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Results for “expression quantitative trait loci”

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PubMed2003

Analysis of the transcriptional response to Rice Yellow Mottle Virus infection in Oryza sativa indica and japonica cultivars.

Several cDNA libraries were constructed using mRNA isolated from roots, panicles, cell suspensions and leaves of non-stressed Oryza sativa indica (IR64) and japonica (Azucena) plants, from wounded leaves, and from leaves of both cultivars inoculated with Rice Yellow Mottle Virus (RYMV). A total of 5549 cleaned expressed sequence tags (ESTs) were generated from these libraries. They were classified into functional categories on the basis of homology, and analyzed for redundancy within each library. The expression profiles represented by each library revealed great differences between indica and japonica backgrounds. EST frequencies during the early stages of RYMV infection indicated that changes in the expression of genes involved in energy metabolism and photosynthesis are differentially accentuated in susceptible and partially resistant cultivars. Mapping of these ESTs revealed that several co-localize with previously described resistance gene analogs and QTLs (quantitative trait loci).

Chromosome Mapping↗
PubMed2005

Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits.

Genetic loci that regulate inherited traits are routinely identified using quantitative trait locus (QTL) mapping methods. However, the genotype-phenotype associations do not provide information on the gene expression program through which the genetic loci regulate the traits. Transcription modules are 'self-consistent regulatory units' and are closely related to the modular components of gene regulatory network [Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176]. We used genome-wide genotype and gene expression data of a genetic reference population that consists of mice of 32 recombinant inbred strains to identify the transcription modules and the genetic loci regulating them. Twenty-nine transcription modules defined by genetic variations were identified. Statistically significant associations between the transcription modules and 18 classical physiological and behavioral traits were found. Genome-wide interval mapping showed that major QTLs regulating the transcription modules are often co-localized with the QTLs regulating the associated classical traits. The association and the possible co-regulation of the classical trait and transcription module indicate that the transcription module may be involved in the gene pathways connecting the QTL and the classical trait. Our results show that a transcription module may associate with multiple seemingly unrelated classical traits and a classical trait may associate with different modules. Literature mining results provided strong independent evidences for the relations among genes of the transcription modules, genes in the regions of the QTLs regulating the transcription modules and the keywords representing the classical traits.

Animals↗
PubMed2006

Regulation of gene expression in the mammalian eye and its relevance to eye disease.

We used expression quantitative trait locus mapping in the laboratory rat (Rattus norvegicus) to gain a broad perspective of gene regulation in the mammalian eye and to identify genetic variation relevant to human eye disease. Of >31,000 gene probes represented on an Affymetrix expression microarray, 18,976 exhibited sufficient signal for reliable analysis and at least 2-fold variation in expression among 120 F(2) rats generated from an SR/JrHsd x SHRSP intercross. Genome-wide linkage analysis with 399 genetic markers revealed significant linkage with at least one marker for 1,300 probes (alpha = 0.001; estimated empirical false discovery rate = 2%). Both contiguous and noncontiguous loci were found to be important in regulating mammalian eye gene expression. We investigated one locus of each type in greater detail and identified putative transcription-altering variations in both cases. We found an inserted cREL binding sequence in the 5' flanking sequence of the Abca4 gene associated with an increased expression level of that gene, and we found a mutation of the gene encoding thyroid hormone receptor beta2 associated with a decreased expression level of the gene encoding short-wavelength sensitive opsin (Opn1sw). In addition to these positional studies, we performed a pairwise analysis of gene expression to identify genes that are regulated in a coordinated manner and used this approach to validate two previously undescribed genes involved in the human disease Bardet-Biedl syndrome. These data and analytical approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease.

Analysis of Variance↗
PubMed2004

FunMap: functional mapping of complex traits.

