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At least 1,153 records · Page 64Linked to original sources
PubMed2003

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

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

Animals↗
PubMed2000

Strategy for uncovering complex determinants of hypertension using animal models.

Hypertension is a complex, multifactorial disorder resulting from the interaction of multiple genetic and environmental factors. While rodent models of hypertension have proved useful for identifying chromosomal regions containing blood pressure quantitative trait loci (QTLs), the gene(s) responsible for strain-differences in blood pressure remain to be identified. A strategy for identifying the genetic factors underlying blood pressure in animal models is presented, grouped according to the following themes: 1) choice of hypertension model, 2) identification of chromosomal regions containing QTLs, 3) confirming the presence of QTLs and delimiting the chromosomal region containing them, 4) developing a physical map of the QTL-containing region of the chromosome, 5) identification of strong candidate gene(s), and 6) requirements for proving that a gene is responsible, in part, for blood pressure differences.

Animals↗
PubMed2001

Marker pair selection for mapping quantitative trait loci.

Mapping of quantitative trait loci (QTL) for backcross and F(2) populations may be set up as a multiple linear regression problem, where marker types are the regressor variables. It has been shown previously that flanking markers absorb all information on isolated QTL. Therefore, selection of pairs of markers flanking QTL is useful as a direct approach to QTL detection. Alternatively, selected pairs of flanking markers can be used as cofactors in composite interval mapping (CIM). Overfitting is a serious problem, especially if the number of regressor variables is large. We suggest a procedure denoted as marker pair selection (MPS) that uses model selection criteria for multiple linear regression. Markers enter the model in pairs, which reduces the number of models to be considered, thus alleviating the problem of overfitting and increasing the chances of detecting QTL. MPS entails an exhaustive search per chromosome to maximize the chance of finding the best-fitting models. A simulation study is conducted to study the merits of different model selection criteria for MPS. On the basis of our results, we recommend the Schwarz Bayesian criterion (SBC) for use in practice.

Chromosome Mapping↗
PubMed2006

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis.

Expression microarrays hybridized with RNA can simultaneously provide both phenotypic (gene expression) and genotypic (marker) data. We developed two types of genetic markers from Affymetrix GeneChip expression data to generate detailed haplotypes for 148 recombinant inbred lines (RILs) derived from Arabidopsis thaliana accessions Bayreuth and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a gene's expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression QTL analyses without the need for separate genotyping. We have demonstrated that gene expression measurements from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied species.

Arabidopsis↗
PubMed2002

A genetic map of Gibberella zeae (Fusarium graminearum).

We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing complementary nitrate-nonutilizing (nit) mutants of G. zeae strains R-5470 (from Japan) and Z-3639 (from Kansas). We selected 99 nitrate-utilizing (recombinant) progeny and analyzed them for amplified fragment length polymorphisms (AFLPs). We used 34 pairs of two-base selective AFLP primers and identified 1048 polymorphic markers that mapped to 468 unique loci on nine linkage groups. The total map length is approximately 1300 cM with an average interval of 2.8 map units between loci. Three of the nine linkage groups contain regions in which there are high levels of segregation distortion. Selection for the nitrate-utilizing recombinant progeny can explain two of the three skewed regions. Two linkage groups have recombination patterns that are consistent with the presence of intercalary inversions. Loci governing trichothecene toxin amount and type (deoxynivalenol or nivalenol) map on linkage groups IV and I, respectively. The locus governing the type of trichothecene produced (nivalenol or deoxynivalenol) cosegregated with the TRI5 gene (which encodes trichodiene synthase) and probably maps in the trichothecene gene cluster. This linkage map will be useful in population genetic studies, in map-based cloning, for QTL (quantitative trait loci) analysis, for ordering genomic libraries, and for genomic comparisons of related species.

Chromosome Mapping↗
PubMed2003

QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments.

