptibility to the malaria parasite, Plasmodium gallinaceum, and yellow fever virus. These results suggest that this region of chromosome 2 contains one or more genes that influence susceptibility of A. aegypti to several mosquito-transmitted pathogens.

Aedes↗
PubMed1999

Colonization history and introduction dynamics of capsella bursa-pastoris (Brassicaceae) in north america: isozymes and quantitative traits

Multilocus isozyme genotypic composition for aspartate aminotransferase (AAT), leucine aminopeptidase (LAP) and glutamate dehydrogenase (GDH) was studied for Capsella in the source continent, Europe (9000 plants from 593 populations), and in the colonized continent, North America (2700 plants from 88 populations). North America was depauperate in the number of genotypes (by approximately 50%), but in terms of frequencies, a few genotypes were common and shared by both continents. Although some, very rare, genotypes were, however, unique for North America, our data provided no evidence to indicate that the introduced gene pools were reconstructed on a multilocus genetic basis after introduction. Instead, they argued for a considerable number of independent introduction events. Geographical distribution patterns of multilocus genotypes in Europe and North America were pronounced and enabled us to trace the colonization history of Californian Capsella back to Spanish ancestral populations and those of temperate North America back to temperate European gene pools. A random-block field experiment with 14 Californian populations from different climatic regions revealed that variation patterns of quantitative traits reflect ecotypic variation, and the ecological amplitude of Capsella in North America is similar to that in Europe, which can be traced back to the introduction of preadapted genotypes. It appears that certain multilocus isozyme genotypes are associated with certain ecotypes. The variable European gene pool of Capsella was essentially introduced into North America without major genetic changes.

Journal Article↗
PubMed1997

Quantitative trait loci associated with promoting effects of sodium L-ascorbate on two-stage bladder carcinogenesis in rats.

In the two-stage rat bladder carcinogenesis model using N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) as an initiator and sodium L-ascorbate (SA) as a promoter, we found a notable strain difference between F344/DuCrj (F344) and WS/Shi (WS) rats in susceptibility to the promoting effect of SA. Twenty each of F344, WS and reciprocal F1 hybrid rats were given 0.05% BBN in their drinking water for 4 weeks and then a basal diet with (BBN-SA group) or without (BBN group) a 5% SA supplement for 32 weeks. In F344 and also in reciprocal F1 hybrids, the number of tumors per rat was significantly higher in the BBN-SA group than in the BBN group (P < 0.0001). In contrast, WS rats were not significantly affected by either treatment (P = 0.8). These findings indicate that F344 rats are highly susceptible to the promoter effect of SA, but WS rats are not. Linkage analysis of 108 WSx (WS x F344) F1 backcrosses revealed that this difference was related to a quantitative trait locus mapped on rat Chr. 17 (maximum LOD score, 3.86) named Bladder Tumor Susceptible-1 and possibly another locus on Chr. 5 (maximum LOD score, 2.39). This study has provided the first evidence that host genes influence the risk of bladder cancer development.

Animals↗
PubMed2005

Large-scale studies of the Leu72Met polymorphism of the ghrelin gene in relation to the metabolic syndrome and associated quantitative traits.

AIM: Recently, low-frequency polymorphisms in the coding region of the ghrelin gene were suggested to be involved in the aetiology of obesity and to modulate glucose-induced insulin secretion in different ethnic study groups. The objective of the present large study was to investigate whether the Leu72Met polymorphism of the ghrelin gene associates with features of the metabolic syndrome (MS) in the Danish population. METHODS: The variant was examined, using PCR-RFLP, in the DanMONICA cohort, a population-based sample of 2413 subjects. The metabolic syndrome was defined using the National Cholesterol Education Program-Adult Treatment Panel III (NCEP-ATPIII) criteria. RESULTS: The allelic frequency of the Met72 allele was 8.6%[6.3-10.9%] in the MS group and 7.8%[7.0-8.6%] among subjects classified as not having the MS (NS). Similarly, there were no significant differences across the three groups of genotypes with respect to any of the examined variables, including BMI, waist circumference, fasting serum lipids, plasma glucose, serum insulin and HOMA estimates of insulin resistance and insulin secretion. CONCLUSION: In conclusion, the Leu72Met polymorphism of the ghrelin gene is not associated with the metabolic syndrome or related quantitative traits in the Danish population.

