A quantitative trait locus not associated with cognitive ability in children: a failure to replicate.
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Apolipoprotein A-IV genetic polymorphism and its impact on quantitative traits in normoglycemic and non-insulin-dependent diabetic Hispanics from the San Luis Valley, Colorado.
Apolipoprotein A-IV exhibits a common two-allele polymorphism in several human populations studied to date. Using isoelectric focusing and immunoblotting, we have analyzed plasmas from 188 non-insulin-dependent diabetic and 238 normoglycemic Hispanic individuals from the San Luis Valley, Colorado, to determine APOA4 genotype frequencies and to estimate the impact of the genotypes on quantitative traits. The frequencies of the two common alleles, APOA4*1 and APOA4*2, were 0.929 and 0.069, respectively, in normal subjects and 0.901 and 0.096, respectively, in diabetics. The third rare allele, APOA4*3, was detected sporadically in both groups. We studied the impact of APOA4 polymorphism on the levels of total plasma cholesterol, HDL cholesterol and its subfractions (HDL3 and HDL2), LDL cholesterol, triglycerides, glucose, and insulin. We observed no significant effect of the APOA4 polymorphism on any trait in diabetics. However, we did note a significant sex-specific effect in normoglycemic females on the level of total HDL cholesterol (p = 0.001) and its subfractions HDL2 (p = 0.043) and HDL3 (p = 0.001). The effect of the APOA4*2 allele in normal Hispanic females was to lower the total HDL, HDL2, and HDL3 cholesterol by 8.75 mg/dl, 2.37 mg/dl, and 5.36 mg/dl, respectively, compared to the common APOA4*1 allele.
Adult↗
Mapping quantitative trait loci (QTLs) for resistance to Gibberella zeae infection in maize.
The basic prerequisite for an efficient breeding program to improve levels of resistance to pathogens in plants is the identification of genes controlling the resistance character. If the response to pathogens is under the control of a multilocus system, the utilization of molecular markers becomes essential. Stalk and ear rot caused by Gibberella zeae is a widespread disease of corn: resistance to G. zeae is quantitatively inherited. Our experimental approach to understanding the genetic basis of resistance to Gibberella is to estimate the genetic linkage between available molecular markers and the character, measured as the amount of diseased tissue 40 days after inoculation of a suspension of Fusarium graminearum, the conidial form of G. zeae, into the first stalk internode. Sensitive and resistant parental inbreds were crossed to obtain F1 and F2 populations: the analysis of the segregation of 95 RFLP (restriction fragment length polymorphism) clones and 10 RAPD (random amplified polymorphic DNA) markers was performed on a population of 150 F2 individuals. Analysis of resistance was performed on the F3 families obtained by selfing the F2 plants. Quantitative trait loci (QTL) detection was based either on analysis of regression coefficients between family mean value and allele values in the F2 population, or by means of interval mapping, using MAPMAKER-QTL. A linkage map of maize was obtained, in which four to five genomic regions are shown to carry factors involved in the resistance to G. zeae.
Chromosome Mapping↗
Quantitative trait loci for refractoriness of Anopheles gambiae to Plasmodium cynomolgi B.
The severity of the malaria pandemic in the tropics is aggravated by the ongoing spread of parasite resistance to antimalarial drugs and mosquito resistance to insecticides. A strain of Anopheles gambiae, normally a major vector for human malaria in Africa, can encapsulate and kill the malaria parasites within a melanin-rich capsule in the mosquito midgut. Genetic mapping revealed one major and two minor quantitative trait loci (QTLs) for this encapsulation reaction. Understanding such antiparasite mechanisms in mosquitoes may lead to new strategies for malaria control.
Animals↗
Identification and fine mapping of quantitative trait loci for growth traits on bovine chromosomes 2, 6, 14, 19, 21, and 23 within one commercial line of Bos taurus.
