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At least 1,639 records · Page 91Linked to original sources
PubMed2002

AFLP and STS tagging of a major QTL for Fusarium head blight resistance in wheat.

Large-scale field screening for Fusarium head blight (FHB) resistance in wheat is difficult because environmental factors strongly influences the expression of resistance genes. Marker-assisted selection (MAS) may provide a powerful alternative. Conversion of amplified fragment length polymorphism (AFLP) markers into sequence-tagged site (STS) markers can generate breeder-friendly markers for MAS. In a previous study, one major quantitative trait locus (QTL) on chromosome 3BS was identified by using EcoRI-AFLP and a recombinant inbred population derived from the cross Ning 7840/Clark. Further mapping with PstI-AFLPs identified five markers that were significantly associated with the QTL. Three of them individually explained 38% to 50% of the phenotypic variation for FHB resistance. Two of them (pAGT/mCTG57, pACT/mCTG136) were linked to the QTL in coupling, and another (pAG/mCAA244) was linked to the QTL in repulsion. Successful conversion of one AFLP marker (pAG/mCAA244) yielded a co-dominant STS marker that explains about 50% of the phenotypic variation for FHB resistance in the population. The STS was validated in 14 other cultivars and is the first STS marker for a FHB resistance QTL converted from an AFLP marker.

Base Sequence↗
PubMed2003

Quantitative trait loci mapping for fatty acid contents in the backfat on porcine chromosomes 1, 13, and 18.

A partial genome scan using microsatellite markers was conducted in order to detect quantitative trait loci (QTLs) for 10 fatty acid contents of the backfat in a pig reference population. Two QTLs were found by studying SSC1, SSC13, and SSC18, where QTLs had already been identified for backfat thickness. A QTL was located between marker loci S0113 and SW974 on chromosome 1; this QTL was only significantly detected (P < 0.05) for linoleic acid. The other QTL was discovered between markers S0062 and S0120 on chromosome 18, and its significance only showed (P < 0.05) for myristic acid. The two QTLs mapped to the same location as the backfat thickness QTL. A third of the phenotypic variation was explained for linoleic acid by the QTL on chromosome 1, and a quarter for myristic acid by the QTL on chromosome 18. Further studies on fine mapping and positional comparative candidate gene analyses will be the next step toward a better understanding of the genetic architecture of fatty acid contents.

Adipose Tissue↗
PubMed2001

Genetic control of susceptibility to experimental Lyme arthritis is polygenic and exhibits consistent linkage to multiple loci on chromosome 5 in four independent mouse crosses.

C3H/He mice infected with Borrelia burgdorferi develop severe arthritis and are high antibody responders, while infected C57BL/6 and BALB/c mice develop mild arthritis and less robust humoral responses. Genetic analysis using composite interval mapping (CIM) on reciprocal backcross populations derived from C3H/HeN and C57BL/6N or C3H/HeJ and BALB/cAnN mice identified 12 new quantitative trait loci (QTL) linked to 10 murine Lyme disease phenotypes. These QTL reside on chromosomes 1, 2, 4, 6, 7, 9, 10, 12, 14, 15, 16, and 17. A reanalysis of an F(2) intercross between C57BL/6N and C3H/HeN mice using CIM identified two new QTL on chromosomes 4 and 15 and confirmed the location of seven previously identified loci. Two or more experimental crosses independently verified six QTL controlling phenotypes after B. burgdorferi infection. Additionally, Bb2 on chromosome 5 was reproduced in four experimental populations and was linked to the candidate locus Cora1. Evidence of four distinct QTL residing within the 30-cM region of chromosome 5 encompassing the previously mapped Bb2 and Bb3 loci was shown by CIM. Interestingly, some alleles contributing to susceptibility to Lyme arthritis were derived from C57BL/6N and BALB/cAnN mice, showing that disease-resistant strains harbor susceptibility alleles.

Animals↗
PubMed2003

Mapping of yield-related QTLs in pepper in an interspecific cross of Capsicum annuum and C. frutescens.

