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Results for “Expression quantitative trait locus”

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At least 289 records · Page 16Linked to original sources
PubMed2000

Quantitative trait loci for floral morphology in Arabidopsis thaliana.

A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these same traits in the Landsberg erecta x Columbia recombinant inbred line population. There was significant genetic variation for all traits in both the sample of naturally occurring ecotypes and in the Ler x Col recombinant inbred line population. In addition, broad-sense genetic correlations among the traits were positive and high. A composite interval mapping (CIM) analysis detected 18 significant QTL affecting at least one floral character. Eleven QTL were associated with several floral traits, supporting either pleiotropy or tight linkage as major determinants of flower morphological integration. We propose several candidate genes that may underlie these QTL on the basis of positional information and functional arguments. Genome-wide QTL mapping is a promising tool for the discovery of candidate genes controlling morphological development, the detection of novel phenotypic effects for known genes, and in generating a more complete understanding of the genetic basis of floral development.

Arabidopsis↗
PubMed2006

FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock.

Temperature compensation contributes to the accuracy of biological timing by preventing circadian rhythms from running more quickly at high than at low temperatures. We previously identified quantitative trait loci (QTL) with temperature-specific effects on the circadian rhythm of leaf movement, including a QTL linked to the transcription factor FLOWERING LOCUS C (FLC). We have now analyzed FLC alleles in near-isogenic lines and induced mutants to eliminate other candidate genes. We showed that FLC lengthened the circadian period specifically at 27 degrees C, contributing to temperature compensation of the circadian clock. Known upstream regulators of FLC expression in flowering time pathways similarly controlled its circadian effect. We sought to identify downstream targets of FLC regulation in the molecular mechanism of the circadian clock using genome-wide analysis to identify FLC-responsive genes and 3503 transcripts controlled by the circadian clock. A Bayesian clustering method based on Fourier coefficients allowed us to discriminate putative regulatory genes. Among rhythmic FLC-responsive genes, transcripts of the transcription factor LUX ARRHYTHMO (LUX) correlated in peak abundance with the circadian period in flc mutants. Mathematical modeling indicated that the modest change in peak LUX RNA abundance was sufficient to cause the period change due to FLC, providing a molecular target for the crosstalk between flowering time pathways and circadian regulation.

Arabidopsis↗
PubMed2006

QTL mapping for plant architecture traits in upland cotton using RILs and SSR markers.

Xiangzamian 2 (XZM2) is the most widely cultivated cotton hybrid in China. By crossing two parents Zhongmiansuo12 and 8891 and upon subsequent selfings, we got F8 and F9 populations having 180 recombinant inbred lines. Ten plant architecture traits were investigated in two years with this population. A genetic map was constructed mainly with SSR markers. Quantitative trait loci (QTL) conditioning plant architecture traits were determined at the single-locus and double-locus levels. The results showed that epistastic effects as well as additive effects of QTL played an important role as the genetic basis of cotton plant architecture. The QTL detected in our research might provide new information on improving plant architecture traits. The polymorphism of molecular markers between ZMS12 and 8891 were quite limited, while significant differences between their phenotypes were found and the hybrid XZM2 expressed high heterosis in yield. All these could be partly explained by the effect of epistatic QTL.

Breeding↗
PubMed2003

What's new in neurogenetics? Focus on "primary microcephaly".

Primary microcephaly is a specific form of microcephaly that is inherited in an autosomal recessive manner. Six loci have been mapped for this condition and the genes at two of these loci have recently been identified. These include the Microcephalin gene at the MCPH1 locus and the ASPM gene at the MCPH5 locus.

Cell Cycle Proteins↗
PubMed2005

Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication.

Phenotypic variation on which selection can act during evolution may be caused by variation in activity level of developmental regulatory genes. In many cases, however, such genes affect multiple traits. This situation can lead to co-evolution of traits, or evolutionary constraint if some pleiotropic effects are detrimental. Here, we present an analysis of quantitative traits associated with gene copy number of two important maize regulatory genes, the duplicate FLORICAULA/LEAFY orthologs zfl1 and zfl2. We found statistically significant associations between several quantitative traits and copy number of both zfl genes in several maize genetic backgrounds. Despite overlap in traits associated with these duplicate genes, zfl1 showed stronger associations with flowering time, while zfl2 associated more strongly with branching and inflorescence structure traits, suggesting some divergence of function. Since zfl2 associates with quantitative variation for ear rank and also maps near a quantitative trait locus (QTL) on chromosome 2 controlling ear rank differences between maize and teosinte, we tested whether zfl2 might have been involved in the evolution of this trait using a QTL complementation test. The results suggest that zfl2 activity is important for the QTL effect, supporting zfl2 as a candidate gene for a role in morphological evolution of maize.