Quantitative-genetic approaches have offered significant insights into phenotypic evolution. However, quantitative-genetic analyses fail to provide information about the evolutionary relevance of specific loci. One complex and ecologically relevant trait for plants is their resistance to herbivory because natural enemies can impose significant damage. To illustrate the insights of combined molecular and ecological research, we present the results of a field study mapping quantitative trait loci (QTL) for resistance and tolerance to natural rabbit herbivory in the genetic model, Arabidopsis thaliana. Replicates of the Ler x Col recombinant inbred lines were planted into field sites simulating natural autumn and spring seasonal germination cohorts. Shortly after flowering, herbivores removed the main flowering inflorescence (apical meristem). We found several main-effect QTL for resistance within each seasonal cohort and significant QTL-season interactions, demonstrating that the loci underlying resistance to a single herbivore differ across seasonal environments. The presence of QTL x environment also shows that variation at specific loci is only available to selection in some environments. Despite significant among-line variance components, no QTL for tolerance were detected. The combined results of the quantitative-genetic and QTL analyses demonstrate that many loci of small effect underlie tolerance to damage by rabbits, and counter the hypothesis of locus-specific tradeoffs between resistance and tolerance. The results also provide insights as to the locus-specific nature of evolutionary constraints, i.e. some loci influence flowering time and resistance in both seasonal cohorts. Our results show how linking molecular-genetic tools with field studies in ecologically relevant settings can clarify the role of specific loci in the evolution of quantitative traits.

Arabidopsis↗
PubMed2004

A large-sample QTL study in mice: I. Growth.

By use of long-term selection lines for high and low growth, a large-sample (n = approximately 1,000 F2) experiment was conducted in mice to further understand the genetic architecture of complex polygenic traits. In combination with previous work, we conclude that QTL analysis has reinforced classic polygenic paradigms put in place prior to molecular analysis. Composite interval mapping revealed large numbers of QTL for growth traits with an exponential distribution of magnitudes of effects and validated theoretical expectations regarding gene action. Of particular significance, large effects were detected on Chromosome (Chr) 2. Regions on Chrs 1, 3, 6, 10, 11, and 17 also harbor loci with significant contributions to phenotypic variation for growth. Despite the large sample size, average confidence intervals of approximately 20 cM exhibit the poor resolution for initial estimates of QTL location. Analysis with genome-wide and chromosomal polygenic models revealed that, under certain assumptions, large fractions of the genome may contribute little to phenotypic variation for growth. Only a few epistatic interactions among detected QTL, little statistical support for gender-specific QTL, and significant age effects on genetic architecture were other primary observations from this study.

Animals↗
PubMed2001

Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize.

To enhance our understanding of the genetic basis of nitrogen use efficiency in maize (Zea mays), we have developed a quantitative genetic approach by associating metabolic functions and agronomic traits to DNA markers. In this study, leaves of vegetative recombinant inbred lines of maize, already assessed for their agronomic performance, were analyzed for physiological traits such as nitrate content, nitrate reductase (NR), and glutamine synthetase (GS) activities. A significant genotypic variation was found for these traits and a positive correlation was observed between nitrate content, GS activity and yield, and its components. NR activity, on the other hand, was negatively correlated. These results suggest that increased productivity in maize genotypes was due to their ability to accumulate nitrate in their leaves during vegetative growth and to efficiently remobilize this stored nitrogen during grain filling. Quantitative trait loci (QTL) for various agronomic and physiological traits were searched for and located on the genetic map of maize. Coincidences of QTL for yield and its components with genes encoding cytosolic GS and the corresponding enzyme activity were detected. In particular, it appears that the GS locus on chromosome 5 is a good candidate gene that can, at least partially, explain variations in yield or kernel weight. Because at this locus coincidences of QTLs for grain yield, GS, NR activity, and nitrate content were also observed, we hypothesize that leaf nitrate accumulation and the reactions catalyzed by NR and GS are coregulated and represent key elements controlling nitrogen use efficiency in maize.

Chromosome Mapping↗
PubMed2004

A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica.

A genetic linkage map of grape was constructed, utilizing 116 progeny derived from a cross of two Vitis rupestris x V. arizonica interspecific hybrids, using the pseudo-testcross strategy. A total of 475 DNA markers-410 amplified fragment length polymorphism, 24 inter-simple sequence repeat, 32 random amplified polymorphic DNA, and nine simple sequence repeat markers-were used to construct the parental maps. Markers segregating 1:1 were used to construct parental framework maps with confidence levels >90% with the Plant Genome Research Initiative mapping program. In the maternal (D8909-15) map, 105 framework markers and 55 accessory markers were ordered in 17 linkage groups (756 cM). The paternal (F8909-17) map had 111 framework markers and 33 accessory markers ordered in 19 linkage groups (1,082 cM). One hundred eighty-one markers segregating 3:1 were used to connect the two parental maps' parents. This moderately dense map will be useful for the initial mapping of genes and/or QTL for resistance to the dagger nematode, Xiphinema index, and Xylella fastidiosa, the bacterial causal agent of Pierce's disease.