An advanced backcross QTL study was performed in pepper using a cross between the cultivated species Capsicum annuum cv. Maor and the wild C. frutescens BG 2816 accession. A genetic map from this cross was constructed, based on 248 BC(2) plants and 92 restriction fragment length polymorphism (RFLP) markers distributed throughout the genome. Ten yield-related traits were analyzed in the BC(2) and BC(2)S(1) generations, and a total of 58 quantitative trait loci (QTLs) were detected; the number of QTLs per trait ranged from two to ten. Most of the QTLs were found in 11 clusters, in which similar QTL positions were identified for multiple traits. Unlike the high percentage of favorable QTL alleles discovered in wild species of tomato and rice, only a few such QTL alleles were detected in BG 2816. For six QTLs (10%), alleles with effects opposite to those expected from the phenotype were detected in the wild species. The use of common RFLP markers in the pepper and tomato maps enabled possible orthologous QTLs in the two species to be determined. The degree of putative QTL orthology for the two main fruit morphology traits-weight and shape-varied considerably. While all eight QTLs identified for fruit weight in this study could be orthologous to tomato fruit weight QTLs, only one out of six fruit shape QTLs found in this study could be orthologous to tomato fruit shape QTLs.

Capsicum↗
PubMed2002

Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars.

The value of exotic germplasm in broadening the genetic base of most crops has been demonstrated many times. However, the difficulties involved in working with exotic germplasm have limited their utility in plant breeding. Unwanted linkages often thwart the successful incorporation of beneficial exotic genes into commercial lines. Thus, the use of exotics in traditional breeding makes the process of crop improvement a tedious, time-consuming and expensive endeavor. The availability of molecular markers makes it possible to isolate specific genomic regions and transfer them into commercial varieties with minimal linkage drag. We found a yield-enhancing quantitative trait locus (QTL) from Glycine soja (Siebold and Zucc.) by evaluating a population of 265 BC(2) individuals from a cross between HS-1 and PI 407305. The yield QTL was located on linkage group B2(U26) of the soybean [Glycine max (L.) Merrill] genetic linkage map. In a 2-year, multi-location study, individuals carrying the PI 407305 haplotype at the QTL locus demonstrated a 9.4% yield advantage over individuals that did not contain the exotic haplotype. When tested in a more uniform "HS-1-like" background in two locations, we observed an 8% yield advantage for lines that carry the PI 407305 haplotype. We further assessed the QTL effect in various elite soybean genetic backgrounds. The yield effect was consistently observed in only two of six genetic backgrounds. Individuals carrying the PI 407305 haplotype at the QTL locus had a 9% yield advantage in yield trials across locations. Despite the limited adaptability of this yield-QTL across genetic backgrounds, this study demonstrates the potential of exotic germplasm for yield enhancement in soybean.

Alleles↗
PubMed2004

Analysis of genetic marker-phenotype relationships by jack-knifed partial least squares regression (PLSR).

The utility of a relatively new multivariate method, bi-linear modelling by cross-validated partial least squares regression (PLSR), was investigated in the analysis of QTL. The distinguishing feature of PLSR is to reveal reliable covariance structures in data of different types with regard to the same set objects. Two matrices X (here: genetic markers) and Y (here: phenotypes) are interactively decomposed into latent variables (PLS components, or PCs) in a way which facilitates statistically reliable and graphically interpretable model building. Natural collinearities between input variables are utilized actively to stabilise the modelling, instead of being treated as a statistical problem. The importance of cross-validation/jack-knifing as an intuitively appealing way to avoid overfitting, is emphasized. Two datasets from chromosomal mapping studies of different complexity were chosen for illustration (QTL for tomato yield and for oat heading date). Results from PLSR analysis were compared to published results and to results using the package PLABQTL in these data sets. In all cases PLSR gave at least similar explained validation variances as the reported studies. An attractive feature is that PLSR allows the analysis of several traits/replicates in one analysis, and the direct visual identification of individuals with desirable marker genotypes. It is suggested that PLSR may be useful in structural and functional genomics and in marker assisted selection, particularly in cases with limited number of objects.

Crosses, Genetic↗
PubMed2006

A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L.

The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal.

Animals↗
PubMed1998

Mapping quantitative trait loci affecting sternopleural bristle number in Drosophila melanogaster using changes of marker allele frequencies in divergently selected lines.

