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At least 1,243 records · Page 69Linked to original sources
PubMed1998

Mapping quantitative trait loci for carcass and meat quality traits in a wild boar x Large White intercross.

An intercross between wild boar and a domestic Large White pig population was used to map quantitative trait loci (QTL) for body proportions, weight of internal organs, carcass composition, and meat quality. The results concerning growth traits and fat deposition traits have been reported elsewhere. In the present study, all 200 F2 animals, their parents, and their grandparents were genotyped for 236 markers. The marker genotypes were used to calculate the additive and dominance coefficients at fixed positions in the genome of each F2 animal, and the trait values were regressed onto these coefficients in intervals of 1 cM. In addition, the effect of proportion of wild boar alleles was tested for each chromosome. Significant QTL effects were found for percentage lean meat and percentage lean meat plus bone in various cuts, proportion of bone in relation to lean meat in ham, muscle area, and carcass length. The significant QTL were located on chromosomes 2, 3, 4, and 8. Each QTL explained 9 to 16% of the residual variance of the traits. Gene action for most QTL was largely additive. For meat quality traits, there were no QTL that reached the significance threshold. However, the average proportion of wild boar alleles across the genome had highly significant effects on reflectance and drip loss. The results show that there are several chromosome regions with a considerable effect on carcass traits in pigs.

Animals↗
PubMed2005

Polymorphism of the pig 2,4-dienoyl CoA reductase 1 gene (DECR1) and its association with carcass and meat quality traits.

We characterized the nearly complete coding sequence of the pig 2,4-dienoyl CoA reductase 1 (DECR1) gene, which encodes an enzyme involved in the beta-oxidation of polyunsaturated fatty enoyl-CoA esters and maps on a linoleic QTL located on Chromosome 4. Sequencing of a 937-bp fragment encompassing exons 2 and 10 revealed the existence of two missense SNP at exon 2 (C181 --> G181) and exon 5 (C458 -->G458). These two SNP are associated with Val (C) --> Leu (G) and Ser (C) --> Thr (G) conservative AA replacements at positions 61 and 153 of the DECR1 protein, respectively. Moreover, DECR1 genotyping in a representative sample of 184 pigs from the Large White, Pietrain, Iberian, Duroc, and Landrace breeds demonstrated the existence of disequilibrium linkage between these two SNP (Haplotype 1: C181C458; Haplotype 2: G181G458). An association analysis between DECR1 genotype and growth, carcass, and meat quality traits in a highly selected Landrace population (n = 470) revealed differences among genotypes for isocitrate dehydrogenase activity (highest posterior density [HPD] of 90%), longissimus thoracis pH (HPD of 95%), lightness (HPD of 90 to 95%), and redness (HPD of 95%). Because these associations were not consistently found in the three available genotype comparisons, we believe that exon 2 and 5 polymorphisms at the DECR1 gene might be in linkage disequilibrium with the true causal mutation influencing isocitrate dehydrogenase activity and muscle color and pH.

Animals↗
PubMed2001

[Inferring genotype of DNA molecular marker by Bayesian theorem].

Bayesian theorem is applied to infer DNA molecular marker genotype (DNA chain type) from its phenotype (electrophoresis band type). The results indicate that large difference often presents in the genotype probability of a molecular marker with incomplete genetic information when it is obtained from the assumption of independence among markers as compared with that inferred from the genotypes of the flanking markers with the complete genetic information and the recombination fractions among them based on the Bayesian theorem. Therefore, before utilizing the marker information, such as in mapping quantitative trait loci (QTL), marker assisted selection (MAS) etc., Bayes' probability of the genotype for all markers with incomplete genetic information must be calculated over the whole genome for every individual. This study provided detailed procedure for the calculation of the Bayes' probability of the unknown DNA genotype. Several extensions were also discussed for the application of the Bayesian theorem in genetics.

Bayes Theorem↗
PubMed2001

Structural and functional genomics in domestic animals: the way to understand the phenotype.