Biological Evolution↗
PubMed2004

Zooming in on a quantitative trait for tomato yield using interspecific introgressions.

To explore natural biodiversity we developed and examined introgression lines (ILs) containing chromosome segments of wild species (Solanum pennellii) in the background of the cultivated tomato (S. lycopersicum). We identified Brix9-2-5, which is a S. pennellii quantitative trait locus (QTL) that increases sugar yield of tomatoes and was mapped within a flower- and fruit-specific invertase (LIN5). QTL analysis representing five different tomato species delimited the functional polymorphism of Brix9-2-5 to an amino acid near the catalytic site of the invertase crystal, affecting enzyme kinetics and fruit sink strength. These results underline the power of diverse ILs for high-resolution perspectives on complex phenotypes.

Alleles↗
PubMed2006

Genetic analysis of NHLH2 and its putative role in bovine body weight control.

The control of energy balance is fundamental to adult animals and is necessary for weight gain/loss, reproductive capacity and general health. In mice, targeted deletion of the neuronal transcription factor Nhlh2 results in adult-onset obesity because of reduced exercise and infertility because of reduced sexual behaviour. Nhlh2 (NHLH2 for humans) is expressed in the hypothalamus, particularly in neurons that have been shown to regulate energy balance. We have cloned the bovine Nhlh2 gene (bNHLH2) and we have shown that bNHLH2 is also expressed in the hypothalamus. Phylogenetic analysis of Nhlh2 reveals that it is very highly conserved in humans, mice, chimps and cattle, and found in organisms with simpler nervous systems, including Caenorhabditis elegans and Drosophila. Using a cattle-human comparative map and online databases, we have evidence that bNHLH2 is located near a quantitative trait locus for marbling on bovine chromosome 3 between microsatellite markers BM723 and BMS963. Cloning of the bNHLH2 gene from Holstein cattle and a mixed breed individual and comparison with Hereford sequences shows that the gene is highly conserved among bovine breeds.

Amino Acid Sequence↗
PubMed1996

Cytochrome P4504A genotype cosegregates with hypertension in Dahl S rats.

Recent studies indicate that the production of 20-HETE by a P4504A2 enzyme in the outer medulla of the kidney is reduced in Dahl salt-sensitive (SS/Jr) rats, but the contribution of this abnormality to the elevation in loop Cl- transport and development of hypertension in this model is unknown. THe present study found that alleles at the locus for the P4504A2 gene cosegregate with blood pressure in an F2 population (n=151) derived from a cross between SS/Jr and Lewis rats (P < .0001). The P4504A2 locus is located in a region on rat chromosome 5 where a blood pressure quantitative trait locus was previously detected. Systolic blood pressure averaged 201 +/- 6 mm Hg in rats with the SS genotype (n=36), 192 +/- 4 mm Hg in SL genotype rats (n=77), and 169 +/- 3 mm Hg in LL genotype rats (n=38). In further studies, we confirmed that there are phenotypic differences in the expression of the P4504A2 gene in the kidneys of SS/Jr and Lewis rats. Although the production of 20-HETE from 14C-arachidonic acid was similar in microsomes prepared from the renal cortex of SS/Jr and Lewis rats (54 +/- 3 versus 55 +/- 3 pmol/min/mg protein), the production of 20-HETE in microsomes prepared from the outer medulla (OM) was markedly reduced in SS/Jr rats (2.8 +/- 0.8 versus 6.7 +/- 1 pmol/min/mg protein). The diminished production of 20-HETE in the OM was due to a threefold reduction in the level of P4504A2 protein. These results suggest that an altered expression of the P4504A2 enzyme in the OM may contribute to the development of hypertension in SS/Jr rats.

Alleles↗
PubMed2005

QTLs for enzyme activities and soluble carbohydrates involved in starch accumulation during grain filling in maize.