Adult↗
PubMed1996

Genetic mapping of two blood pressure quantitative trait loci on rat chromosome 1.

A genetic map for rat chromosome 1 was constructed using 66 microsatellite markers typed on either or both of two populations derived from inbred Dahl salt-sensitive (S) rats: F2(LEW x S) n = 151, and F2(WKY x S) n = 159. These populations had been raised on a high salt (8% NaCl) diet. Systolic blood pressure and heart weight were found to be genetically linked to two separate regions on rat chromosome 1 in the F2(LEW x S) population. One region was centered around the anonymous SA locus and accounted for 24 mmHg of blood pressure. The other region was 55 cM from the SA locus centered around a cluster of cytochromes P450 loci, and accounted for 30 mmHg of blood pressure. Since blood pressure and heart weight were highly correlated these same regions were also linked to heart weight. These results were cross-specific as linkage of these chromosome 1 regions to blood pressure and heart weight was not observed in several other F2 populations derived by crossing S and other normotensive control strains. This is presumably due to different alleles and/or different genetic backgrounds in the various populations. The SA region of chromosome 1 was found to influence body weight in F2(LEW x S) rats. Combining the present data with our previously published data on the F2(LEW x S) population showed that four separate quantitative trait loci with additive effects accounted for 106 mmHg and 38% of the total variance of blood pressure and for 506 mg and 34% of the total variance of heart wt.

Animals↗
PubMed1984

Fear-related responses of white Leghorn hens of several genetic stocks in five-bird cages and associations with quantitative traits.

Hens of 8 genetic stocks derived from a common foundation population were compared at three ages for latency to recover from tonic immobility (TI) and from an avoidance response following exposure to a metronome. Body weight, feather score, and egg-production traits also were measured. A total of 350 hens was involved and individuals of the same genetic stock were kept together in 5-hen cages from 19 to 70 weeks old. The TI and metronome avoidance tests were conducted in three rounds at mean ages of 35, 48, and 61 weeks. Hens of stocks with increased egg mass, resulting from selection, did not differ from unselected controls for TI or avoidance responses. Straincross hens also did not differ from parental strain means for these fear-related behaviors. Time to recover from induced TI decreased with repeated testing at 13-week intervals. Hens exposed to the metronome a second time within the first round recovered more rapidly than did those tested in this way for the first time. Previous indirect exposure to the metronome also resulted in reduction in avoidance time. Correlation analysis revealed only a moderate association between TI and avoidance responses (r = .23, P less than .01). Avoidance responses were not associated with any other quantitative trait in the 5-hen cage environment. Duration of TI was moderately associated with body weight (r = .22, P less than .01) and had a complex relationship with total egg mass produced, which was associated with the interval in cages prior to testing. There was no apparent correlation of TI and egg mass when TI was measured on 35-week-old hens, heterogeneity of correlations was present among genetic stocks tested at 48 weeks, and a negative association was detected when TI tests were conducted at 61 weeks (r = -.46, P less than .01).

Animals↗
PubMed1995

Quantitative trait loci (QTL) for circadian rhythms of locomotor activity in mice.

The locomotor activity of male mice (Mus musculus) was monitored by infrared photo-electric beams under three lighting regimens: LD (12 h of light and 12 h of dark), DD (constant dark), and LL (constant broad-spectrum light, 10 lux). Circadian period of locomotor activity (tau) was compared among 3 inbred strains of mice, C57BL/6J (B6), BALB/c (C), and DBA/2J (D2), and 26 recombinant inbred strains B x D (B6 x D2). The tau under both continuous low-intensity light and continuous darkness varied significantly among strains. Under DD the mean tau was 23.8 h for B6, 23.7 h for D2, and 23.6 h for C. Under LL the mean tau was 25.1 h for B6, 23.9 h for D2, and 25.5 h for C. Frequency histograms of the mean tau of 26 B x D RI mouse strains (three to seven animals per strain) in either DD or LL and the difference between them, delta tau, had distributions which appeared unimodal, suggesting polygenic inheritances. The narrow-sense heritability determined using 26 strains of B x D RI mice was about 55% for tau and about 38% for both tau in LL and delta tau. An estimated four loci contribute to the variance of tau in constant darkness and five to the variance of tau in constant low-intensity light among the strains studied. Quantitative trait locus (QTL) analysis identified several potential genetic loci associated with tau in constant darkness, tau in constant low-intensity light, and delta tau. The associations of highest probability for each of these traits were the D1Nds4 locus (p < .001) on mouse chromosome 1, the D5Ncvs52 locus (p < .05) on mouse chromosome 5, and the Pmv12 locus (p < .01) at 70 cM on mouse chromosome 5, respectively. A QTL identified for tau was associated (p < .05) with the D2NDS1 marker at 45 cM on chromosome 2 near the Ea 6 marker at 46 cM associated (p < .05) with that reported for the period of wheel running activity in seven C x B RI strains (Schwartz, W.J., and Zimmerman, P., J. Neurosci. 10:3685 1990).