Base Sequence↗
PubMed2002

Quantitative trait loci affecting fatness in the chicken.

An F2 chicken population of 442 individuals from 30 families, obtained by crossing a broiler line with a layer line, was used for detecting and mapping Quantitative Trait Loci (QTL) affecting abdominal fat weight, skin fat weight and fat distribution. Within-family regression analyses using 102 microsatellite markers in 27 linkage groups were carried out with genome-wide significance thresholds. The QTL for abdominal fat weight were found on chromosomes 3, 7, 15 and 28; abdominal fat weight adjusted for carcass weight on chromosomes 1, 5, 7 and 28; skin and subcutaneous fat on chromosomes 3, 7 and 13; skin fat weight adjusted for carcass weight on chromosomes 3 and 28; and skin fat weight adjusted for abdominal fat weight on chromosomes 5, 7 and 15. Interactions of the QTL with sex or family were unimportant and, for each trait, there was no evidence for imprinting or of multiple QTL on any chromosome. Significant dominance effects were obtained for all but one of the significant locations for QTL affecting the weight of abdominal fat, none for skin fat and one of the three QTL affecting fat distribution. The magnitude of each QTL ranged from 3.0 to 5.2% of the residual phenotypic variation or 0.2-0.8 phenotypic standard deviations. The largest additive QTL (on chromosome 7) accounted for more than 20% of the mean weight of abdominal fat. Significant positive and negative QTL were identified from both lines.

Abdomen↗
PubMed2006

Genetic analyses and quantitative trait loci detection, using a partial genome scan, for intramuscular fatty acid composition in Scottish Blackface sheep.

Genetic parameters for LM fatty acid composition were estimated in Scottish Blackface sheep, previously divergently selected for carcass lean content (LEAN and FAT lines). Furthermore, QTL were identified for the same fatty acids. Fatty acid phenotypic measurements were made on 350 male lambs, at approximately 8 mo of age, and 300 of these lambs were genotyped across candidate regions on chromosomes 1, 2, 3, 5, 14, 18, 20, and 21. Fatty acid composition measurements included in total 17 fatty acids of 3 categories: saturated, monounsaturated, and polyunsaturated. Total i.m. fat content was estimated as the sum of the fatty acids. The FAT line had a greater i.m. fat content and more oleic acid, but less linoleic acid (18:2 n-6) and docosapentaenoic acid (22:5 n-3) than did the LEAN line. Saturated fatty acids were moderately heritable, ranging from 0.19 to 0.29, and total SFA were highly heritable (0.90). Monounsaturated fatty acids were moderately to highly heritable, with cis-vaccenic acid (18:1 n-7) being the most heritable (0.67), and total MUFA were highly heritable (0.73). Polyunsaturated fatty acids were also moderately to highly heritable; arachidonic acid (20:4 n-6) and CLA were the most heritable, with values of 0.60 and 0.48, respectively. The total PUFA were moderately heritable (0.40). The QTL analyses were performed using regression interval mapping techniques. In total, 21 chromosome-wide QTL were detected in 6 out of 8 chromosomal regions. The chromosome-wide, significant QTL affected 3 SFA, 5 MUFA, and 13 PUFA. The most significant result was a QTL affecting linolenic acid (18:3 n-3) on chromosome 2. This QTL segregated in 2 of the 9 families and explained 37.6% of the phenotypic variance. Also, 10 significant QTL were identified on chromosome 21, where 8 out of 10 QTL were segregating in the same families and detected at the same position. The results of this study demonstrate that altering carcass fatness will simultaneously change i.m. fat content and oleic, linoleic, and docosapentaenoic acid content. The heritabilities of the fatty acids indicate opportunities for genetically altering most fatty acids. Moreover, this is the first report of detection of QTL directly affecting fatty acid composition in sheep.