SUMMARY: FunMap is a Web-based user interface designed to map quantitative trait loci (QTL) affecting function-valued traits or infinite-dimensional traits in well-structured pedigrees or natural populations. User input includes three files: longitudinal trait data, marker genotypes and/or a linkage map. This software allows for a systematic genome-wide scan and significance test of QTL throughout the map. The dynamic change of QTL effects during the time course of growth is automatically drawn, from which specific biological hypotheses regarding the genetic control mechanisms of growth and development can be tested. AVAILABILITY: http://web.biostat.ufl.edu/~cma/genetics/software.html

Chromosome Mapping↗
PubMed2004

Use of new EST markers to elucidate the genetic differences in grain protein content between European and North American two-rowed malting barleys.

A population comprising 102 doubled haploid lines were produced from a cross between Beka, a barley cultivar widely grown in Spain, and Logan, a north American cultivar with inherently low protein content, a character considered to derive from the cultivar Karl. The intentions were to determine whether low-nitrogen malting barleys could be developed in Spain, and if genetic factors that influenced protein content were similarly expressed in widely diverse environments, i.e. northeastern Spain and eastern Scotland. An extensive map comprising 187 molecular markers was developed. Expressed sequence-tagged-derived markers were used in addition to anonymous simple sequence repeats to determine the potential for identifying candidate genes for quantitative trait loci (QTLs), and 22 such markers were mapped for the first time. There was transgressive segregation for both yield and protein content, and the gene for low protein from Logan was not expressed in the Scottish environment. In 2002, high yield was associated with earlier heading date in Spain, while late heading at the Scottish site was associated with greater lodging and lower thousand-kernel weight. These appeared to be possible pleiotropic effects of a factor detected on chromosome 2H. Using information from a consensus map, it was shown that this locus on 2H was in the region of the photoperiod response gene Eam6. A QTL explaining 18% of the variation in grain protein content was detected on chromosome 5H in a region in which a gene for nitrate reductase was previously observed. No effect on grain protein was associated with chromosome 6H, which has been suggested as the location of the low protein gene from Karl. However, it is likely that Karl contained more than one genetic factor reducing protein, and we postulate that the gene on 6H may have been lost during the breeding of Logan.

Base Sequence↗
PubMed2006

A method for identification of the expression mode and mapping of QTL underlying embryo-specific characters.

Embryos of crop seeds are one of the major sources of the plant protein and lipid for human nutrition. The genetic expression for embryo-specific characters in crop seeds can be controlled exclusively by the embryo or the maternal genotypes and sometimes by both simultaneously. However, current methods for mapping quantitative trait loci (QTLs) underlying characters of maternal plants have not been effective in dealing with the QTL analysis of embryo characters. On the basis of the expression feature of embryo, a statistical method was proposed for the identification of expression mode and mapping of QTL controlling embryo traits. The maximum likelihood method implemented via the expectation maximization algorithm was used to estimate parameters of a putative embryo-specific QTL. The QTL expression mode was identified by the likelihood ratio test statistic. Statistical power and other properties of the proposed method were investigated under a variety of scenarios through simulation studies. The results showed that the mapping method neglecting the effects of embryo genotype or maternal effects could neither identify the expression mode of QTL nor estimate its genetic effects accurately, whereas the proposed method could effectively map the embryo-specific QTL of various expression modes.

Algorithms↗
PubMed2005

Identification of quantitative trait loci across recombinant inbred lines and testcross populations for traits of agronomic importance in rice.

This study was conducted to determine whether quantitative trait loci (QTL) controlling traits of agronomic importance detected in recombinant inbred lines (RILs) are also expressed in testcross (TC) hybrids of rice. A genetic map was constructed using an RIL population derived from a cross between B5 and Minghui 63, a parent of the most widely grown hybrid rice cultivar in China. Four TC hybrid populations were produced by crossing the RILs with three maintaining lines for the widely used cytoplasmic male-sterile (CMS) lines and the genic male-sterile line Peiai64s. The mean values of the RILs for the seven traits investigated were significantly correlated to those of the F1 hybrids in the four TC populations. Twenty-seven main-effect QTL were identified in the RILs. Of these, the QTL that had the strongest effect on each of the seven traits in the RILs was detected in two or more of the TC populations, and six other QTL were detected in one TC population. Epistatic analysis revealed that the effect of epistatic QTL was relatively weak and cross combination specific. Searching publicly available QTL data in rice revealed the positional convergence of the QTL with the strongest effect in a wide range of populations and under different environments. Since the main-effect QTL is expressed across different testers, and in different genetic backgrounds and environments, it is a valuable target for gene manipulation and for further application in rice breeding. When a restorer line that expresses main-effect QTL is bred, it could be used in a number of cross combinations.