Animals↗
PubMed2002

An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix.

A genetic linkage map of Salix (2n = 38), composed of 325 AFLP and 38 RFLP markers has been constructed. The map was based on a population ( n = 87) derived from a cross between the male hybrid clone "Björn" ( Salix viminalis x Salix schwerinii) and the female clone "78183" ( S. viminalis). Three hundred fifty seven AFLPs corresponding to DNA polymorphisms heterozygous in one parent and null in the other were scored. A total of 87 RFLP probes, most (83) derived from the Populus genome, yielded 39 and 11 polymorphic loci segregating in a 1:1 and 1:2:1 ratio respectively. Two maps, one for each parent, were constructed according to the "two-way pseudo-testcross" mapping strategy. The S. viminalis x S. schwerinii map (2,404 cM) included 217 markers and formed 26 major linkage groups while S. viminalis (1,844 cM) consisted of 146 markers placed on 18 major groups. In addition, eight and 14 additional minor linkage groups composed of less than four markers (doubles and triplets) were obtained in the S. viminalis x S. schwerinii and the S. viminalis maps, respectively. Both maps provided 70-80% genome coverage with an average density of markers of 14 cM. To investigate possible homologies between the parental maps, 20 AFLPs and 11 RFLPs segregating in 3:1 or 1:2:1 ratios were included in the linkage analysis. Eight linkage groups homologous between the two maps were detected. The present genetic map was used to identify quantitative trait loci (QTLs) affecting growth-related traits. Eleven QTLs were identified; seven QTLs for height growth, one QTL for stem diameter, one QTL for the height: diameter ratio, one QTL for the number of vegetative buds during flowering time and one QTL for the number of shoots. The estimated magnitude of the QTL effect ranged from 14 to 22% of the total phenotypic variance. One QTL associated with height growth and one affecting the height: diameter ratio were overlapping in the same marker interval with the QTL affecting stem diameter. QTL stability over years was estimated for traits measured in multiple years. Generally, QTLs were only significant in a single year although two QTLs for height growth were close to reaching the significance level in 2 consecutive years.

Journal Article↗
PubMed2001

Genetics, environment and cognitive abilities: review and work in progress towards a genome scan for quantitative trait locus associations using DNA pooling.

BACKGROUND: Multivariate genetic research indicates that genetic effects on diverse cognitive abilities are general rather than specific or modular. General cognitive ability (g), a key factor in learning and memory, is among the most heritable behavioural traits. AIMS: To give a brief overview of quantitative genetic research on g and to describe initial results from a programme of research that aims to identify genes responsible for the substantial heritability of general cognitive ability. METHOD: The research uses a new technique called DNA pooling, which combines DNA from individuals within a group and makes it feasible to screen thousands of DNA markers for a systematic scan of the genome for associations between DNA markers and g. Two independent samples of children with very high g scores and two control samples of children with average g scores were compared in a systematic scan of 147 markers on chromosome 4 and 66 markers on chromosome 22. RESULTS: Three replicated associations on chromosome 4 were identified using DNA pooling and confirmed using individual genotyping. CONCLUSIONS: These first results of the application of DNA pooling in systematic analysis of allelic association are encouraging.

Adult↗
PubMed2006

Identification of quantitative trait loci for ABA sensitivity at seed germination and seedling stages in rice.