Animals↗
PubMed2003

Identification of a single QTL, Mptp1, for susceptibility to MPTP-induced substantia nigra pars compacta neuron loss in mice.

The loss of substantia nigra pars compacta (SNpc) neurons seen in idiopathic Parkinson's disease is hypothesized to result from a genetic susceptibility to an unknown environmental toxin. MPTP has been used as a prototypical toxin, since exposure to this drug results in variable SNpc cell death in several vertebrate species, including man and mouse. Previously, we have shown that C57BL/6J mice are sensitive to this compound, while Swiss-Webster mice are resistant. In this study, we intercrossed these mouse strains to map quantitative trait loci (QTL) for MPTP sensitivity. Using genome wide PCR analysis, we found that a single major QTLs, Mptp1, located near the distal end of chromosome 1 between D1Mit113 and D1Mit293, accounts for the majority of the strain sensitivity to MPTP.

Animals↗
PubMed2006

Assignment of rainbow trout linkage groups to specific chromosomes.

The rainbow trout genetic linkage groups have been assigned to specific chromosomes in the OSU (2N=60) strain using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group. There was a rough correlation between chromosome size and size of the genetic linkage map in centimorgans for the genetic maps based on recombination from the female parent. Chromosome size and structure have a major impact on the female:male recombination ratio, which is much higher (up to 10:1 near the centromeres) on the larger metacentric chromosomes compared to smaller acrocentric chromosomes. Eighty percent of the BAC clones containing duplicate genes mapped to a single chromosomal location, suggesting that diploidization resulted in substantial divergence of intergenic regions. The BAC clones that hybridized to both duplicate loci were usually located in the distal portion of the chromosome. Duplicate genes were almost always found at a similar location on the chromosome arm of two different chromosome pairs, suggesting that most of the chromosome rearrangements following tetraploidization were centric fusions and did not involve homeologous chromosomes. The set of BACs compiled for this research will be especially useful in construction of genome maps and identification of QTL for important traits in other salmonid fishes.

Animals↗
PubMed2006

Identification of quantitative trait loci affecting corpora lutea and number of teats in a Meishan x Duroc F2 resource population.

Understanding of the genetic control of female reproductive performance in pigs would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing 3 to 5 more viable piglets per litter than Western breeds. This difference in prolificacy is attributed to the Meishan's superior prenatal survival. Our study utilized a 3-generation resource population, in which the founder grandparental animals were purebred Meishan and Duroc pigs, in a genome scan for QTL. Grandparent, F1, and F2 animals were genotyped for 180 microsatellite markers. Reproductive traits, including number of corpora lutea (number of animals = 234), number of fetuses per animal (n = 226), number of teats (n = 801), and total number born (n = 288), were recorded for F2 females. Genome-wide significance level thresholds of 1, 5, and 10% were calculated using a permutation approach. We identified 9 QTL for 3 traits at a 10% genome-wise significance level. Parametric interval mapping analysis indicated evidence of a 1% genome-wise significant QTL for corpora lutea on SSC 3. Nonparametric interval mapping for number of teats found 4 significant QTL on chromosomes SSC3 (P < 0.01), SSC7 (P < 0.01), SSC8 (P < 0.01), and SSC12 (P < 0.05). Partial imprinting of a QTL affecting teat number (P < 0.10) was detected on SSC8. Using the likelihood-ratio test for a categorical trait, 2 QTL for pin nipples were detected on SSC2 and SSC16 (P < 0.01). Fine mapping of the QTL regions will be required for their application to introgression programs and gene cloning.

Alleles↗
PubMed2002

Functional genomics in rat models of hypertension: using differential expression and congenic strains to identify and evaluate candidate genes.

