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PubMed2005

Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana.

The underlying mechanisms for hybrid vigor or heterosis are elusive. Here we report a population of recombinant inbred lines (RILs), derived from the two ecotypes, Col and Ler, which can serve as a permanent resource for studying the molecular basis of hybrid vigor in Arabidopsis. Using a North Carolina mating design III (NCIII), we determined the additive and dominant nature of gene action in this population. We detected heterosis among crosses of RILs with one of the two parents (Col and Ler) and analyzed genotypes and heterozygosities for RILs and test cross families (RILs crossed to Col and Ler) using a total of 446 published molecular markers. The performance of RILs and additive and dominant components in the test cross families were used to analyze QTLs for 16 traits, using QTL cartographer and composite interval mapping with 1,000 permutations for each trait. Our data suggest that locus-specific and/or genome-wide differential heterozygosity, including epistasis, plays an important role in the generation of the observed heterosis. Furthermore, the hybrid vigor occurred between two closely related ecotypes, and provides a general mechanism for novel variation generated between genetically similar materials.

Arabidopsis↗
PubMed1999

Genetics of insulin resistance.

Even among young, healthy individuals, there is more than a 10-fold variation in insulin sensitivity; however, taken in combination, all the known modifiers of insulin sensitivity - including obesity and a variety of environmental factors - explain less than one third of this variation. It is possible that genetic factors could account for the bulk of the variance observed, and hence play a major role in the development of impaired insulin sensitivity, ie insulin resistance. From the genetic point of view, insulin resistance is thought to be due to the inheritance of a number of mutations in a variety of genes. Three complementary approaches have been applied in the search for mutations: mutational analysis of candidate genes; linkage analysis of candidate genes or chromosomal regions for insulin resistance in familial type 2 diabetes; and random genome mapping with quantitative trait loci (QTL) analysis. Mutational analysis of the insulin signalling cascade has identified a glycine-arginine (Gly-Arg) substitution at codon 972 of the insulin receptor substrate-1 (IRS-1) gene with a carrier prevalence of 9% among Caucasians. Expression of this variant in 32-D cells is associated with a significant (20-30%) impairment of insulin-stimulated PI3-kinase activity, as well as reduced binding of IRS-1 to the p85 regulatory subunit of PI3-kinase. Genotype/phenotype studies stratified according to body mass index (BMI) indicate that obese subjects who are heterozygous for the mutant allele have a 50% decrease in insulin sensitivity, compared with wild-type obese subjects. This suggests that there may be an interaction between the mutant allele and obesity, such that, in the presence of obesity, the mutant variant may aggravate the obesity-associated insulin resistance. Mutational analysis has also shown that homozygous carriers of a codon Met 326 Ile mutation in the p85 subunit of phosphatidylinositol-3 (PI3)-kinase (about 2% of the Caucasian population) have lower glucose tolerance, glucose effectiveness. A further Asp to Tyr polymorphism has been identified at codon 905 of the gene encoding the regulatory subunit of glycogen-associated protein phosphatase-1 (PP1G). Individuals who are heterozygous for this polymorphism constitute 18% of the Caucasian population and appear to exhibit both tissue-specific and pathway-specific insulin resistance. It is likely that inherited insulin resistance will eventually prove to be related to subtle mutations in many such genes of the insulin signalling network and the numerous genetic components controlling energy metabolism.

Animals↗
PubMed2001

A major quantitative trait locus on chromosome 3 controls colitis severity in IL-10-deficient mice.