We report the identification and fine mapping of QTL for birth weight (BWT), preweaning ADG (PWADG), and postweaning ADG on feed (ADGF) in a commercial line of Bos taurus using an identical-by-descent haplotype sharing method. One hundred seventy-six calves of 12 bulls (9 to 30 male calves from each sire) of the Beefbooster, Inc., M1 line were typed using 71 genetic markers from bovine chromosomes (BTA) 2, 6, 14, 19, 21, and 23 (8 to 16 markers from each chromosome). Sixteen haplotypes were found to have significant (P <0.05) associations with BWT at the comparison-wise threshold. The 16 haplotypes span 13 chromosomal regions, two on BTA 2 (9.1 to 22.5 cM and 95.0 to 100.3 cM), three on BTA 6 (8.2 to 11.8 cM, 35.5 to 49.7 cM, and 83.0 to 86.2 cM), three on BTA 14 (26.0 to 26.7 cM, 36.2 to 46.2 cM, and 52.0 to 67.7 cM), one on BTA 19 (52.0 to 52.7 cM), two on BTA 21 (9.9 to 20.4 cM and 28.2 to 46.1 cM), and two on BTA 23 (23.9 to 36.0 cM and 45.1 to 50.9 cM). Thirteen haplotypes spanning seven chromosomal regions significantly affected (P <0.05) PWADG at the comparison-wise threshold. The seven chromosomal regions include two regions on BTA 6 (11.8 to 44.2 cM and 83.0 to 86.2 cM), one on BTA 14 (26.7 to 50.8 cM), one on BTA 19 (4.8 to 15.9 cM), one on BTA 21 (9.9 to 20.4 cM), and two on BTA 23 (17.3 to 36.0 cM and 45.1 to 50.9 cM). For ADGF, 11 haplotypes were identified to have significant associations (P <0.05) at the comparison-wise threshold. The 11 haplotypes represented eight chromosomal regions, one on BTA 2 (9.1 to 22.5 cM), two on BTA 6 (49.7 to 50.1 cM and 59.6 to 63.6 cM), two on BTA 14 (17.0 to 24.0 cM and 36.2 to 46.2 cM), two on BTA 19 (52.0 to 52.7 cM and 65.1 to 65.7 cM), and one on BTA 21 (46.1 to 53.1 cM). The QTL regions identified and fine mapped in this study will provide a reference for future positional candidate gene research and marker-assisted selection of various growth traits.
Alleles↗
Chromosomal mapping of quantitative trait loci contributing to stroke in a rat model of complex human disease.
Stroke is a complex disorder with a poorly understood multifactorial and polygenic aetiology. We used the stroke-prone spontaneously hypertensive rat (SHRSP) as a model organism, mated it with the stroke-resistant spontaneously hypertensive rat (SHR) and performed a genome-wide screen in the resultant F2 cohort where latency until stroke, but not hypertension (a major confounder) segregated. We identified three major quantitative trait loci, STR1-3, with lod scores of 7.4, 4.7 and 3.0, respectively, that account for 28% of the overall phenotypic variance. STR2 colocalizes with the genes encoding atrial and brain natriuretic factor, peptides with important vasoactive properties. Our results demonstrate the existence of primary, blood pressure-independent genetic factors predisposing to a complex form of stroke.
Animals↗
Genetic basis of climatic adaptation in scots pine by bayesian quantitative trait locus analysis.
We examined the genetic basis of large adaptive differences in timing of bud set and frost hardiness between natural populations of Scots pine. As a mapping population, we considered an "open-pollinated backcross" progeny by collecting seeds of a single F(1) tree (cross between trees from southern and northern Finland) growing in southern Finland. Due to the special features of the design (no marker information available on grandparents or the father), we applied a Bayesian quantitative trait locus (QTL) mapping method developed previously for outcrossed offspring. We found four potential QTL for timing of bud set and seven for frost hardiness. Bayesian analyses detected more QTL than ANOVA for frost hardiness, but the opposite was true for bud set. These QTL included alleles with rather large effects, and additionally smaller QTL were supported. The largest QTL for bud set date accounted for about a fourth of the mean difference between populations. Thus, natural selection during adaptation has resulted in selection of at least some alleles of rather large effect.
Acclimatization↗
[The chromosomal localization of the major genes for the quantitative traits (QTL) of wheat by using D chromosome gene markers].