Abscisic acid (ABA) is one of the important plant hormones, which plays a critical role in seed development and adaptation to abiotic stresses. The sensitivity of rice (Oryza sativa L.) to exogenous ABA at seed germination and seedling stages was investigated in the recombinant inbred line (RIL) population derived from a cross between irrigated rice Zhenshan 97 and upland rice IRAT109, using relative germination vigor (RGV), relative germination rate (RGR) and leaf rolling scores of spraying (LRS) or culturing (LRC) with ABA as sensitivity indexes. The phenotypic correlation analysis revealed that only RGV at germination stage was positively correlated to ABA sensitivity at seedling stage. QTL detection using composite interval mapping (CIM) and mixed linear model was conducted to dissect the genetic basis of ABA sensitivity, and the single-locus QTLs detected by both methods are in good agreement with each other. Five single QTLs and six pairs of epistatic QTLs were detected for ABA sensitivity at germination stage. Eight single QTLs and five pairs of epistatic QTLs were detected for ABA sensitivity at seedling stage. Two QTLs were common between LRS and LRC; and one common QTL was detected for RGV, LRS and LRC simultaneously. These results indicated that both single and epistatic loci were involved in the ABA sensitivity in rice, and the genetic basis of ABA sensitivity at seed germination and seedling stage was largely different.

Abscisic Acid↗
PubMed2006

Quantitative trait locus on chromosome 20q13 for plasma levels of C-reactive protein in healthy whites: the HERITAGE Family Study.

C-reactive protein (CRP) is a sensitive marker of systemic low-grade inflammation. Increased plasma levels of CRP predict the risk of cardiovascular and metabolic diseases. Although genetic factors account for 30-40% of individual differences in plasma CRP levels, genomic regions contributing to CRP levels remain unknown. We performed a genome-wide linkage scan for plasma CRP levels in healthy whites from the HERITAGE Family Study. CRP was measured with a high-sensitivity assay. Multipoint linkage analyses were performed in 280 sibling pairs with 654 markers using regression and variance components-based methods. Data were adjusted for independent correlates of plasma CRP. We showed the strongest evidence of linkage for plasma CRP levels on chromosome 20q13. Markers which gave suggestive linkages in this region were D20S52 [logarithm of odds (LOD) score 3.18, P = 0.00006], D20S857 (LOD score 2.87, P = 0.00014), D20S869 (LOD score 2.75, P = 0.0002), D20S480 (LOD score 2.59, P = 0.0003), D20S501 (LOD score 2.55, P = 0.0003), D20S840 (LOD score 2.18, P = 0.0008), and D20S876 (LOD score 2.07, P = 0.001). We also detected suggestive linkage on chromosome 5p13 for marker D5S1470 (LOD score 2.23, P = 0.0007). Chromosome 20q13 may contribute to plasma CRP levels in healthy whites. This region contains genes that are important in the inflammatory process and may play a role in the development of chronic inflammatory diseases. The present findings may be useful in the ongoing effort to search for genes contributing to inflammation and to identify individuals at an increased risk of chronic inflammatory diseases.

Age Factors↗
PubMed2003

Fine mapping a quantitative trait locus affecting ovulation rate in swine on chromosome 8.

Ovulation rate is an integral component of litter size in swine, but is difficult to directly select for in commercial swine production. Because a QTL has been detected for ovulation rate at the terminal end of chromosome 8p, genetic markers for this QTL would enable direct selection for ovulation rate in both males and females. Eleven genes from human chromosome 4p16-p15, as well as one physiological candidate gene, were genetically mapped in the pig. Large insert swine genomic libraries were screened, clones were isolated and then screened for microsatellite repeats, and informative microsatellite markers were developed for seven genes (GNRHR, IDUA, MAN2B2, MSX1, PDE6B, PPP2R2C, and RGS12). Three genes (LRPAP1, GPRK2L, and FLJ20425) were mapped using genotyping assays developed from single nucleotide polymorphisms. Two genes were assigned since they were present in clones that contained mapped markers (HGFAC and HMX1). The resulting linkage map of pig chromosome 8 contains markers associated with 14 genes in the first 27 cM. One inversion spanning at least 3 Mb in the human genome was detected; all other differences could be explained by resolution of mapping techniques used. Fourteen of the most informative microsatellite markers in the first 27 cM of the map were genotyped across the entire MARC swine resource population, increasing the number of markers typed from 2 to 14 and more than doubling the number ofgenotyped animals with ovulation rate data (295 to 600). Results from the revised data set for the QTL analysis, assuming breed specific QTL alleles, indicated that the most likely position of the QTL resided at 4.85 cM on the new linkage map (F1,592 = 20.5150, genome-wide probability less than 0.015). The updated estimate of the effect of an allele substitution was -1.65 ova for the Meishan allele. The F-ratio peak was closest to markers for MAN2B2 (4.80 cM) and was flanked on the other side by markers for PPP2R2C. Two positional candidate genes included in this study are MAN2B2 and RGS12. These results validate the presence of a QTL affecting ovulation rate on chromosome 8 and facilitate selection of positional candidate genes to be evaluated.