Chromosome Mapping↗
PubMed2006

Vernalization response in perennial ryegrass (Lolium perenne L.) involves orthologues of diploid wheat (Triticum monococcum) VRN1 and rice (Oryza sativa) Hd1.

Flowering time is important when adapting crop plants to different environments. While high feeding quality of forage grasses is facilitated by repression of flowering, flowering should also be inducible to facilitate grass seed production. Consequently, the identification and characterization of the genes controlling flowering time in forage grasses, including perennial ryegrass (Lolium perenne L.), is of great interest. In this study, three candidate genes for vernalization response genes in perennial ryegrass were identified based on DNA sequence homology to TmVRN1 and TmVRN2 of diploid wheat (Triticum monococcum), and Hd1 of rice (Oryza sativa). High sequence similarity between LpVRN1 and TmVRN1, co-localization of LpVRN1 with a major quantitative trait loci (QTL) for vernalization response in perennial ryegrass, synteny between map-positions of LpVRN1 and TmVRN1, mRNA expression analysis of LpVRN1 alleles during vernalization, and the correspondence between LpVRN1 mRNA expression levels and flowering time leads us to conclude that LpVRN1 is orthologous to TmVRN1 and that its function is conserved between diploid wheat and perennial ryegrass. Of the remaining two candidate genes, a putative Hd1 orthologue, LpCO, co-localized with a second QTL for vernlization response. LpCO has recently been shown to be involved in the photoperiodic regulation of flowering time. While epistasis, at the level of LpVRN1 transcription, was observed between the LpVRN1 and LpCO genomic regions, no differential expression of LpCO transcripts was observed during vernalization. While orthologous genes controlling flowering time can thus be identified, future allele sequencing efforts will reveal if causative polymorphisms are conserved across the grasses.

Amino Acid Sequence↗
PubMed1997

Structure and sequence of the bovine butyrophilin gene.

The complete sequence of the bovine butyrophilin gene (BTN) is described and compared with the mouse gene (Btn). Both genes contain seven exons separated by six introns, and the organisation of exons is closely associated with structural domains of the protein. Individual exons of BTN and Btn are 68-87% similar in sequence. There are no canonical TATA or CCAAT boxes associated with the transcription initiation sites in the genes of either species. However, a number of potential binding sites for transcription factors were identified in the 5'-flanking DNA, some of which may function in regulating expression of the gene in mammary tissue. Conservation of a 110-bp region in the promoters of BTN and Btn may have some functional significance. Cloning and sequencing of BTN provides an additional mammary-specific gene promoter that may be used for driving the expression of transgenes in the lactating mammary gland, and for determining the basis for tissue-specific gene expression. In addition, the sequence of BTN may be used to map intragenic polymorphisms and identify quantitative trait loci in commercial livestock.

Animals↗
PubMed2000

Quantitative trait loci controlling allergen-induced airway hyperresponsiveness in inbred mice.

Identification of the genetic loci underlying asthma in humans has been hampered by variability in clinical phenotype, uncontrolled environmental influences, and genetic heterogeneity. To circumvent these complications, the genetic regulation of asthma-associated phenotypes was studied in a murine model. We characterized the strain distribution patterns for the asthma-related phenotypes airway hyperresponsiveness (AHR), lung eosinophils, and ovalbumin (OVA)-specific serum immunoglobulin (Ig) E induced by allergen exposure protocols in A/J, AKR/J, BALB/cJ, C3H/HeJ, and C57BL/6J inbred strains and in (C3H/HeJ x A/J)F1 mice. Expression of AHR differed between strains and was sometimes discordant with lung eosinophils or serum IgE. Furthermore, we identified two distinct quantitative trait loci (QTL) for susceptibility to allergen-induced AHR, Abhr1 (allergen-induced bronchial hyperresponsiveness) (lod = 4. 2) and Abhr2 (lod = 3.7), on chromosome 2 in backcross progeny from A/J and C3H/HeJ mice. In addition, a QTL on chromosome 7 was suggestive of linkage to this trait. These QTL differ from those we have previously found to control noninflammatory AHR in the same crosses. Elucidation of the genes underlying these QTL will facilitate the identification of biochemical pathways regulating AHR in animal models of asthma and may provide insights into the pathogenesis of human disease.