Molecular approaches to genome analysis in livestock are reviewed by discussing the contribution of molecular genome analysis to the identification of the genetic variation underlying phenotypic variation (structural genome analysis) and to the definition of the trait-associated and environment-affected gene expression (functional genome analysis) as an important prerequisite to understanding the formation of a phenotype. Aspects of using mapped 'quantitative trait loci' (QTL) or gene variants as well as the identified trait-associated and environment-affected gene expression profile in livestock production are expounded.

Journal Article↗
PubMed2004

Identification of chromosome regions associated with seedling vigor in rice.

Seedling vigor is important for optimum stand establishment in rice cropping. In this paper,a set of 264 F12 recombinant inbred lines (RILs) derived by single seed descent from a cross between Lemont (japonica) and Teqing (indica) was phenotyped for three seedling vigor related traits, including seed germination rate (GR), seedling shoot length and dry weight by the rolled paper towel tests. The phenotype data and a linkage map consisting of 198 DNA markers were combined to map quantitative trait loci (QTL) for seedling vigor by using a computer program QTLMapper1.0. A total of 13 putative main-effect QTL were detected. All of these QTL had much smaller effects on the traits with a mean R2 of 6.2%, ranging from 2.9% to 12.7%. As for digenic interaction, 18 pairs of epistatic loci with R2 > or = 5% were resolved with a mean R2 of 6.9% ,ranging from 5.1% to 11.8%, which was slightly larger than that of the main-effect QTL identified for the traits. The majority of the main-effect and epistatic loci detected for seedling vigor related traits were clustered in a few chromosome regions. Together, seven such chromosome regions (CRs), each with three or more seedling vigor main-effect and epistatic loci, were found to be highly associated with seedling vigor. These CRs can be classified into three types, i.e. M-CRs, E-CRs and ME-CRs. For some CRs just like CR(SV-6), the QTL within one CR were found to interact simultaneously with QTL within more than one other CRs to affect different seedling vigor related traits. The above results revealed that seedling vigor in rice is controlled by many loci, most of which have relatively small effects. Comparatively, epistasis as a genetic factor would be more important than main-effects of QTL for seedling vigor in rice. Nevertheless, the effects of the QTL are still large enough to be detected and in fact several chromosome regions were found to be highly associated with seedling vigor in very different populations as compared with previous studies. Molecular tagging of favorable alleles and marker-aided selection strategy may, therefore, be a promising approach to the improvement of rice seedling vigor.

Hybrid Vigor↗
PubMedDate not supplied

The search for human osteoporosis genes.

Osteoporosis is the most prevalent metabolic bone disease and a major clinical and public health problem. Heredity plays an important and well-established role in determining the lifetime risk of this disease. Major efforts are currently underway to identify the specific genes and their allelic variations that contribute to the heritable component to osteoporosis. A number of laboratories are using quantitative trait locus (QTL) methods of genome scanning in families and animal models to identify candidate genomic regions and, ultimately, the genes and genetic variations that lead to osteoporosis. Several chromosomal regions of the human genome have now been linked to osteoporosis-related phenotypes. Although the specific genes contributing to the majority of these linkage signals have not been identified, two positional candidate genes have now been identified: low density lipoprotein receptor-related protein 5 (LRP5) and bone morphogenetic protein 2 (BMP2). A number of QTL has also been identified by cross-breeding strains of mice with variable bone density and several of these QTL have been fine mapped, providing a rich new base for understanding osteoporosis. Genetic association analyses have also provided evidence for a modest relationship between allelic variants in several biological candidate genes and bone mass and the risk of fracture. These ongoing animal and human studies will provide a continuing source of new insight into the genetic regulation of bone and mineral metabolism and the molecular etiology of osteoporosis. The new insight that will emerge from this ongoing research should lead to new ways of diagnosing, preventing and treating the growing clinical and public health problem of osteoporosis.

Animals↗
PubMed2005

Characterization and RH mapping of bovine microsatellites generated from a microdissected BTA20-specific DNA library.