Hypertension is a leading contributor to cardiovascular diseases such as heart attack and stroke. Genetic and environmental factors contribute to the development of hypertension. Animal models have been developed to study the genetic contributions to blood pressure (BP) regulation and to identify chromosomal regions harboring candidate genes causative of differences in BP regulation (i.e., BP quantitative trait loci [QTL]). Advances in both mammalian genome projects and global gene expression analysis present opportunities to study functional genomics in these animal models. In this article, novel approaches for designing experiments and interpreting global gene expression data using the Dahl salt-sensitive hypertension rat model are presented. We describe two-step screening protocols that can be used to identify BP QTL candidate genes. Genetically determined expression differences are identified in the target organs of inbred strains of contrasting phenotype in the first screen. Expression patterns in a panel of congenic strains or expression differences stemming from gene x environment interactions are examined in the second screen. Chromosomal locations of these genes can then be examined to determine whether they map to BP QTL-containing regions. Another approach is to study the expression of genes identified from public databases to be located within BP QTL-containing congenic regions. Several candidate genes have been identified using these strategies.

Animals↗
PubMed1997

Murine susceptibility to radiation-induced pulmonary fibrosis is influenced by a genetic factor implicated in susceptibility to bleomycin-induced pulmonary fibrosis.

From evidence of interpatient variability in normal tissue sensitivity to radiotherapy and from radiation studies using inbred mouse strains, it is hypothesized that individual variation in susceptibility to radiation-induced pulmonary fibrosis is genetically controlled. A genetic model has been developed from the fibrosis-prone C57BL/6J and the fibrosis-resistant C3Hf/Kam mouse strains. Inheritance of the fibrotic phenotype was characterized in F1 and F2 (F1 intercross) generations derived from the parental strains. Genetic mapping was used to determine whether the quantitative trait loci (QTL), which influence susceptibility to bleomycin-induced lung fibrosis in these progenitor strains, could be implicated in susceptibility to radiation-induced lung fibrosis. Mice were treated with 14 or 16 Gy (60Co) to the whole thorax. The doses were selected to investigate the response at the LD50 and LD100 of C3Hf/Kam mice. The animals were sacrificed 33 weeks after treatment or when moribund. The percentage of lung with fibrosis for each mouse was quantified with image analysis of a histological section of the lung. For both the 14- and 16-Gy data sets, heritability was estimated at 38 +/- 11%, and the number of genetic factors influencing susceptibility to pulmonary fibrosis was estimated to be one or two. Two hundred fifty-five F2 intercross mice were genotyped with markers at the bleomycin loci on chromosomes 11 and 17 (chromosome 17 marker is at the major histocompatibility complex). Genetic linkage was established for the marker on chromosome 17 (P = 3.0 x 10(-6)), which accounts for 6.6% of the F2 phenotypic variance but not for the markers surrounding the QTL on chromosome 11 (P = 0.37). The inheritance data suggested that susceptibility to radiation-induced pulmonary fibrosis is a heritable trait controlled by two genetic loci, and through genomic mapping, a QTL on chromosome 17 was identified as one of the loci.

Animals↗
PubMed2002

Genetic analysis of scab resistance QTL in wheat with microsatellite and AFLP markers.

Three chromosomal regions associated with scab resistance were detected in a common cultivar, Ning7840, by microsatellite and AFLP analysis. Six microsatellites on chromosome 3BS, Xgwm389, Xgwm533, Xbarc147, Xgwm493, Xbarc102, and Xbarc131, were integrated into an amplified fragment length polymorphism (AFLP) linkage group containing a major quantitative trait locus (QTL) for scab resistance in a mapping population of 133 recombinant inbred lines (RILs) derived from 'Ning7840' x 'Clark'. Based on single-factor analysis of variance of scab infection data from four experiments, Xgwm533 and Xbarc147 were the two microsatellite markers most tightly associated with the major scab resistance QTL. Interval analysis based on the integrated map of AFLP and microsatellite markers showed that the major QTL was located in a chromosome region about 8 cM in length around Xgwm533 and Xbarc147. Based on mapping of six microsatellite markers on eight 3BS deletion lines, the major QTL was located distal to breakage point 3BS-8. In total, 18 microsatellites were physically located on different subarm regions on 3BS. Two microsatellites, Xgwm120 and Xgwm614, were significantly associated with QTL for scab resistance on chromosome 2BL and 2AS, respectively. The resistance alleles on 3BS, 2BL, and 2AS were all derived from 'Ning7840'. Significant interaction between the major QTL on 3BS and the QTL on 2BL was detected based on microsatellite markers linked to them. Using these microsatellite markers would facilitate marker-assisted selection to improve scab resistance in wheat.

Chromosome Mapping↗