ADPglucose, the essential substrate for starch synthesis, is synthesized in maize by a pathway involving at least invertases, sucrose synthase, and ADPglucose pyrophosphorylase, as shown by the starch-deficient mutants, mn1, sh1, and bt2 or sh2, respectively. To improve understanding of the relationship between early grain-filling traits and carbohydrate composition in mature grain, QTLs linked to soluble invertase, sucrose synthase, and ADPglucose pyrophosphorylase activities and to starch, sucrose, fructose, and glucose concentrations were investigated. In order to take into account the specific time-course of each enzyme activity during grain filling, sampling was carried out at three periods (15, 25, and 35 d after pollination) on 100 lines from a recombinant inbred family, grown in the field. The MQTL method associated with QTL interaction analysis revealed numerous QTLs for all traits, but only one QTL was consistently observed at the three sampling periods. Some chromosome zones were heavily labelled, forming clusters of QTLs. Numerous possible candidate genes of the starch synthetic pathway co-located with QTLs. Four QTLs were found close to the locus Sh1 (bin 9.01) coding for the sucrose synthase. In order to confirm the importance of this locus, the CAPS polymorphism of the Sh1 gene was analysed in 45 genetically unrelated maize lines from various geographical origins. The DNA polymorphism was significantly associated with phenotypic traits related to grain filling (starch and amylose content, grain matter, and ADPglucose pyrophosphorylase activity at 35 DAP). Thus, the Sh1 locus could provide a physiologically pertinent marker for maize selection.

Carbohydrate Metabolism↗
PubMed1993

Sequence and single-base polymorphisms of the bovine alpha-lactalbumin 5'-flanking region.

The alpha-lactalbumin (alpha LA)-encoding gene is a potential quantitative trait locus in dairy animals. In cattle, the production of alpha LA is tightly coupled to the onset of lactation and it serves as a regulatory subunit of the enzyme responsible for lactose synthesis. Lactose is the major osmole controlling water movement in the mammary gland. To better understand the control of bovine alpha LA expression, the 5'-flanking region of a Holstein alpha LA gene was cloned and sequenced. The sequenced clone contains 1952 bp of 5'-flanking region and 66-bp of the protein-coding region. Three single-bp polymorphisms were identified within this region. These polymorphisms occur at positions +15, +21 and +54 relative to the mRNA transcription start point (tsp). The +15 and +21 variations occur in the region encoding the 5'-untranslated region of the mRNA-coding sequence. The +54 polymorphism is a silent mutation in the SP-coding region of the gene. A polymerase chain reaction (PCR, Cetus)-based screening method has been employed to analyze the genotype of cattle at the +15 position. A total of 501 randomly selected cattle from seven breeds were screened for this allele. Of these animals, only the Holstein breed of cattle was found to contain the +15 variation and it occurs at a gene frequency of 32%. Sequence comparisons were conducted between the 5'-flanking regions of the bovine-milk-protein encoding genes, alpha LA, beta-casein and alpha S1-casein, which are coordinately expressed. Regions of similarity extending to 350 bp in length were observed between these sequences.

Animals↗
PubMed2004

High-resolution comparative mapping of pig Chromosome 4, emphasizing the FAT1 region.

The first quantitative trait locus (QTL) in pigs, FAT1, was found on Chromosome 4 (SSC4) using a Wild Boar intercross. Further mapping has refined the FAT1 QTL to a region with conserved synteny to both human Chromosomes 1 and 8. To both improve the comparative map of the entire SSC4 and to define the specific human chromosome region with conserved synteny to FAT1, we have now mapped 103 loci to pig Chromosome 4 using a combination of radiation hybrid and linkage mapping. The physical data and linkage analysis results are in very good agreement. Comparative analysis revealed that gene order is very well conserved across SSC4 compared to both HSA1 and HSA8. The breakpoint in conserved synteny was refined to an area of about 23 cR on the q arm of SSC4 corresponding to a genetic distance of less than 0.5 cM. Localizations of the centromeres do not seem to have been conserved between the two species. No remnants of the HSA1 centromere were detected on the corresponding region on SSC4 and traces from the centromeric region of SSC4 cannot clearly be revealed on the homologous region on HSA8. This refined SSC4 map and the comparative analysis will be a great aid in the search for the genes underlying the FAT1 locus.

Animals↗
PubMed1999

Quantitative trait locus mapping of airway responsiveness to chromosomes 6 and 7 in inbred mice.