Quantitative trait loci (QTLs) responsible for variation in sternopleural bristle number in crosses between the laboratory lines of Drosophila melanogaster OregonR and CantonS were mapped using information from allele frequency changes of two families of retrotransposon markers in divergently selected populations. QTL effects and positions were inferred by likelihood, using transition matrix iteration and Monte Carlo interval mapping. Individuals from the selected population were genotyped for markers spaced at an average distance 4.4 cM. Four QTLs of moderate effect ranging from 0.6 to 1.32 bristles accounted for most of the selection response. A permutation test of the correspondence between the mapped QTLs and the positions of bristle number candidate genes suggested that alleles at these candidate genes were no more strongly associated with selected changes in marker allele frequency than were randomly chosen positions in the genome.

Alleles↗
PubMed2006

In search of new targets for plasma high-density lipoprotein cholesterol levels: promise of human-mouse comparative genomics.

Many lines of evidence suggest that raising plasma high-density lipoprotein cholesterol (HDL-C) levels may inhibit, perhaps even reverse, atherosclerosis. Quantitative trait locus (QTL) analysis has been performed in both humans and mice. So far, approximately 40 high-density lipoprotein (HDL)-regulating QTLs have been identified in each species. To compare human and mouse HDL-C QTLs, we generate human-mouse comparative chromosome maps based on homologous genes in humans and mice. The comparative maps reveal that most human and mouse HDL-C QTLs are concordant, which suggests that identifying the underlying QTL genes in mice will facilitate identifying their homologs in humans. The maps also help to narrow QTLs by mouse-human homologous QTL comparison. By using a combination of classic genetic approaches and newer bioinformatics tools (including comparative genomics as highlighted in this study), identifying new drug targets for plasma HDL-C levels holds more promise than ever.

Animals↗
PubMed2006

Identification of genetic loci associated with ear-emergence in bread wheat.

A doubled haploid population constructed from a cross between the South Australian wheat cultivars 'Trident' and 'Molineux' was grown under winter field conditions, under field conditions over summer and under artificial light both with and without vernalisation. The duration from planting to ear-emergence was recorded and QTL associated with heading date were detected using a previously constructed genetic linkage map. Associations were shown with chromosomal regions syntenous to previously identified photoperiod (Ppd-B1) and vernalisation (Vrn-A1) sensitive loci. Additional QTL associated with time to heading were also identified on chromosomes 1A, 2A, 2B, 6D, 7A and 7B. Comparisons between the genetic associations observed under the different growing conditions allowed the majority of these loci to be classified as having either photoperiod-sensitive, vernalisation-sensitive or earliness per se actions. The identification of a photoperiod-sensitive QTL on chromosome 1A provides evidence for a wheat gene possibly homoeologous to Ppd-H2 previously identified on chromosome 1H of barley. The occurrence of a putative major gene for photoperiod sensitivity observed on chromosome 7A is presented. The combined additive effects at these loci accounted for more than half the phenotypic variance in the duration from planting to ear-emergence in this population. The possible role of these loci on the adaptation of wheat in Australia is discussed.

Chromosomes, Plant↗
PubMed2002

Genetic linkage mapping of quantitative trait loci for behavioral and neuroendocrine stress response traits in pigs.

A QTL analysis of behavioral and neuroendocrine responses to a "novel environment" stress was conducted in a three-generation experimental cross between Meishan and Large White pig breeds. A total of 186 F2 males and 182 F2 females were studied for their behavioral and neuroendocrine reactivity to a novel environment test at 6 wk of age. Locomotion, vocalization, and defecation rate, as well as exploration time, were measured for 10 min. Blood samples were taken immediately before and after the test to measure plasma levels of ACTH, cortisol, and glucose. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using two interval mapping methods: a line-cross regression method, where founder lines were assumed to be fixed for different QTL alleles, and a half-/full-sib maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Both methods revealed a highly significant gene effect for poststress cortisol level (P < 0.001) and a significant effect for basal cortisol level (P < 0.05) at the end of the q arm of chromosome 7, explaining, respectively, 20% and 7% of the phenotypic variance. Meishan alleles are associated with higher cortisol levels and are partially dominant (for poststress levels) over Large White alleles. Other significant gene effects on biological measures were detected on chromosomes 1 and 17 (ACTH response to stress), 3, 5, and 8 (glucose levels). The SSC 17 QTL explains 12% of the phenotypic variance of poststress ACTH levels, with a suggestive evidence of imprinting effects. Meishan alleles are associated with lower poststress ACTH levels. Gene effects of low amplitude only were found for behavioral reactivity traits. Considering the effects of stress neuroendocrine systems on energy fluxes and protein deposition, and the importance of stress reactivity for meat quality and animal welfare, these results open new perspectives for pig selection.