Colitic lesions are much more severe in C3H/HeJBir (C3H) than C57BL/6J (B6) mice after 10 backcrosses of a disrupted interleukin-10 (Il10) gene. This study identified cytokine deficiency-induced colitis susceptibility (Cdcs) modifiers by using quantitative trait locus (QTL) analysis. A segregating F(2) population (n = 408) of IL-10-deficient mice was genotyped and necropsied at 6 weeks of age. A major C3H-derived colitogenic QTL (Cdcs1) on chromosome (Chr.) 3 contributed to lesions in both cecum [logarithm of odds ratio (LOD) = 14.6)] and colon (LOD = 26.5) as well as colitis-related phenotypes such as spleen/body weight ratio, mesenteric lymph node/body weight ratio, and secretory IgA levels. Evidence for other C3H QTL on Chr. 1 (Cdcs2) and Chr. 2 (Cdcs3) was obtained. Cdcs1 interacted epistatically or contributed additively with loci on other chromosomes. The resistant B6 background also contributed colitogenic QTL: Cdcs4 (Chr. 8), Cdcs5 (Chr. 17, MHC), and Cdcs6 (Chr. 18). Epistatic interactions between B6 QTL on Chr. 8 and 18 contributing to cecum hyperplasia were particularly striking. In conclusion, a colitogenic susceptibility QTL on Chr. 3 has been shown to exacerbate colitis in combination with modifiers contributed from both parental genomes. The complex nature of interactions among loci in this mouse model system, coupled with separate deleterious contributions from both parental strains, illustrates why detection of human inflammatory bowel disease linkages has proven to be so difficult. A human ortholog of the Chr. 3 QTL, if one exists, would map to Chr. 4q or 1p.

Animals↗
PubMed2003

Harvesting the genomic promise: recombineering sequences for phenotypes.

The past decade has witnessed the construction of linkage and physical maps defining quantitative trait loci (QTL) in various domesticated species. Targeted chromosomal regions are being further characterized through the construction of bacterial artificial chromosome (BAC) contigs in order to isolate and characterize genes contributing towards phenotypic variation. Whole-genome BAC contigs are also being constructed that will serve as the tiling path for genomic sequencing. Harvesting this genetic information for biological gain requires either genetic selection or the production of genetically modified animals. This later approach when coupled with nuclear transfer technology (NT) provides "clones" of genetically modified animals. However, to date, the production of genetically modified animals has been limited to either microinjection of small gene constructs into embryos with random insertion or complex gene constructs designed to knock-out targeted gene expression. Neither of these approaches provides for introducing directed genetic manipulation allowing for allelic substitution [knock-in], subsequent analyses of gene expression, and cloning. An alternative approach utilizing genomic sequence information and recombineering to direct gene targeting of specific porcine BACs is presented here.

Animals↗
PubMed2002

Detection of quantitative trait loci for resistance/susceptibility to pseudorabies virus in swine.

This study describes genetic differences in resistance/susceptibility to pseudorabies virus (PrV) between European Large White and Chinese Meishan pigs, with a mapping of quantitative trait loci (QTL) obtained from a genome-wide scan in F(2) animals. Eighty-nine F(2) pigs were challenged intranasally at 12 weeks with 10(5) p.f.u. of the wild-type PrV strain NIA-3. For QTL analysis, 85 microsatellite markers, evenly spaced on the 18 porcine autosomes and on the pseudoautosomal region of the X chromosome, were genotyped. All pigs developed clinical signs, i.e. fever, from 3 to 7 days p.i. The pure-bred Large White pigs, the F(1) and three-quarters of the F(2) animals, but none of the Meishan pigs, developed neurological symptoms and died or were euthanized. QTLs for appearance/non-appearance of neurological symptoms were found on chromosomes 9, 5, 6 and 13. They explained 10.6-17.9% of F(2) phenotypic variance. QTL effects for rectal temperature after PrV challenge were found on chromosomes 2, 4, 8, 10, 11 and 16. Effects on chromosomes 9, 10 and 11 were significant on a genome-wide level. The results present chromosomal regions that are associated with presence/absence of neurological symptoms as well as temperature course after intranasal challenge with NIA-3. The QTLs are in proximity to important candidate genes that are assumed to play crucial roles in host defence against PrV.

Animals↗
PubMed2006

The gene controlling the quantitative trait locus EPITHIOSPECIFIER MODIFIER1 alters glucosinolate hydrolysis and insect resistance in Arabidopsis.