The possibility of biochemical and morphological marker genes application for QTL and determination of their association with definite D chromosomes was shown on F2 populations of bread wheat from crossing of hexaploids AABBDD with different D subgenomes and the same genome AB part. Algorithm for calculation of the theoretical means for evaluation of differences according t-criterion was proposed and examined. The results of biometrical genetic analysis of the quantitative traits obtained by joint scaling Cavalli test using 6-10 different generations were used for calculation of theoretical means.
Chromosome Mapping↗
Identification of sex-specific quantitative trait loci controlling alcohol preference in C57BL/ 6 mice.
Mice from various inbred strains consume alcoholic beverages at highly reproducible and strain-specific levels. While most mice consume alcohol in moderate amounts, C57BL/6J animals exhibit sustained oral ingestion of high levels of alcohol in the presence of competing water and food. We now report a genetic investigation of this phenotype as one potential model for alcoholism. An intercross-backcross breeding protocol was used to identify two recessive alcohol preference quantitative trait loci (QTLs) that are both sex-restricted in expression. A comparison of our results with those of an earlier morphine preference study argues against the hypothesis of a single unified phenotype defined by a preference for all euphoria-producing drugs.
Alcohol Drinking↗
An introgression analysis of quantitative trait loci that contribute to a morphological difference between Drosophila simulans and D. mauritiana.
Drosophila simulans and D. mauritiana differ markedly in morphology of the posterior lobe, a male-specific genitalic structure. Both size and shape of the lobe can be quantified by a morphometric variable, PCl, derived from principal components and Fourier analyses. The genetic architecture of the species difference in PCl was investigated previously by composite interval mapping, which revealed largely additive inheritance, with a minimum of eight quantitative trait loci (QTL) affecting the trait. This analysis was extended by introgression of marked segments of the mauritiana third chromosome into a simulans background by repeated backcrossing. The two types of experiment are consistent in suggesting that several QTL on the third chromosome may have effects in the range of 10-15% of the parental difference and that all or nearly all QTL have effects in the same direction. Since the parental difference is large (30.4 environmental standard deviations), effects of this magnitude can produce alternative homozygotes with little overlap in phenotype. However, these estimates may not reflect the effects of individual loci, since each interval or introgressed segment may contain multiple QTL. The consistent direction of allelic effects suggests a history of directional selection on the posterior lobe.
Animals↗
Quantitative trait loci controlling vegetative growth rate in the edible basidiomycete Pleurotus ostreatus.
Mycelium growth rate is a quantitative characteristic that exhibits continuous variation. This trait has applied interest, as growth rate is correlated with production yield and increased advantage against competitors. In this work, we studied growth rate variation in the edible basidiomycete Pleurotus ostreatus growing as monokaryotic or dikaryotic mycelium on Eger medium or on wheat straw. Our analysis resulted in identification of several genomic regions (quantitative trait loci [QTLs]) involved in the control of growth rate that can be mapped on the genetic linkage map of this fungus. In some cases monokaryotic and dikaryotic QTLs clustered at the same map position, indicating that there are principal genomic areas responsible for growth rate control. The availability of this linkage map of growth rate QTLs can help in the design of rational strain breeding programs based on genomic information.
Chromosome Mapping↗
Genome-wide cis-expression Quantitative Trait Loci (eQTL) and transcriptomic signals reveal distinct molecular regulation across correlated feed efficiency traits.