Adrenocorticotropic Hormone↗
PubMed2002

Mapping of quantitative trait loci underlying ethanol metabolism in BXD recombinant inbred mouse strains.

BACKGROUND: Genetic factors are well known to play an important role in determining individual differences in the metabolism of ethanol (EtOH), and several specific polymorphic loci have been identified that significantly contribute to the variability of EtOH metabolism in humans. However, these variant genes are either alcohol or aldehyde dehydrogenases, and the identification of new gene products that contribute to variation in alcohol metabolism would be useful. METHODS: To identify quantitative trait loci (QTLs), we correlated variation in polymorphic markers with blood EtOH concentration and the rate of EtOH metabolism (beta) in C57BL/6J and DBA/2J strains and in 25 of their recombinant inbred strains after 2 and 3 g/kg of EtOH intraperitoneally. RESULTS: A QTL associated with beta values for both doses was definitively mapped to the proximal region of chromosome 17, syntenic with human chromosome 6q25-27. Seven to 12 chromosomal regions were provisionally identified for each phenotype; several were associated with 2 or more phenotypes. Each QTL suggests the location of a gene or genes affecting EtOH pharmacokinetics. Candidate genes suggested by these analyses included several whose gene products are known to be induced by EtOH (e.g., superoxide dismutase, glutathione transferase, and cytochrome P450 2E1), as well as several whose gene products have signaling functions likely to contribute to this induction. CONCLUSIONS: These studies provide evidence for the existence of genes affecting EtOH metabolism in multiple chromosomal regions. Future studies will be required to identify the chromosome 17 gene product. Use of other genetic populations, such as B6D2F2 crosses, will be required to determine which of the provisional loci represent true and which represent false-positive associations.

Animals↗
PubMed1995

New seizure frequency QTL and the complex genetics of epilepsy in EL mice.

EL/Suz (EL) mice experience recurrent seizures that are similar to common partial complex epilepsy in humans. In the mice, seizures occur naturally at 90-100 days of age, but can be induced in younger mice and analyzed as a semi-quantitative trait after gentle rhythmic stimulation. A previous genetic mapping study of EL backcrosses to the strains ABP/LeJ or DBA/2J showed two quantitative trait loci (QTL) with large effects on seizure frequency (El1, Chr 9; El2, Chr 2) and implied the existence of other QTL with lesser effects. To further the understanding of EL-derived seizure alleles, we examined intercross progeny of EL and the strains ABP/LeJ and DDY/Jcl, and also a backcross of (EL x DDY)F1 hybrids to DDY. A new large-effect seizure frequency QTL was found (El5, Chr 14), a more minor QTL confirmed (El3, Chr 10), and two additional QTL proposed (El4, Chr 9; El6, Chr 11). The serotonin receptor gene, Htr2a, maps near and is a candidate for El5, and linkages of other serotonin receptor genes to seizure frequency QTL are noted. In addition, a strong gender effect was revealed, and epistasis was found between Chr 9 and Chr 14 markers. Despite this progress, however, our results revealed a more complex determinism of epilepsy in EL mice than previously described. In particular, no single El locus or pair was essential for frequent seizures, as QTL with large effects, such as El5, El2, and El1, were highly dependent on genetic context. Our studies highlight the importance of gene interaction in some complex mammalian traits defined by natural variation.

Animals↗
PubMed2002

Assignment of 280 swine genomic inserts including 31 microsatellites from BAC clones to the swine RH map (IMpRH map).