Bovine chromosome 20 (BTA20) is associated with several quantitative trait loci (QTL) for meat tenderness, birth weight, milk yield and composition. Fine mapping of these QTL requires the development of additional informative markers to increase the resolution of the BTA20 genetic and physical maps. A BTA20-specific library was constructed by means of microdissection and microcloning, and screened for dinucleotide repeats with (CA)16 and (GT)16 oligos. A total of 60 new microsatellites (MS) were developed and characterized for polymorphism using the U.S. Department of Agriculture (USDA)/Meat Animal Research Center (MARC) bovine reference family, of which 53 markers were informative in this family. The number of alleles for these loci varied from 1 to 14, with an average of 6.5. Thirty-three of these MSs, together with 105 markers previously mapped to BTA20, were scored on a 7000-rad cattle-hamster whole-genome radiation hybrid panel (SUNbRH), resulting in a high-resolution RH7000 rad map for BTA20.

Animals↗
PubMed2001

Mapping of multiple quantitative trait loci by simple regression in half-sib designs.

Detection of QTL in outbred half-sib family structures has mainly been based on interval mapping of single QTL on individual chromosomes. Methods to account for linked and unlinked QTL have been developed, but most of them are only applicable in designs with inbred species or pose great demands on computing facilities. This study describes a strategy that allows for rapid analysis, involving multiple QTL, of complete genomes. The methods combine information from individual analyses after which trait scores for a specific linkage group are adjusted for identified QTL at other linkage groups. Regression methods are used to estimate QTL positions and effects; permutation tests are used to obtain empirical threshold values. The description of the methods is complemented by an example of the combined analysis of 28 bovine chromosomes and their associations with milk yield in Finnish Ayrshire cattle. In this example, the individual analysis revealed five suggestive QTL affecting milk yield. Following the strategy presented in this paper, the final combined analysis showed eight significant QTL affecting milk yield. This clearly demonstrates the potential gain of using the combined analysis. The use of regression methods, with low demands on computing resources, makes this approach very practical for total genome scans.

Animals↗
PubMed2006

Simultaneous fine mapping of multiple closely linked quantitative trait Loci using combined linkage disequilibrium and linkage with a general pedigree.

Within a small region (e.g., <10 cM), there can be multiple quantitative trait loci (QTL) underlying phenotypes of a trait. Simultaneous fine mapping of closely linked QTL needs an efficient tool to remove confounded shade effects among QTL within such a small region. We propose a variance component method using combined linkage disequilibrium (LD) and linkage information and a reversible jump Markov chain Monte Carlo (MCMC) sampling for model selection. QTL identity-by-descent (IBD) coefficients between individuals are estimated by a hybrid MCMC combining the random walk and the meiosis Gibbs sampler. These coefficients are used in a mixed linear model and an empirical Bayesian procedure combines residual maximum likelihood (REML) to estimate QTL effects and a reversible jump MCMC that samples the number of QTL and the posterior QTL intensities across the tested region. Note that two MCMC processes are used, i.e., an (internal) MCMC for IBD estimation and an (external) MCMC for model selection. In a simulation study, the use of the multiple-QTL model clearly removes the shade effects between three closely linked QTL located at 1.125, 3.875, and 7.875 cM across the region of 10 cM, using 40 markers at 0.25-cM intervals. It is shown that the use of combined LD and linkage information gives much more useful information compared to using linkage information alone for both single- and multiple-QTL analyses. When using a lower marker density (11 markers at 1-cM intervals), the signal of the second QTL can disappear. Extreme values of past effective size (resulting in extreme levels of LD) decrease the mapping accuracy.

Chromosome Mapping↗
PubMed2004

Genetic dissection of embryo sac fertility, pollen fertility, and their contributions to spikelet fertility of intersubspecific hybrids in rice.