INTRODUCTION: Feed efficiency (FE) is a complex trait which determines livestock production profitability, yet the molecular mechanisms behind it remain unclear. This study investigated the blood transcriptomic profile of lambs, alongside genotype data with the aim to uncover the genetic basis of FE traits such as absolute dry matter intake (DMIabsolute), DMI adjusted for body size (DMIadjusted), average daily live weight gain (ADG), and residual feed intake (RFI). MATERIALS AND METHODS: Bulk RNA-Seq and genotype data were analysed using three complementary approaches: differential gene expression (DGE) analysis, weighted gene co-expression network analysis (WGCNA), and cis-expression Quantitative Trait Loci (cis-eQTL) mapping. These methods were used independently to identify genes and regulatory networks associated with FE traits and to investigate evidence supporting multi-trait candidate gene selection. RESULTS: DGE analysis revealed 2, 24, 85 and 4 differentially expressed genes for DMIabsolute, DMIadjusted, ADG, and RFI (Padjusted < 0.05), functionally enriched in sensory perception, ATP-dependent chromatin remodeling, Notch signaling and immune response pathways. 9 gene modules significantly associated with the FE traits (P ≤ 0.05) with correlations ranging from r = -0.56 to 0.49, were identified using WGCNA. Single nucleotide polymorphism (SNP)-level cis-eQTL analysis identified 93 eSNPs associated with 74 genes (false discovery rate (FDR) < 0.05), while permutation-derived gene level analysis identified 280 eGenes (FDR < 0.2, empirical P < 0.03). Across the three analyses, applying thresholds of DGE (Padjusted < 0.05), WGCNA (correlation, P ≤ 0.05), and cis-eQTL gene-level significance (empirical P < 0.05), multiple overlapping genes were identified including DNMT3A, KANSL1, NCOR1 for DMIadjusted, ACOX2, FANCF, CIMIP2B, LOC101115106, ARMH2, LOC132657496 for ADG, and LOC114114576 for RFI representing regulators of variations in FE. DISCUSSION: The integration of DGE, WGCNA, and cis-eQTL analyses identified key genes and regulatory mechanisms associated with variation in FE traits. These results highlight that integrated multi-trait candidate gene identification approaches can reveal key genes that lower feed intake while maintaining animal growth, supporting breeding strategies aimed at improving efficiency and long-term economic sustainability in sheep.
average daily gain (ADG)↗
Genetic mapping of blood pressure quantitative trait loci in Milan hypertensive rats.
In a previous study, by using a candidate gene approach, we detected in both Milan hypertensive rats and humans a polymorphism in the alpha-adducin gene (ADD1) that was associated with blood pressure and renal sodium handling. In the present study, a genomewide search with 264 informative markers was undertaken in 251 (Milan hypertensive strain x Milan normotensive strain) F2 rats to further investigate the contribution of the adducin gene family (Add1, Add2, and Add3) and to identify novel quantitative trait loci (QTLs) that affect blood pressure. The influence of 2 different methods of blood pressure measurement, the intracarotid catheter and the tail-cuff method, was also evaluated. We found evidence that QTLs affected systolic blood pressure (SBP) measured at the carotid (direct SBP) on rat chromosome 1 with a logarithm of the odds (LOD) score peak of 3.3 on D1Rat121 and on rat chromosome 14 on Add1 locus (LOD=3.2). A QTL for SBP measured at the tail (indirect SBP) was found on rat chromosome 10 around D10Rat33 (LOD=5.0). All of these QTLs identified chromosomal regions not detected in other rat studies and harbor genes (Na(+)/H(+) exchanger A3; alpha-adducin; alpha(1B)-adrenergic receptor) that may be involved in blood pressure regulation. Therefore, these findings may be relevant to human hypertension, also in consideration of the biochemical and pathophysiological similarities between MHS and a subgroup of patients of primary hypertension, which led to the identification of alpha-adducin as a candidate gene in both species.
Animals↗
Genetic mapping of quantitative trait loci for growth and fatness in pigs.
The European wild boar was crossed with the domesticated Large White pig to genetically dissect phenotypic differences between these populations for growth and fat deposition. The most important effects were clustered on chromosome 4, with a single region accounting for a large part of the breed difference in growth rate, fatness, and length of the small intestine. The study is an advance in genome analyses and documents the usefulness of crosses between divergent outbred populations for the detection and characterization of quantitative trait loci. The genetic mapping of a major locus for fat deposition in the pig could have implications for understanding human obesity.
Adipose Tissue↗
Heritability and number of quantitative trait loci of neurocognitive functions in families with schizophrenia.