A precise genetic map containing anonymous markers and genes is indispensable for the efficient selection of candidate gene(s) responsible for quantitative trait loci (QTL) traits. For this purpose, a first version of a radiation hybrid cell (RH) map has been constructed by using the INRA-University of Minnesota RH panel for 757 markers (IMpRH) (Hawken et al. 1999, Mamm. Genome 10: 824--830). In this study, 280 swine genomic fragments in BAC clones were assigned to the IMpRH map; 255 BAC clones were successfully linked to first-generation linkage groups (LOD > 4.8). The remaining 25 clones could not be mapped, because their lod-scores to the closest markers in the first generation map were less than 4.8. In addition, 16 BAC clones, mapped to swine Chromosome (Chr) 1 by IMpRH mapping, were subjected to isolation of microsatellites (MSs). Thirty-one MSs were isolated from 15 BAC clones, and 24 of 31 (77%) MSs derived from 14 clones were found to be polymorphic. We also mapped both termini of 12 BAC clones to the IMpRH map, in order to measure resolution of the IMpRH map; the resolution was found to range from 8 kb/centiRay to more than 126 kb/centiRay depending on the region.

Animals↗
PubMed1999

Interval mapping of growth in divergent swine cross.

A genomic scan of 18 swine autosomal chromosomes was constructed with 119 polymorphic microsatellite (ms) markers to identify quantitative trait loci (QTL) for 11 growth traits in the University of Illinois Meishan x Yorkshire Swine Resource Family. A significant QTL effect was found for post-weaning average daily gain (ADG) between 5.5 and 56 kg of body weight that mapped between markers SW373 and SW1301 near the telomere of Chromosome (Chr) 1 q (SSC1). This QTL effect had a nominal (pointwise) p-value of 0.000007, a genome wide p-value of 0.012, and accounted for 26% of the F2 phenotypic variance. The same chromosome region also had significant effects on ADG between birth and 56 kg body weight (p-value =. 000227), and on ADG between 35 and 56 kg (p-value =.00077). These observations suggest that a significant QTL for post-weaning growth resides on SSC1.

Animals↗
PubMedDate not supplied

Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize.

Vgt1 (Vegetative to generative transition 1) is a quantitative trait locus (QTL) for flowering time in maize (Zea mays L.). Vgt1 was initially mapped in a ca. 5-cM interval on chromosome bin 8.05, using a set of near-isogenic lines (NILs) in the genetic background of the late dent line N28, with the earliness allele introgressed from the early variety Gaspé Flint. A new large mapping population was produced by crossing N28 and one early NIL with a ca. 6-cM long Gaspé Flint introgression at the Vgt1 region. Using PCR-based assays at markers flanking Vgt1, 69 segmental NILs homozygous for independent crossovers near the QTL were developed. When the NILs were tested in replicated field trials for days to pollen shed (DPS) and plant node number (ND), the QTL followed a Mendelian segregation. Using bulk segregant analysis and AFLP profiling, 17 AFLP markers linked to the QTL region were identified. Statistical analysis indicated a substantial coincidence of the effects of Vgt1 on both DPS and ND. Vgt1 was mapped at ca. 0.3 cM from an AFLP marker. As compared to DPS, the higher heritability of ND allowed for a more accurate assessment of the effects of Vgt1. The feasibility of the positional cloning of Vgt1 is discussed.

Base Sequence↗
PubMed2004

First-generation linkage map of the gray, short-tailed opossum, Monodelphis domestica, reveals genome-wide reduction in female recombination rates.

The gray, short-tailed opossum, Monodelphis domestica, is the most extensively used, laboratory-bred marsupial resource for basic biologic and biomedical research worldwide. To enhance the research utility of this species, we are building a linkage map, using both anonymous markers and functional gene loci, that will enable the localization of quantitative trait loci (QTL) and provide comparative information regarding the evolution of mammalian and other vertebrate genomes. The current map is composed of 83 loci distributed among eight autosomal linkage groups and the X chromosome. The autosomal linkage groups appear to encompass a very large portion of the genome, yet span a sex-average distance of only 633.0 cM, making this the most compact linkage map known among vertebrates. Most surprising, the male map is much larger than the female map (884.6 cM vs. 443.1 cM), a pattern contrary to that in eutherian mammals and other vertebrates. The finding of genome-wide reduction in female recombination in M. domestica, coupled with recombination data from two other, distantly related marsupial species, suggests that reduced female recombination might be a widespread metatherian attribute. We discuss possible explanations for reduced female recombination in marsupials as a consequence of the metatherian characteristic of determinate paternal X chromosome inactivation.

Animals↗