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PubMed2006

Genome-wide genetic association of complex traits in heterogeneous stock mice.

Difficulties in fine-mapping quantitative trait loci (QTLs) are a major impediment to progress in the molecular dissection of complex traits in mice. Here we show that genome-wide high-resolution mapping of multiple phenotypes can be achieved using a stock of genetically heterogeneous mice. We developed a conservative and robust bootstrap analysis to map 843 QTLs with an average 95% confidence interval of 2.8 Mb. The QTLs contribute to variation in 97 traits, including models of human disease (asthma, type 2 diabetes mellitus, obesity and anxiety) as well as immunological, biochemical and hematological phenotypes. The genetic architecture of almost all phenotypes was complex, with many loci each contributing a small proportion to the total variance. Our data set, freely available at http://gscan.well.ox.ac.uk, provides an entry point to the functional characterization of genes involved in many complex traits.

Animals↗
PubMed2002

Relationship between microsatellite marker alleles on chromosomes 1-5 originating from the Rhode Island Red and Green-legged Partrigenous breeds and egg production and quality traits in F(2) mapping population.

The objective of this study was to determine the relationship between the origin of marker alleles from the Rhode Island Red (RIR) and Green-legged Partrigenous (GlP) breeds and chosen egg production and quality traits in F(2) generation consisting of 10 full-sib families. Polymorphism analysis of 23 microsatellite markers within the mapping population (519 F(2)) was made. In parental generation 17 alleles were identified as specific for the GlP and 23 for the RIR. The least squares method was used to evaluate the significance of effects of genotype (GlP/GlP, RIR/RIR, GlP/RIR) on the analysed quantitative traits. Thirty traits of egg production and quality were measured during the laying period. It was shown that the effects of the genotype (GlP/GlP, RIR/RIR, GlP/RIR) at the loci on analysed traits of F(2) animals were diversified. Significant effects were found for 16 traits. These results confirm that the analysed microsatellite loci may be linked to the genes affecting egg production and quality traits. The loci examined and the experimental population constitutes a valuable material for QTL mapping (linkage analysis).

Alleles↗
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↗
PubMed2004

Genetic basis of barley caryopsis dormancy and seedling desiccation tolerance at the germination stage.

The genomic regions controlling caryopsis dormancy and seedling desiccation tolerance were identified using 152 F4 lines derived from a cross between Mona, a Swedish cultivar, and an Israeli xeric wild barley Hordeum spontaneum genotype collected at Wadi Qilt, Israel. Dormancy, the inability of a viable seed to germinate, and desiccation tolerance, the ability of the desiccated seedlings to revive after rehydration, were characterized by fitting the germination and revival data with growth curves, using three parameters: minimum, maximum, and slope of germination or revival rate derived by the least square method. The genetic map was constructed with 85 genetic markers (SSRs, AFLPs, STSs, and Dhn genes) using the MULTIPOINT: -mapping algorithm. Quantitative trait loci (QTLs) mapping was conducted with the MULTIQTL: package. Ten genomic regions were detected that affected the target traits, seven of which affected both dormancy and desiccation tolerance traits. Both the wild barley genotype and the Swedish cultivar contributed the favorite alleles for caryopsis dormancy, whereas seedling desiccation tolerance was attributed to alleles descending from the cultivar. The results indicate that some barley dormancy genes are lost during domestication and that dormancy QTLs are associated with abiotic stress tolerance.

Chromosome Mapping↗
PubMed2006

Using genomic inbreeding coefficient estimates for homozygosity mapping of rare recessive traits: application to Taybi-Linder syndrome.

The use of inbred patients whose exact genealogy may not be available is of primary interest in mapping genes involved in rare recessive diseases. We show here that this can be achieved by estimating inbreeding coefficients from the patients' genomic information and using these estimates to perform homozygosity mapping. We show the interest of the approach by mapping a gene for Taybi-Linder syndrome to chromosome 2q, with the use of a key patient with no genealogical information.

Chromosomes, Human, Pair 2↗
PubMed2001

Comparative analysis of a BAC contig of the porcine RN region and the human transcript map: implications for the cloning of trait loci.