Animals↗
PubMed2002

On the detection of imprinted quantitative trait loci in experimental crosses of outbred species.

In this article, the quantitative genetic aspects of imprinted genes and statistical properties of methods to detect imprinted QTL are studied. Different models to detect imprinted QTL and to distinguish between imprinted and Mendelian QTL were compared in a simulation study. Mendelian and imprinted QTL were simulated in an F2 design and analyzed under Mendelian and imprinting models. Mode of expression was evaluated against the H(0) of a Mendelian QTL as well as the H(0) of an imprinted QTL. It was shown that imprinted QTL might remain undetected when analyzing the genome with Mendelian models only. Compared to testing against a Mendelian QTL, using the H(0) of an imprinted QTL gave a higher proportion of correctly identified imprinted QTL, but also gave a higher proportion of false inference of imprinting for Mendelian QTL. When QTL were segregating in the founder lines, spurious detection of imprinting became more prominent under both tests, especially for designs with a small number of F1 sires.

Computer Simulation↗
PubMed2005

Quantitative trait loci for hip dysplasia in a cross-breed canine pedigree.

Canine hip dysplasia is a common developmental inherited trait characterized by hip laxity, subluxation or incongruity of the femoral head and acetabulum in affected hips. The inheritance pattern is complex and the mutations contributing to trait expression are unknown. In the study reported here, 240 microsatellite markers distributed in 38 autosomes and the X chromosome were genotyped on 152 dogs from three generations of a crossbred pedigree based on trait-free Greyhound and dysplastic Labrador Retriever founders. Interval mapping was undertaken to map the QTL underlying the quantitative dysplastic traits of maximum passive hip laxity (the distraction index), the dorsolateral subluxation score, and the Norberg angle. Permutation testing was used to derive the chromosome-wide level of significance at p<0.05 for each QTL. Chromosomes 4, 9, 10, 11 (p<0.01), 16, 20, 22, 25, 29 (p<0.01), 30, 35, and 37 harbor putative QTL for one or more traits. Successful detection of QTL was due to the cross-breed pedigree, multiple-trait measurements, control of environmental background, and marked advancement in canine mapping tools.

Animals↗
PubMed1991

Isolation by distance in a quantitative trait.

Random genetic drift in a quantitative character is modeled for a population with a continuous spatial distribution in an infinite habitat of one or two dimensions. The analysis extends Wright's concept of neighborhood size to spatially autocorrelated sampling variation in the expected phenotype at different locations. Weak stabilizing selection is assumed to operate toward the same optimum phenotype in every locality, and the distribution of dispersal distances from parent to offspring is a (radially) symmetric function. The equilibrium pattern of geographic variation in the expected local phenotype depends on the neighborhood size, the genetic variance within neighborhoods, and the strength of selection, but is nearly independent of the form of the dispersal function. With all else equal, geographic variance is smaller in a two-dimensional habitat than in one dimension, and the covariance between expected local phenotypes decreases more rapidly with the distance separating them in two dimensions than in one. The equilibrium geographic variance is less than the phenotypic variance within localities, unless the neighborhood size is small and selection is extremely weak, especially in two dimensions. Nevertheless, dispersal of geographic variance created by random genetic drift is an important mechanism maintaining genetic variance within local populations. For a Gaussian dispersal function it is shown that, even with a small neighborhood size, a population in a two-dimensional habitat can maintain within neighborhoods most of the genetic variance that would occur in an infinite panmictic population.

Gene Frequency↗