Allergens↗
PubMed2004

A Leishmania major response locus identified by interval-specific congenic mapping of a T helper type 2 cell bias-controlling quantitative trait locus.

The propensity of naive CD4 T cells to become T helper (Th) type 2 cells correlates with susceptibility to infection by the protozoal parasite Leishmania major. Using genetic linkage analysis, we earlier identified Dice1 as a Th2 cell bias-controlling quantitative trait locus on chromosome 16. Using interval-specific congenic mapping, we now resolve Dice1 into two independent genetic loci, Dice1.1 and Dice1.2, which control Il4 expression from naive Th cells and thereby indirectly control Th2 cell bias. Interestingly, only one of the two congenic intervals containing Dice1.1 and Dice1.2, respectively, also contained an L. major response locus, indicating that L. major responsiveness can be insensitive to determinants that influence Th2 cell bias by controlling naive T cell Il4 expression. These results lay the groundwork for identifying the Dice1.1 and Dice1.2 genes controlling naive T cell Il4 expression and L. major responses, and for testing whether these control other Th2 cell-dependent processes such as worm expulsion, allergic asthma, and dermatitis.

Animals↗
PubMed2005

Cytokinin oxidase regulates rice grain production.

Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.

Alleles↗
PubMed2005

Characterisation of a barley (Hordeum vulgare L.) homologue of the Arabidopsis flowering time regulator GIGANTEA.

Barley cDNA and genomic clones homologous to the Arabidopsis flowering time regulator GIGANTEA were isolated. Genetic mapping showed that GIGANTEA is present as a single copy gene in barley (3HS) and rice (1S), while two copies are present in maize (3S and 8S) at locations consistent with previous comparative mapping studies. Comparison of the barley peptide with rice and Arabidopsis gave 94% and 79% similarity, respectively. Northern and semi-quantitative RT-PCR analysis of the barley gene (HvGI) showed the presence of a single mRNA species, with a peak of expression between 6 h and 9 h after dawn in short days (8 h light) and a peak 15 h after dawn in long days (16 h light). This behaviour is similar to that seen in Arabidopsis and rice, showing that sequence and expression pattern were well conserved. A lack of correspondence with the map positions of QTL affecting flowering time (heading date) suggests that variation at HvGI does not provide a major source of adaptive variation in photoperiod response.

Amino Acid Sequence↗
PubMed2005

Identification of a new class of pistil-specific proteins of Petunia inflata that is structurally similar to, but functionally distinct from, the self-incompatibility factor HT.

Pollen-pistil interactions are thought to involve a wide variety of intercellular recognition events controlled by diverse proteins and other molecules. One of the best characterized interactions is the S-RNase-based gametophytic self-incompatibility (GSI) system found in Solanaceae, Rosaceae and Scrophulariaceae. Although the S specificity of the pistil and the pollen in these families is determined by the S locus-encoded proteins S-RNase and SLF/SFB, respectively, these proteins alone are not sufficient for operation of the GSI reaction. Other factors are also required and are classified into three groups. To date, the only known factor is the pistil-expressed small asparagine-rich protein HT-B in three solanaceous genera Nicotiana, Lycopersicon and Solanum. HT-B is a Group 2 factor that is required for pollen rejection but do not affect S-RNase expression; factors in the other groups have not yet cloned. Here, we identified a new class of HT-like proteins in the style of Petunia inflata and named it HTL. Through alternative splicing, it was found that two isolated homologous HTL cDNAs, HTL-A and HTL-B, derived from a single gene. Like HT-B, HTL showed pistil-specific accumulation as well as significant sequence similarity to HT including conserved cystein residues at the C-terminal region and a signal peptide for extracellular localization. However, unlike HT-B, HTL lacked an asparagine-rich domain. Thus, it represents a new class of HT proteins. To determine whether HTL is involved in GSI function, RNA silencing constructs for HTL-A and HTL-B were introduced into self-incompatible P. inflata. Although several transgenic lines showed no detectable levels of both HTL-A and HTL-B transcripts, they retained normal GSI function and produced large fruits upon compatible pollination. This suggests that since silencing of the HTL gene alone is not sufficient to affect reproductive physiology, the gene is functionally distinct from the GSI factor HT-B.