The partial sterility of hybrids has been a major barrier for utilization of the strong heterosis expressed in hybrids between Oryza sativa ssp. indica and O. sativa ssp. japonica. Wide-compatibility varieties, comprising a special class of germplasm, are able to produce fertile hybrids when crossed to both indica and japonica varieties. However, all the work on wide compatibility and majority of studies on indica/japonica hybrid sterility reported so far were based only on spikelet fertility; thus, it is not known to what extent male and female gamete abortions influence hybrid sterility. In this study, we investigated pollen fertility, embryo sac fertility, and spikelet fertility in an F1 population of 202 true hybrid plants derived from a three-way cross ('02428'/'Nanjing 11'//'Balilla'). A partial regression analysis showed that the pollen and embryo sac fertility contributed almost equally to spikelet fertility. QTL analysis based on a linkage map of 191 polymorphic marker loci identified two QTLs for pollen fertility, one QTL for embryo sac fertility, and three QTLs for spikelet fertility. The S5 locus, previously identified as a locus for wide compatibility by spikelet fertility analysis, is a major locus for embryo sac fertility, and a QTL on chromosome 5 had a major effect on pollen fertility. These two loci coincided with the two major QTLs for spikelet fertility. The study also detected a QTL on chromosome 8, showing a large effect on spikelet fertility but no effect on either pollen or embryo sac fertility. Very little interaction among the QTLs was detected. The implications of the findings in rice breeding programs are discussed.

Chromosome Mapping↗
PubMed2007

Fine-mapping and comprehensive transcript analysis reveals nonsynonymous variants within a novel 1.17 Mb blood pressure QTL region on rat chromosome 10.

The presence of blood pressure (BP) quantitative trait loci (QTL) on rat chromosome 10 has been clearly demonstrated by linkage analysis and substitution mapping. Using congenic strains containing the LEW rat chromosomal segments on the Dahl salt-sensitive (S) rat background, further iterations of congenic substrains were constructed and characterized to fine-map a chromosome 10 region (QTL1) linked to blood pressure. Comparison of seven congenic substrains refined QTL1 to a 1.17 Mb segment flanked by D10Mco88 and D10Mco89, which are located at 71,513,116 and 72,684,774 bp, respectively. The newly defined QTL1, containing 18 genes, is captured in its entirety within a single congenic substrain. A thorough transcript analysis revealed that 3 of these 18 genes, Ccl5, Ddx52, and RGD1559577, had nonsynonymous allelic variations between the S rat and the LEW rat. None of the detected transcripts within the newly defined QTL1 are implicated directly in BP control in humans or model organisms. Therefore, the present work defines a novel blood pressure QTL with three potential quantitative trait nucleotides.

Animals↗
PubMed1998

Quantitative trait loci affecting body weight and fatness from a mouse line selected for extreme high growth.

Quantitative trait loci (QTL) influencing body weight were mapped by linkage analysis in crosses between a high body weight selected line (DU6) and a control line (DUKs). The two mouse lines differ in body weight by 106% and in abdominal fat weight by 100% at 42 days. They were generated from the same base population and maintained as outbred colonies. Determination of line-specific allele frequencies at microsatellite markers spanning the genome indicated significant changes between the lines on 15 autosomes and the X chromosome. To confirm these effects, a QTL analysis was performed using structured F2 pedigrees derived from crosses of a single male from DU6 with a female from DUKs. QTL significant at the genome-wide level were mapped for body weight on chromosome 11; for abdominal fat weight on chromosomes 4, 11, and 13; for abdominal fat percentage on chromosomes 3 and 4; and for the weights of liver on chromosomes 4 and 11, of kidney on chromosomes 2 and 9, and of spleen on chromosome 11. The strong effect on body weight of the QTL on chromosome 11 was confirmed in three independent pedigrees. The effect was additive and independent of sex, accounting for 21-35% of the phenotypic variance of body weight within the corresponding F2 populations. The test for multiple QTL on chromosome 11 with combined data from all pedigrees indicated the segregation of two loci separated by 36 cM influencing body weight.

Alleles↗
PubMed2004

Genetics of species differences in the wild annual sunflowers, Helianthus annuus and H. petiolaris.