Glucosinolates are sulfur-rich plant secondary metabolites whose breakdown products have a wide range of biological activities in plant-herbivore and plant-pathogen interactions and anticarcinogenic properties. In Arabidopsis thaliana, hydrolysis by the enzyme, myrosinase, produces bioactive nitriles, epithionitriles, or isothiocyanates depending upon the plant's genotype and the glucosinolate's structure. A major determinant of this structural specificity is the epithiospecifier locus (ESP), whose protein causes the formation of epithionitriles and nitriles. A quantitative trait locus (QTL) on chromosome 3 epistatically affects nitrile formation in combination with ESP; this QTL has been termed EPITHIOSPECIFIER MODIFIER1 (ESM1). We identified a myrosinase-associated protein as the ESM1 QTL in Arabidopsis using map-based cloning with recombinant inbred lines, natural variation transcriptomic analysis, and metabolic profiling. In planta and in vitro analyses with natural ESM1 alleles, ESM1 knockouts, and overexpression lines show that ESM1 represses nitrile formation and favors isothiocyanate production. The glucosinolate hydrolysis profile change influenced by ESM1 is associated with the ability to deter herbivory by Trichoplusia ni. This gene could provide unique approaches toward improving human nutrition.

Animals↗
PubMed2006

Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling.

Genetical genomics is an approach that blends the mapping of quantitative trait loci (QTL) with microarray analysis. The approach can be used to identify associations between the allelic state of a genomic region and a gene's transcript abundance. However, the large number of microarrays required for adequate power results in high material and labor costs that prevent wide adoption of the genetical genomics strategy outside of some well-funded laboratories. We present a method called selective transcriptional profiling that involves selecting an optimal subset of individuals to microarray from a larger set of individuals for which relatively inexpensive quantitative trait and molecular marker data are available. We show how to use microarray data from the selected individuals, along with the trait and marker data from all individuals, to identify genes whose transcript abundance is associated with a quantitative trait of interest through linkage to a trait QTL or correlation with the trait. Our methods for selection and analysis are derived within a missing data framework.

Alleles↗
PubMed2001

Genetic loci determining bone density in mice with diet-induced atherosclerosis.

This study investigates the phenotypic and genetic relationships among bone-density-related traits and those of adipose tissue and plasma lipids in mice with diet-induced atherosclerosis. Sixteen-month-old female F2 progeny of a C57BL/6J and DBA/2J intercross, which had received an atherogenic diet for 4 mo, were examined for multiple measures of femoral bone mass, density, and biomechanical properties using both computerized tomographic and radiographic methods. In addition, body weight and length, adipose tissue mass, plasma lipids and insulin, and aortic fatty lesions were assessed. Bone mass was inversely correlated with extent of atherosclerosis and with a prooxidant lipid profile and directly correlated with body weight, length, and, most strongly, adipose tissue mass. Quantitative trait locus (QTL) analysis, using composite interval mapping (CIM) and multi-trait analysis, identified six loci with multi-trait CIM LOD scores > 5. Three of these coincided with loci linked with adipose tissue and plasma high-density lipoprotein. Application of statistical tests for distinguishing close linkage vs. pleiotropy supported the presence of a potential pleiotropic effect of two of the loci on these traits. This study shows that bone mass in older female mice with atherosclerosis has multiple genetic determinants and provides phenotypic and genetic evidence linking the regulation of bone density with adipose tissue and plasma lipids.

Adipose Tissue↗
PubMed2006

A statistical framework for genetic association studies of power curves in bird flight.

How the power required for bird flight varies as a function of forward speed can be used to predict the flight style and behavioral strategy of a bird for feeding and migration. A U-shaped curve was observed between the power and flight velocity in many birds, which is consistent to the theoretical prediction by aerodynamic models. In this article, we present a general genetic model for fine mapping of quantitative trait loci (QTL) responsible for power curves in a sample of birds drawn from a natural population. This model is developed within the maximum likelihood context, implemented with the EM algorithm for estimating the population genetic parameters of QTL and the simplex algorithm for estimating the QTL genotype-specific parameters of power curves. Using Monte Carlo simulation derived from empirical observations of power curves in the European starling (Sturnus vulgaris), we demonstrate how the underlying QTL for power curves can be detected from molecular markers and how the QTL detected affect the most appropriate flight speeds used to design an optimal migration strategy. The results from our model can be directly integrated into a conceptual framework for understanding flight origin and evolution.