Despite evidence for several chromosomal loci linked to schizophrenia, no susceptibility genes have been identified for the disorder. Using quantitative measures of phenotypic affection in place of clinical diagnostic categories or dichotomous classification of the affection status may be more effective in searching for susceptibility genes. Neurocognitive traits have been suggested as putative quantitative endophenotypes of the disorder, but their heritability estimates are not well known. We investigated the heritability of working memory, verbal declarative memory and its different components, and both verbal and visual ability functions in schizophrenia families with a well-ascertained pedigree structure. We also estimated the number of quantitative trait loci (QTLs) contributing to these neurocognitive functions. Additive genetic heritability of the neurocognitive functions was estimated in a sample of schizophrenia patients and their first-degree relatives (N = 264) from an isolated geographical subregion in Finland. The number of QTLs was analyzed using Markov chain Monte Carlo segregation analysis. Significant heritabilities were found in working memory and ability functions. Furthermore, the working memory functions revealed the most restricted number of QTLs. The mean numbers of loci for verbal and visual working memory were 1.2 and 1.0, respectively, with corresponding posterior probabilities of 73% and 70% for at least one locus. In declarative memory variables, the number of loci was more dispersed. Our results suggest that neurocognitive measures, particularly working memory, may provide valid quantitative phenotypic traits for linkage analyses searching predisposing genes for schizophrenia.
Adult↗
Genetic analysis of NIDDM. The study of quantitative traits.
Many studies are in progress worldwide to elucidate the genetics of NIDDM. Nevertheless, few articles are available that combine the interdisciplinary fields of medicine, genetics, physiology, and statistics in order to provide the scientific rationale for such an endeavor. Here we describe the methodology and background necessary to study the genetics of NIDDM and discuss how to analyze the data. We also provide a detailed bibliography for researchers and a glossary for those who are not experts in the field. In particular, we wish to emphasize the analysis of intermediate quantitative traits as a means to dissect the genetic basis of NIDDM.
Diabetes Mellitus, Type 2↗
A quantitative trait locus in major histocompatibility complex determining latent period of mouse lymphomas.
The effects of two host genes on retrovirus-induced murine lymphoma were evaluated by studying 114 F2 intercross mice between SL/Kh and AKR/Ms mice. Out of 47 T-lymphoma-bearing F2 mice, 45 had the AKR-derived dominant allele at Tism-1. The length of the lymphoma latent period was not related to type of tumor. Instead, it was significantly shortened by a recessive SL/Kh-derived allele at a major histocompatibility complex (MHC)-linked locus on Chr. 17. A quantitative trait analysis of the latent period yielded a maximal logarithm of likelihood ratio for linkage (LOD) score of 7.06 at a class II gene within MHC. The SL/Kh-derived recessive gene was named lla (lymphoma latency acceleration).
Alleles↗
Quantitative trait loci associated with brain weight in the BXD/Ty recombinant inbred mouse strains.
Adult C57BL/6J (B6) male mice had 37% heavier brains than did DBA/2J (D2) mice, while their body weights did not differ. The BXD recombinant inbred (RI) series of 20 strains, derived from a cross between B6 and D2 inbred strains, was used as the initial screen to determine significant associations between male brain weight and brain:body weight ratio, with allelic variation at 360 known marker gene loci. For brain weight, this yielded five candidate chromosome regions, each reflecting a possible quantitative trait locus (QTL) site affecting brain weight. The second step was to test as many of these five as possible using standard (non-RI) inbred strain data for brain weight previously reported in the literature. For this purpose, only strains possessing the same alleles as the B6 or D2 strains were used. Sufficient data to test two of the five candidate QTL were available. Of these, one was strongly supported as a site affecting brain weight--the D7rp2 region of chromosome 7. For the brain to body weight ratio, four chromosome regions emerged as significantly associated in the BXD series, but none were amenable to testing due to a lack of allelic information for the standard inbred strains. However, two of these regions showed highly significant associations (p less than 0.001, single test) that merit consideration as QTL sites for future testing. These two are the Hba region on chromosome 11 and the D17Tu7 region on chromosome 17. The genetic correlation between brain and body weight was low (r = 0.28), indicating that these two traits are largely genetically independent in the BXD RI series.
Animals↗