The poorly developed transcript maps and the limited resources for genome analysis hamper positional cloning of trait loci in farm animals. This study demonstrates that this will now be easier by the combined use of BAC contigs and the import of the near complete human transcript map. The conclusion was obtained by a comparative analysis of a 2.4-Mb BAC contig of the RN region in pigs. The contig was constructed as part of a successful positional cloning project, which identified PRKAG3 as the causative gene for the RN phenotype. A comparative map including the corresponding regions on human chromosome 2q35 and mouse chromosome 1 (region 36-44 cM) is reported. Sixteen coding sequences were mapped on the BAC contig. The majority of these were identified by BLAST searches of BAC end sequences and BAC shotgun sequences generated during the positional cloning project. Map data for the orthologues in humans were available for 12 of the 16 coding sequences, and all 12 have been assigned to 2q35. Furthermore, no evidence for any rearrangement in gene order was obtained. The extensive linkage conservation indicates that the near complete human transcript map will be an invaluable resource for positional cloning projects in pigs and other domestic animals.

Animals↗
PubMed2005

[QTL mapping of five agronomic traits in maize].

Agronomic traits have significant influence on stability and adaptability in maize production. In this investigation, using a population with 266 F2:3 families from Yuyu22 (Zong3 x 87-1), two-location field tests were conducted in Wuhan and Xiangfan in 2001, with a randomized complete block design, to characterize five agronomic traits: ear height, tassel branch number, stalk diameter, days to pollen, and days to silk. Correlation analysis of field performance indicated that ear height, tassel branch number and stalk diameter were significantly positive correlative with single-plant yield, days to pollen and days to silk were highly positive correlative with each other, and tassel branch number was significantly positive correlative with stalk diameter too. Utilizing data of field tests and molecular markers, Composite Interval Mapping (CIM) method was used to localize the quantitative trait loci of these traits and 500 times permutation test was conducted to have proper LOD threshold value. As the results, total seven QTL of ear height, nine QTL of tassel branch number, eight QTL of stalk diameter, nine QTL of days to pollen, and seven QTL of days to silk were mapped on 10 chromosomes of maize; all of these QTL distributed unevenly on chromosomes and trended to cluster together. According to analysis of this investigation, the phenotype correlations of quantitative traits may result from the correlations of QTL controlling those traits. Those will be helpful to further understand genetic basis of agronomic traits in maize.

Chromosome Mapping↗
PubMed1999

Whole genome scan in chickens for quantitative trait loci affecting carcass traits.

An experiment was conducted to enable quantitative trait loci (QTL) mapping for carcass traits. The population consisted of 10 full-sib families originating from a cross between male and female founders chosen from two different outcross broiler lines. Founder animals, parents, offspring, and grandoffspring are denoted as generation (G) 0, 1, 2, and 3 animals, respectively. Microsatellite marker genotypes were collected on G1 and G2 animals. Phenotypic observations were collected on G3 animals. Recorded traits were BW at 48 d, carcass weight, carcass percentage, breast meat color, and leg score. Average adjusted progeny trait values were calculated for each G2 animal and for each trait after adjusting phenotypic observations on G3 animals for fixed effects, covariables, the additive genetic contribution of the other parent, and differences between sexes. The average adjusted progeny trait values were used as the dependent variable in the QTL analysis. A QTL analysis was undertaken by modeling the segregation from G1 to G2, using a full-sib across family regression interval mapping approach. In total, 27 autosomal linkage groups covered with 420 markers were analyzed. Genomewise significance thresholds were derived using the permutation test and a Bonferroni correction. Two QTL, affecting two of the five analyzed traits, exceeded suggestive linkage. The most significant QTL was located on Chromosome 1 at 466 cM and showed an effect on carcass percentage. The other QTL, which affected meat color, was located on Chromosome 2 and gave a peak at 345 and 369 cM.

Animals↗
PubMed2003

Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs.

An earlier study identified quantitative trait loci (QTLs) lb4, lb5b, and lb11b for quantitative resistance to Phytophthora infestans (late blight) in a backcross population derived from crossing susceptible cultivated tomato ( Lycopersicon esculentum) with resistant L. hirsutum. The QTLs were located in intervals spanning 28-47 cM. Subsequently, near-isogenic lines (NILs) were developed for lb4, lb5b, and lb11b by marker-assisted backcrossing to L. esculentum. Sub-NILs containing overlapping L. hirsutum segments across each QTL region were selected and used to validate the QTL effects, fine-map QTLs, and evaluate potential linkage drag between resistance QTLs and QTLs for horticultural traits. The NILs and sub-NILs were evaluated for disease resistance and eight horticultural traits at three field locations. Resistance QTLs were detected in all three sets of NIL lines, confirming the BC(1) mapping results. Lb4 mapped near TG609, and between TG182 and CT194, on chromosome 4, a 6.9-cM interval; lb5b mapped to an 8.8-cM interval between TG69a and TG413 on chromosome 5, with the most likely position near TG23; and lb11b mapped to a 15.1-cM interval on chromosome 11 between TG194 and TG400, with the peak centered between CT182 and TG147. Most QTLs for horticultural traits were identified in intervals adjacent to those containing the late blight resistance QTLs. Fine mapping of these QTLs permits the use of marker-assisted selection for the precise introgression of L. hirsutum segments containing late blight resistance alleles separately from those containing deleterious alleles at horticulturally important QTLs.