Journal Article↗
PubMed2006

Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy.

Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in recombinant inbred line (RIL) populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The single-nucleotide polymorphism haplotype data of B73 and 25 diverse maize inbreds were used to simulate the production of various RIL populations. Compared to the three-step genome scan, the power to detect three-way interactions was higher with the four-step genome scan. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distance-based designs than from nested designs or diallel designs. The power and PFP to detect three-way interactions using a nested design with 5000 RILs were for both the 4-QTL and the 12-QTL scenario of a magnitude that seems promising for their identification.

Chromosome Mapping↗
PubMed2007

Environmental influence on the genetic correlations between life-history traits in Caenorhabditis elegans.

Empirical evidence is mounting to suggesting that genetic correlations between life-history traits are environment specific. However, detailed knowledge about the loci underlying genetic correlations in different environments is scant. Here, we studied the influence of temperature (12 degrees C and 24 degrees C) on the genetic correlations between egg size, egg number and body mass in the nematode Caenorhabditis elegans. We used a quantitative trait loci (QTL) approach based on a genetic map with evenly spaced single nucleotide polymorphism markers in an N2 x CB4856 recombinant inbred panel. Significant genetic correlations between various traits were found at both temperatures. We detected pleiotropic or closely linked QTL, which supported the negative correlation between egg size and egg number at 12 degrees C, the positive correlation across temperatures for body mass, and the positive correlation between body mass and egg size at 12 degrees C. The results indicate that specific loci control the covariation in these life-history traits and the locus control is prone to environmental conditions.

Animals↗
PubMed2002

Locus controlling LDL cholesterol response to dietary cholesterol is on baboon homologue of human chromosome 6.

OBJECTIVE: Cholesterolemic responses to dietary lipids are known to be heritable, but the genes that may affect this response have yet to be identified. Using segregation analysis, we previously detected a potential quantitative trait locus (QTL) in baboons that influenced low density lipoprotein cholesterol response to dietary cholesterol. We performed linkage analyses to locate this QTL by using data on the baboon genetic linkage map. METHODS AND RESULTS: We obtained evidence for linkage of this potential QTL to the same locus (D6S311) on the baboon homologue of human chromosome 6 by using variance components and parametric linkage analysis methods (2-point lod scores 4.17 [genomic probability value 0.008] and 2.81 [genomic P=0.10], respectively). Linkage analyses of serum levels of apolipoprotein B dietary response, a correlated trait, also gave weak suggestive evidence of linkage to this chromosomal region (maximum 2-point lod score 1.91). Although the LPA locus is nearby, we found no evidence of linkage with LPA. CONCLUSIONS: This report is the first to localize, in any primate species, a potential QTL that influences low density lipoprotein cholesterol response to dietary cholesterol.

Animals↗
PubMed2005

The map expansion obtained with recombinant inbred strains and intermated recombinant inbred populations for finite generation designs.

The generation of special crosses between different inbred lines such as recombinant inbred strains (RIS) and intermated recombinant inbred populations (IRIP) is being used to improve the power of QTL detection techniques, in particular fine mapping. These approaches acknowledge the fact that recombination of linked loci increases with every generation, caused by the accumulation of crossovers appearing between the loci at each meiosis. This leads to an expansion of the map distance between the loci. While the amount of the map expansion of RIS and IRIP is known for infinite inbred generations, it is not known for finite numbers of generations. This gap was closed here. Since the recursive evaluation of the map expansion factors turned out to be complex, a useful approximation was derived.

Chromosome Mapping↗
PubMed2003

Mapping quantitative trait loci mediating sensitivity to etomidate.