Much of our knowledge of speciation genetics stems from quantitative trait locus (QTL) studies. However, interpretations of the size and distribution of QTL underlying species differences are complicated by differences in the way QTL magnitudes are estimated. Also, many studies fail to exploit information about QTL directions or to compare inter- and intraspecific QTL variation. Here, we comprehensively analyze an extensive QTL data set for an interspecific backcross between two wild annual sunflowers, Helianthus annuus and H. petiolaris, interpret different estimates of QTL magnitudes, identify trait groups that have diverged through selection, and compare inter- and intraspecific QTL magnitudes. Our results indicate that even minor QTL (in terms of backcross variance) may be surprisingly large compared to levels of standing variation in the parental species or phenotypic differences between them. Morphological traits, particularly flower morphology, were more strongly or consistently selected than life history or physiological traits. Also, intraspecific QTL were generally smaller than interspecific ones, consistent with the prediction that larger QTL are more likely to spread to fixation across a subdivided population. Our results inform the genetics of species differences in Helianthus and suggest an approach for the simultaneous mapping of inter- and intraspecific QTL.

Alleles↗
PubMed2006

The genetic basis of floral traits associated with mating system evolution in Leptosiphon (Polemoniaceae): an analysis of quantitative trait loci.

Mapping of quantitative trait loci (QTL) was used to investigate the genetic architecture of divergence in floral characters associated with the mating system, an important adaptive trait in angiosperms. Two species of Leptosiphon (Polemoniaceae), one strongly self-fertilizing (L. bicolor) and the other partially outcrossing (L. jepsonii), were crossed to produce F2 and both backcross progenies. For each crossing population, a linkage map was created using amplified fragment length polymorphism markers, and QTL were identified for several dimensions of floral size. For each of the five traits examined, three to seven QTL were detected, with independent datasets yielding congruent results in some but not all cases. The phenotypic effect of individual QTL was generally moderate. We estimated that many of the QTL were additive or showed dominance toward L. bicolor, whereas comparison of mean trait values for parental and cross progenies showed apparent overall dominance of L. jepsonii traits. Colocalization of QTL for different dimensions of floral size was consistent with high phenotypic correlations between floral traits. Substantial segregation distortion was observed in marker loci, the majority favoring alleles from the large-flowered parent. A low frequency of male sterility in the F2 population is consistent with the Dobzhansky-Muller model for the evolution of reproductive isolation.

Biological Evolution↗
PubMed2003

Candidate defense genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice.

Candidate genes involved in both recognition (resistance gene analogs [RGAs]) and general plant defense (putative defense response [DR]) were used as molecular markers to test for association with resistance in rice to blast, bacterial blight (BB), sheath blight, and brown plant-hopper (BPH). The 118 marker loci were either polymerase chain reaction-based RGA markers or restriction fragment length polymorphism (RFLP) markers that included RGAs or putative DR genes from rice, barley, and maize. The markers were placed on an existing RFLP map generated from a mapping population of 116 doubled haploid (DH) lines derived from a cross between an improved indica rice cultivar, IR64, and a traditional japonica cultivar, Azucena. Most of the RGAs and DR genes detected a single locus with variable copy number and mapped on different chromosomes. Clusters of RGAs were observed, most notably on chromosome 11 where many known blast and BB resistance genes and quantitative trait loci (QTL) for blast, BB, sheath blight, and BPH were located. Major resistance genes and QTL for blast and BB resistance located on different chromosomes were associated with several candidate genes. Six putative QTL for BB were located on chromosomes 2, 3, 5, 7, and 8 and nine QTL for BPH resistance were located to chromosomes 3, 4, 6, 11, and 12. The alleles of QTL for BPH resistance were mostly from IR64 and each explained between 11.3 and 20.6% of the phenotypic variance. The alleles for BB resistance were only from the Azucena parent and each explained at least 8.4% of the variation. Several candidate RGA and DR gene markers were associated with QTL from the pathogens and pest. Several RGAs were mapped to BB QTL. Dihydrofolate reductase thymidylate synthase co-localized with two BPH QTL associated with plant response to feeding and also to blast QTL. Blast QTL also were associated with aldose reductase, oxalate oxidase, JAMyb (a jasmonic acid-induced Myb transcription factor), and peroxidase markers. The frame map provides reference points to select candidate genes for cosegregation analysis using other mapping populations, isogenic lines, and mutants.