Analysis of Variance↗
PubMed2006

Relaxed significance criteria for linkage analysis.

Linkage analysis involves performing significance tests at many loci located throughout the genome. Traditional criteria for declaring a linkage statistically significant have been formulated with the goal of controlling the rate at which any single false positive occurs, called the genomewise error rate (GWER). As complex traits have become the focus of linkage analysis, it is increasingly common to expect that a number of loci are truly linked to the trait. This is especially true in mapping quantitative trait loci (QTL), where sometimes dozens of QTL may exist. Therefore, alternatives to the strict goal of preventing any single false positive have recently been explored, such as the false discovery rate (FDR) criterion. Here, we characterize some of the challenges that arise when defining relaxed significance criteria that allow for at least one false positive linkage to occur. In particular, we show that the FDR suffers from several problems when applied to linkage analysis of a single trait. We therefore conclude that the general applicability of FDR for declaring significant linkages in the analysis of a single trait is dubious. Instead, we propose a significance criterion that is more relaxed than the traditional GWER, but does not appear to suffer from the problems of the FDR. A generalized version of the GWER is proposed, called GWERk, that allows one to provide a more liberal balance between true positives and false positives at no additional cost in computation or assumptions.

Algorithms↗
PubMed2002

Statistical methods for dissecting triploid endosperm traits using molecular markers. An autogamous model.

The endosperm, a result of double fertilization in flowering plants, is a triploid tissue whose genetic composition is more complex than diploid tissue. We present a new maximum-likelihood-based statistical method for mapping quantitative trait loci (QTL) underlying endosperm traits in an autogamous plant. Genetic mapping of quantitative endosperm traits is qualitatively different from traits for other plant organs because the endosperm displays complicated trisomic inheritance and represents a younger generation than its mother plant. Our endosperm mapping method is based on two different experimental designs: (1) a one-stage design in which marker information is derived from the maternal genome and (2) a two-stage hierarchical design in which marker information is derived from both the maternal and offspring genomes (embryos). Under the one-stage design, the position and additive effect of a putative QTL can be well estimated, but the estimates of the dominant and epistatic effects are upward biased and imprecise. The two-stage hierarchical design, which extracts more genetic information from the material, typically improves the accuracy and precision of the dominant and epistatic effects for an endosperm trait. We discuss the effects on the estimation of QTL parameters of different sampling strategies under the two-stage hierarchical design. Our method will be broadly useful in mapping endosperm traits for many agriculturally important crop plants and also make it possible to study the genetic significance of double fertilization in the evolution of higher plants.

Chromosome Mapping↗
PubMed2004

Pleiotropic effects on mandibular morphology II: differential epistasis and genetic variation in morphological integration.

The evolution of morphological modularity through the sequestration of pleiotropy to sets of functionally and developmentally related traits requires genetic variation in the relationships between traits. Genetic variation in relationships between traits can result from differential epistasis, where epistatic relationships for pairs of loci are different for different traits. This study maps relationship quantitative trait loci (QTLs), specifically QTLs that affect the relationship between individual mandibular traits and mandible length, across the genome in an F2 intercross of the LG/J and SM/J inbred mouse strains (N = 1045). We discovered 23 relationship QTLs scattered throughout the genome. All mandibular traits were involved in one or more relationship QTL. When multiple traits were affected at a relationship QTL, the traits tended to come from a developmentally restricted region of the mandible, either the muscular processes or the alveolus. About one-third of the relationship QTLs correspond to previously located trait QTLs affecting the same traits. These results comprise examples of genetic variation necessary for an evolutionary response to selection on the range of pleiotropic effects.