Long- and Short-Sleep (LS and SS) mice were selectively bred for differences in ethanol-induced loss of the righting reflex (LORR) and have been found to differ in LORR induced by various anesthetic agents. We used a two-stage mapping strategy to identify quantitative trait loci (QTLs) affecting duration of LORR caused by the general anesthetic etomidate and brain levels of etomidate (BEL) following regain of the righting reflex. Analysis of recombinant-inbred strains derived from a cross between LS and SS mice (LSXSS) yielded a heritability estimate of 0.23 for etomidate-induced LORR and identified one marker that showed suggestive linkage for a QTL, on mouse Chromosome (chr) 12. Mapping in an F(2) population derived from a cross between inbred LS and SS (ILS and ISS) revealed a significant QTL for etomidate-induced LORR on Chr 12, and two significant QTLs mediating BEL on Chrs 6 and 12. Several QTLs showing suggestive linkage for etomidate-induced LORR and BEL were also identified in the F(2) population. Brain levels of etomidate in the RI and F(2) mice suggested that differences in LORR were due to differential central nervous system sensitivity, rather than differential etomidate metabolism. Interestingly, the region on Chr 7 has also been identified as a region influencing ethanol-induced LORR, suggesting the possibility of a common genetic mechanism mediating etomidate and ethanol sensitivity. These QTL regions need to be further narrowed before the testing of candidate genes is feasible.

Analysis of Variance↗
PubMed2005

Identification of quantitative trait loci that regulate Arabidopsis root system size and plasticity.

Root system size (RSS) is a complex trait that is greatly influenced by environmental cues. Hence, both intrinsic developmental pathways and environmental-response pathways contribute to RSS. To assess the natural variation in both types of pathways, we examined the root systems of the closely related Arabidopsis ecotypes Landsberg erecta (Ler) and Columbia (Col) grown under mild osmotic stress conditions. We found that Ler initiates more lateral root primordia, produces lateral roots from a higher percentage of these primordia, and has an overall larger root system than Col under these conditions. Furthermore, although each of these parameters is reduced by osmotic stress in both ecotypes, Ler shows a decreased sensitivity to osmotica. To understand the genetic basis for these differences, QTL for RSS under mild osmotic stress were mapped in a Ler x Col recombinant inbred population. Two robust quantitative trait loci (QTL) were identified and confirmed in near-isogenic lines (NILs). The NILs also allowed us to define distinct physiological roles for the gene(s) at each locus. This study provides insight into the genetic and physiological complexity that determines RSS and begins to dissect the molecular basis for naturally occurring differences in morphology and developmental plasticity in the root system.

Arabidopsis↗
PubMed2003

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

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

Adenoma↗
PubMed2002

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea).

RAPD markers were employed for construction of a linkage map and localization of QTLs for oleic acid level using a set of 94 recombinant inbred lines (RILs) of mustard (Brassica juncea L.) as a mapping population. Only 30% of the 235 random primers used were useful in terms of polymorphism detected and the reproducibility of those patterns. Normal Mendelian segregation was observed for the majority of the 130 markers obtained with 71 informative primers; only 13.1% deviated (P < 0.01) from the expected 1:1 ratio. One-hundred and fourteen markers were assigned to 21 linkage groups (LGs) covering a total length of 790.4 cM with an average distance of 6.93 cM between markers. Two quantitative trait loci (QTL) for oleic acid level were mapped to 14- and 10.6-cM marker intervals on two different LGs. Both loci together explained 32.2% of phenotypic variance. One major QTL explained 28.5% of the trait variance observed in this species.

Breeding↗
PubMed2004

Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (Triticum aestivum L.).

We report here the second advanced backcross quantitative trait locus (AB-QTL) analysis carried out in winter wheat. Seven agronomic traits were studied in a BC2F1 population derived from a cross between the German winter wheat variety Flair and the synthetic wheat line XX86 developed in Japan. We selected 111 BC2F1 lines and genotyped these with 197 microsatellite markers. Field data for seven agronomic traits were collected from corresponding BC2F3 families that were grown at up to six locations in Germany. QTL analyses for yield and yield components were performed using single-marker regression and interval mapping. A total of 57 putative QTLs derived from XX86 were detected, of which 24 (42.1%) were found to have a positive effect from the synthetic wheat XX86. These favourable QQTLs were mainly associated with thousand-grain weight and grain weight per ear. Many QTLs for correlated traits were mapped in similar chromosomal regions. The AB-QTL data obtained in the present study are discussed and compared with results from previous QTL analyses.

Agriculture↗