Aldehyde Reductase↗
PubMed1999

Disequilibrium mapping of a quantitative-trait locus in an expanding population.

Linkage disequilibrium (LD) mapping can be successful if there is strong nonrandom association between marker alleles and an allele affecting a trait of interest. The principles of LD mapping of dichotomous traits are well understood, but less is known about LD mapping of a quantitative-trait locus (QTL). It is shown in this report that selective genotyping can increase the power to detect and map a rare allele of large effect at a QTL. Two statistical tests of the association between an allele and a quantitative character are proposed. These tests are approximately independent, so information from them can be combined. Analytic theory is developed to show that these two tests are effective in detecting the presence of a low-frequency allele with a relatively large effect on the character when the QTL is either already a candidate locus or closely linked to a marker locus that is in strong LD with the QTL. The latter situation is expected in a rapidly growing population in which the allele of large effect was present initially in one copy. Therefore, the proposed tests are useful under the same conditions as those for successful LD mapping of a dichotomous trait or disease. Simulations show that, for detection of the presence of a QTL, these tests are more powerful than a simple t-test. The tests also provide a basis for defining a measure of association, gamma, between a low-frequency allele at a putative QTL and a low-frequency allele at a marker locus.

Genetics, Population↗
PubMedDate not supplied

Multipoint genomic scanning for quantitative loci: effects of map density, sibship size and computational approach.

Multipoint interval mapping (MIM) and the MAPMAKER/SIBS program (M/S) are two methods of mapping quantitative loci by examining identity by descent (IBD) sharing in a region spanned by multiple microsatellite DNA markers. For the purpose of comparison, we simulated a quantitative trait controlled by a two-locus model, and evaluated the power and genome-wide false positive rate of both approaches. Based on our simulation, we examined the effects of marker density (5 cM, 10 cM and 20 cM) and sibship size (2, 3, 4 and 5) on the power to detect linkage. Our results indicate that a 10 cM map provides the optimal trade-off between power and type I error, and that the power of MIM increases with sibship size and, in general, performs better than MAPMAKER/SIBS. Furthermore, we conclude that using a reasonable sample of randomly ascertained sibships, it is possible to map a quantitative trait locus (QTL) which accounts for 25% of the phenotypic variance.

Chromosome Mapping↗
PubMed2001

Identification of a polymorphic mucin-like gene expressed in the midgut of the mosquito, Aedes aegypti, using an integrated bulked segregant and differential display analysis.

The identification of putative differentially expressed genes within genome regions containing QTL determining susceptibility of the mosquito, Aedes aegypti, to the malarial parasite, Plasmodium gallinaceum, was investigated using an integrated, targeted approach based on bulked segregant and differential display analysis. A mosquito F2 population was obtained from pairwise matings between the parasite-susceptible RED strain and the resistant MOYO-R substrain. DNA from female carcasses was used to genotype individuals at RFLP markers of known chromosomal position around the major QTL (pgs 1). Midguts, dissected 48 hr after an infected blood meal, were used to prepare two RNA bulks, each representing one of the parental genotypes at the QTL interval. The RNA bulks were compared by differential display PCR. A mucin-like protein gene (AeIMUC1) was isolated and characterized. The gene maps within the pgs 1 QTL interval and is expressed in the adult female midgut. AeIMUC1 RNA abundance decreased with time after blood meal ingestion. No differential expression was observed between the two mosquito strains but three different alleles with inter- and intrastrain allelic polymorphisms including indels and SNPs were characterized. The AeIMUC1 gene chromosome location and allelic polymorphisms raise the possibility that the protein might be involved in parasite-mosquito interactions.

Aedes↗