Animals↗
PubMed2002

Unified sampling approach for multipoint linkage disequilibrium mapping of qualitative and quantitative traits.

Rapid development in biotechnology has enhanced the opportunity to deal with multipoint gene mapping for complex diseases, and association studies using quantitative traits have recently generated much attention. Unlike the conventional hypothesis-testing approach for fine mapping, we propose a unified multipoint method to localize a gene controlling a quantitative trait. We first calculate the sample size needed to detect linkage and linkage disequilibrium (LD) for a quantitative trait, categorized by decile, under three different modes of inheritance. Our results show that sampling trios of offspring and their parents from either extremely low (EL) or extremely high (EH) probands provides greater statistical power than sampling in the intermediate range. We next propose a unified sampling approach for multipoint LD mapping, where the goal is to estimate the map position (tau) of a trait locus and to calculate a confidence interval along with its sampling uncertainty. Our method builds upon a model for an expected preferential transmission statistic at an arbitrary locus conditional on the sampling scheme, such as sampling from EL and EH probands. This approach is valid regardless of the underlying genetic model. The one major assumption for this model is that no more than one quantitative trait locus (QTL) is linked to the region being mapped. Finally we illustrate the proposed method using family data on total serum IgE levels collected in multiplex asthmatic families from Barbados. An unobserved QTL appears to be located at tau; = 41.93 cM with 95% confidence interval of (40.84, 43.02) through the 20-cM region framed by markers D12S1052 and D12S1064 on chromosome 12. The test statistic shows strong evidence of linkage and LD (chi-square statistic = 18.39 with 2 df, P-value = 0.0001).

Asthma↗
PubMed2006

Genetic association tests based on ranks (GATOR) for quantitative traits with and without censoring.

Linkage disequilibrium mapping of quantitative traits is a powerful method for dissecting the genetic etiology of complex phenotypes. Quantitative traits, however, often exhibit characteristics that make their use problematic. For example, the distribution of the trait may be censored, highly skewed, or contaminated with outlying values. We propose here a rank-based framework for deriving tests of gene and trait association that explicitly take censoring into account and are insensitive to skewness and outlying values. Standard methods for mapping quantitative traits do not take these characteristics into account, which leads to the discarding of valuable information or their improper application. We show how this framework can be applied in nuclear families and discuss its implementation in general pedigrees. The power and efficacy of the approach is illustrated through a series of simulation experiments in which the approach is compared to existing methods.

Age of Onset↗
PubMed2003

Mapping viability loci using molecular markers.

In genetic mapping experiments, some molecular markers often show distorted segregation ratios. We hypothesize that these markers are linked to some viability loci that cause the observed segregation ratios to deviate from Mendelian expectations. Although statistical methods for mapping viability loci have been developed for line-crossing experiments, methods for viability mapping in outbred populations have not been developed yet. In this study, we develop a method for mapping viability loci in outbred populations using a full-sib family as an example. We develop a maximum likelihood (ML) method that uses the observed marker genotypes as data and the proportions of the genotypes of the viability locus as parameters. The ML solutions are obtained via the expectation-maximization algorithm. Application and efficiencies of the method are demonstrated and tested using a set of simulated data. We conclude that mapping viability loci can be accomplished using similar statistical techniques used in quantitative trait locus mapping for quantitative traits.

Algorithms↗
PubMed2004

Interval mapping of QTLs controlling yield-related traits and seed protein content in Pisum sativum.

A linkage map of garden pea was constructed on the basis of 114 plants (F2 generation) derived from a cross combination Wt10245 x Wt11238. The map, consisting of 204 morphological, isozyme, AFLP, ISSR, STS, CAPS and RAPD markers, was used for interval mapping of quantitative trait loci (QTLs) controlling seed number, pod number, 1000-seed weight, 1000-yield, and seed protein content. Characterization of each QTL included identification of QTL position with reference to the flanking markers, estimation of the part of variance explained by this QTL, and determination of its gene action. The yield-related traits were measured in F2 plants and in F4 recombinant inbred lines (RILs). The interval mapping revealed two to six QTLs per trait, demonstrating linkage to seven pea chromosomes. A total of 37 detected QTLs accounted for 9.1-55.9% of the trait's phenotypic variation and showed different types of gene action. As many as eight and ten QTLs influencing the analysed traits were mapped in linkage groups III and V, respectively, indicating an important role of these regions of the pea genome in the control of yield and seed protein content.

Chromosome Mapping↗