Flowers↗
PubMed1995

Mapping and manipulating quantitative traits in maize.

Maize has been used effectively as a model organism in the development and evaluation of molecular markers for the identification, mapping and manipulation of major genes affecting the expression of quantitative traits in plants. Although quantitative geneticists have recognized the possibility of major loci, the general dogma had emerged that quantitative traits were controlled by many loci, each with a small effect. This interpretation sent a quantitative traits because it would be essentially impossible to isolate a gene responsible for the trait. Recent results from numerous mapping studies have shown that quantitative traits are controlled by, at least some, factors with major effects, and have given credibility to the conclusion that major loci exist and that one might be able to study them. Positive results from marker-facilitated selection and introgression studies have further strengthened this conclusion.

Chromosome Mapping↗
PubMed2006

Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme.

Large-scale screening studies carried out to date for genetic variants that affect gene regulation are generally limited to descriptions of differences in allele-specific expression (ASE) detected in vivo. Allele-specific differences in gene expression provide evidence for a model whereby cis-acting genetic variation results in differential expression between alleles. Such gene surveys for regulatory variation are a first step in identifying the specific nucleotide changes that govern gene expression differences, but they leave the underlying mechanisms unexplored. Here, we propose a quantitative genetics approach to perform a genome-wide analysis of ASE differences (GASED). The GASED approach is based on a diallel design that is often used in plant breeding programs to estimate general combining abilities (GCA) of specific inbred lines and to identify high-yielding hybrid combinations of parents based on their specific combining abilities (SCAs). In a context of gene expression, the values of GCA and SCA parameters allow cis- and trans-regulatory changes to be distinguished and imbalances in gene expression to be ascribed to cis-regulatory variation. With this approach, a total of 715 genes could be identified that are likely to carry allelic polymorphisms responsible for at least a 1.5-fold allelic expression difference in a total of 10 diploid Arabidopsis thaliana hybrids. The major strength of the GASED approach, compared to other ASE detection methods, is that it is not restricted to genes with allelic transcript variants. Although a false-positive rate of 9/41 was observed, the GASED approach is a valuable pre-screening method that can accelerate systematic surveys of naturally occurring cis-regulatory variation among inbred lines for laboratory species, such as Arabidopsis, mouse, rat and fruitfly, and economically important crop species, such as corn.

Alleles↗
PubMed2007

Expression of positional candidates for shell thickness in the chicken.

Expression of 12 positional candidates for QTL affecting shell thickness at 53 wk of lay age (ST53) was investigated by real-time PCR in the distal part of chicken oviducts (uterus) with a forming eggshell. In the local chicken breed Green-legged Partridgenous, the complete cDNA CR523443 (ChEST985k21) was downregulated with ratio of means 0.49 (P < or = 0.01) in the group with low ST53 (248.6 +/- 16.62 microm) relative to the group with the highest ST53 (372.4 +/- 2.07 microm). Expression of this gene was highly correlated (0.85, P < or = 0.01) with shell thickness. No significant difference in expression between the 2 groups with thick (378.4 +/- 3.65 microm) and thin (227.8 +/- 8.99 microm) shell and no significant correlation of expression level with ST53 were detected in Rhode Island Red, which could be explained by strict selection to egg quality traits, including optimal shell thickness in this commercial layer breed. These data suggested that CR523443 was a candidate gene for QTL ST53 in the chicken.

Animals↗