Quantitative trait locus (QTL) mapping was used to identify chromosomal regions contributing to airway hyperresponsiveness in mice. Airway responsiveness to methacholine was measured in A/J and C3H/HeJ parental strains as well as in progeny derived from crosses between these strains. QTL mapping of backcross [(A/J x C3H/HeJ) x C3H/HeJ] progeny (n = 137-227 informative mice for markers tested) revealed two significant linkages to loci on chromosomes 6 and 7. The QTL on chromosome 6 confirms the previous report by others of a linkage in this region in the same genetic backgrounds; the second QTL, on chromosome 7, represents a novel locus. In addition, we obtained suggestive evidence for linkage (logarithm of odds ratio = 1.7) on chromosome 17, which lies in the same region previously identified in a cross between A/J and C57BL/6J mice. Airway responsiveness in a cross between A/J and C3H/HeJ mice is under the control of at least two major genetic loci, with evidence for a third locus that has been previously implicated in an A/J and C57BL/6J cross; this indicates that multiple genetic factors control the expression of this phenotype.

Animals↗
PubMed2003

Fine mapping and identification of candidate pulmonary adenoma susceptibility 1 genes using advanced intercross lines.

In the present study, we used newly developed F(11) generation mouse advanced intercross lines (AIL) to fine map Pas1-3 quantitative trait loci (QTL). The (A/J x C57BL/6) F(11) AIL mouse population was created by crossing lung tumor-resistant C57BL/6 mice with lung tumor-susceptible A/J mice. By selectively genotyping 30% of the population, we have confirmed the Pas1 QTL and narrowed it to an interval of approximately 1.0 cM or 1.3 Mb in the vicinity of the Kras2 gene. The Pas2 QTL was detected by both ANOVA and regression analysis but not by MapMaker EXP/QTL software. In addition, an interaction between the Pas1 and Pas2 QTLs was revealed. However, the Pas3 QTL was not confirmed in this study. It was either lost during the development of the AIL or too weak to be detected using AIL. The Pas1 locus is now sufficiently fine-mapped that candidate gene(s) for the Pas1 locus can be characterized by positional cloning. In this study, all 27 of the known or predicted genes located in the Pas1 candidate region were characterized as possible candidate Pas genes. Six genes were selected for additional analyses because of their relevant function in tumorigenesis or allelic changes between A/J and C57BL/6 mice. The Lrmp gene bears amino acid polymorphisms among various mouse strains that are highly correlated with the Pas1 allele status. The Pas1c1 gene (RIKEN Ak016641), encoding an intermediate filament tail domain-containing protein, produces alternatively spliced transcripts across inbred strains of mice, and its splicing pattern cosegregates with the Pas1 allele. The genetic and expression data support these two genes as strong candidates for the Pas1 locus. Of the other four genes (Eca39, RIKEN Ak015530, mHoj-1, and Krag), no functional polymorphisms or differential gene expression were found in Eca39, mHoj-1, and Krag between lung tumor-susceptible and -resistant strains. The Ak015530 carries an amino acid polymorphism, but this polymorphism does not cosegregate with mouse lung tumor susceptibility. Thus, these 4 genes are less likely candidates for the Pas1 locus.

Adenoma↗
PubMed2006

Rearranged gene order between pig and human in a quantitative trait loci region on SSC3.

A quantitative trait locus (QTL) for ovulation rate on chromosome 3 that peaks at 36 cM has been identified in a Meishan-White composite resource population with an additive effect of 2.2 corpora lutea. As part of an effort to identify the responsible gene(s), typing of additional genes on the INRA-University of Minnesota porcine radiation hybrid (IMpRH) map of SSC3 and comparative analysis of gene order was conducted. We placed 52 known genes and expressed sequence tags, two BAC-end sequences and one microsatellite (SB42) on a framework map that fills gaps on previous RH maps. Data were analysed for two-point and multipoint linkage with the IMpRH mapping tool and were submitted to the IMpRH database (http://imprh.toulouse.inra.fr/). Gene order was confirmed for 42 loci residing in the QTL region (spanning c. 17 Mb of human sequence) by using the high-resolution IMpRH2 panel. Carthagène (http://www.inra.fr/internet/departments/MIA/T/CarthaGene) was used to estimate multipoint marker distance and order using all public markers on SSC3 in the IMpRH database and those typed in this study. For the high-resolution map, only data for markers typed in both panels were used. Comparative analysis of human and porcine maps identified conservation of gene order for SSC3q and multiple blocks of conserved segments for SSC3p, which included six distinct segments of HSA7 and two segments of HSA16. The results of this study allow significant refinement of the SSC3p region that contains an ovulation rate QTL.

Animals↗
PubMed1986

Autoimmunity to Thy-1.

Conditions are described for the induction of autoimmunity to Thy-1 and a large panel of monoclonal CBA and AKR autoantibodies has been characterized. These reveal a hitherto unrecognized complexity at the Thy-1 locus and evidence for intragenic control. Epitopes recognized by the autoantibodies differed in species and tissue distribution from alloantigenic determinants but their specificity was confirmed by transfection studies with the cloned Thy-1b gene. The quantitative and qualitative differences in epitope expression between Thy-1a and Thy-1b alleles were inherited as single Mendelian traits and in the absence of recombinants, suggesting translational control.

Animals↗
PubMed2004

Disregulated glyceroneogenesis: PCK1 as a candidate diabetes and obesity gene.

Genetics and diet interact to cause type 2 diabetes mellitus and obesity. PCK1 has been implicated as one of many genes associated with type 2 diabetes mellitus. The common assumption is that mutations in PCK1 lead to excessive glucose production through hepatic gluconeogenesis. However, there is an alternative explanation, wherein mutations at the PCK1 locus could selectively affect PCK1 expression in adipose tissue. The result would be changes in glyceroneogenesis that would affect the storage and release of fatty acids. Here, we present the novel hypothesis that a variety of phenotypes could arise from mutations of the various tissue-specific control elements of PCK1. We also suggest specific quantitative metabolic traits that would accompany mutations that selectively affect PCK1 expression in adipose tissue.

Diabetes Mellitus↗
PubMed2006

Quantitative trait locus analysis of male mating success and sperm competition in Drosophila melanogaster.

Much of sexual selection theory depends on assumptions about the genetic basis of variation in male mating success and sperm competitive ability. Despite intense interest in this topic, few genes have been identified that contribute to variation in these traits. Here we report the results of quantitative trait locus (QTL) analyses of mating success of male Drosophila melanogaster when exposed to virgin females, remating success of males with previously mated females, and both defense and offense components of sperm competition. We found two to four significant QTLs for remating success, but no QTLs for mating success, even though mating success was more genetically variable than remating success in the recombinant inbred lines used in this study. By combining these results with data from previous gene-expression experiments, we were able to identify three X-linked candidate genes for variation in remating ability. For two of these genes, QTL and expression data were completely concordant with respect to directionality of effects: high mating success was associated with high levels of gene expression and with beneficial QTL effects on the trait. We found equivocal evidence for genetic variation in sperm offense and defense in the recombinant inbred lines, and we did not find any significant QTLs for either sperm competition trait.

Animals↗
PubMed2003

Identification of a new gene controlling plant height in rice using the candidate-gene strategy.

A gene underlying a quantitative trait locus (QTL) controlling plant height on chromosome 1 (QTLph1) in rice ( Oryza sativa L.) was identified using the candidate-gene strategy. First, the function of a targeted gene was analyzed using near isogenic lines (NILs) in which the chromosomal region of a targeted QTL was substituted with that of another line. Second, for physiological information, the candidate gene was selected in the annotation data by the genome sequencing. Physiological analyses of an NIL-expressing QTLph1 (NIL6) suggested that the targeted gene controls plant height by enabling higher amounts of sucrose to be translocated in leaves. The results indicated that the gene for sucrose phosphate synthase (SPS; EC 2.4.1.14), the major limiting enzyme for sucrose synthesis, is a candidate gene for QTLph1 among the annotation results of the region of QTLph1. The higher level of SPS transcripts and the activity of SPS in NIL6 compared to control plants, and the fact that the relative SPS activity per SPS protein content was almost the same between NIL6 and Nipponbare suggested that the higher plant height in NIL6 compared to Nipponbare was due to the high SPS activity in NIL6. In agreement with this hypothesis, transgenic rice plants with a maize SPS gene that had about 3 times the SPS activity of that in Nipponbare (control plants) were significantly taller than Nipponbare from the early growth stage. From these results and the physiological data from NIL6, we concluded that SPS is the targeted gene underlying QTLph1.

Base Sequence↗