QTL Mapping Studies Research Articles

Identity by descent estimation with dense genome-wide genotype data

We present a novel method, IBDLD, for estimating the probability of identity by descent (IBD) for a pair of related individuals at a locus, given dense genotype data and a pedigree of arbitrary size and complexity. IBDLD overcomes the challenges of exact multipoint estimation of IBD in pedigrees of potentially large size and eliminates the difficulty of accommodating the background linkage disequilibrium (LD) that is present in high-density genotype data. We show that IBDLD is much more accurate at estimating the true IBD sharing than methods that remove LD by pruning SNPs and is highly robust to pedigree errors or other forms of misspecified relationships. The method is fast and can be used to estimate the probability for each possible IBD sharing state at every SNP from a high-density genotyping array for hundreds of thousands of pairs of individuals. We use it to estimate point-wise and genomewide IBD sharing between 185,745 pairs of subjects all of whom are related through a single, large and complex 13-generation pedigree and genotyped with the Affymetrix 500 k chip. We find that we are able to identify the true pedigree relationship for individuals who were misidentified in the collected data and estimate empirical kinship coefficients that can be used in follow-up QTL mapping studies. IBDLD is implemented as an open source software package and is freely available.

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

Directionality of Epistasis in a Murine Intercross Population

Directional epistasis describes a situation in which epistasis consistently increases or decreases the effect of allele substitutions, thereby affecting the amount of additive genetic variance available for selection in a given direction. This study applies a recent parameterization of directionality of epistasis to empirical data. Data stems from a QTL mapping study on an intercross between inbred mouse (Mus musculus) strains LG/J and SM/J, originally selected for large and small body mass, respectively. Results show a negative average directionality of epistasis for body-composition traits, predicting a reduction in additive allelic effects and in the response to selection for increased size. Focusing on average modification of additive effect of single loci, we find a more complex picture, whereby the effects of some loci are enhanced consistently across backgrounds, while effects of other loci are decreased, potentially contributing to either enhancement or reduction of allelic effects when selection acts at single loci. We demonstrate and discuss how the interpretation of the overall measurement of directionality depends on the complexity of the genotype-phenotype map. The measure of directionality changes with the power of scale in a predictable way; however, its expected effect with respect to the modification of additive genetic effects remains constant.

Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background

BackgroundDifferences in gene expression may be caused by nearby DNA polymorphisms (cis regulation) or by interactions of gene control regions with polymorphic transcription factors (trans regulation). Trans acting loci are much harder to detect than cis acting loci and their effects are much more sensitive to genetic background.ResultsTo quantify cis and trans regulation we correlated haplotype data with gene expression in two inbred mouse strains and two derived congenic lines. Upstream haplotype differences between the parental strains suggested that 30-43% of differentially expressed genes were differentially expressed because of cis haplotype differences. These cis regulated genes displayed consistent and relatively tissue-independent differential expression. We independently estimated from the congenic mice that 71-85% of genes were trans regulated. Cis regulated genes were associated with low p values (p < 0.005) for differential expression, whereas trans regulated genes were associated with values 0.005 < p < 0.05. The genes differentially expressed between congenics and controls were not a subset of those that were differentially expressed between the founder lines, showing that these were dependent on genetic background. For example, the cholesterol synthesis pathway was strongly differentially expressed in the congenic mice by indirect trans regulation but this was not observable in the parental mice.ConclusionsThe evidence that most gene regulation is trans and strongly influenced by genetic background, suggests that pathways that are modified by an allelic variant, may only exhibit differential expression in the specific genetic backgrounds in which they were identified. This has significant implications for the interpretation of any QTL mapping study.

Genome‐wide SNP detection in the great titParus majorusing high throughput sequencing

Identifying genes that underlie ecological traits will open exiting possibilities to study gene-environment interactions in shaping phenotypes and in measuring natural selection on genes. Evolutionary ecology has been pursuing these objectives for decades, but they come into reach now that next generation sequencing technologies have dramatically lowered the costs to obtain the genomic sequence information that is currently lacking for most ecologically important species. Here we describe how we generated over 2 billion basepairs of novel sequence information for an ecological model species, the great tit Parus major. We used over 16 million short sequence reads for the de novo assembly of a reference sequence consisting of 550 000 contigs, covering 2.5% of the genome of the great tit. This reference sequence was used as the scaffold for mapping of the sequence reads, which allowed for the detection of over 20 000 novel single nucleotide polymorphisms. Contigs harbouring 4272 of the single nucleotide polymorphisms could be mapped to a unique location on the recently sequenced zebra finch genome. Of all the great tit contigs, significantly more were mapped to the microchromosomes than to the intermediate and the macrochromosomes of the zebra finch, indicating a higher overall level of sequence conservation on the microchromosomes than on the other types of chromosomes. The large number of great tit contigs that can be aligned to the zebra finch genome shows that this genome provides a valuable framework for large scale genetics, e.g. QTL mapping or whole genome association studies, in passerines.

Information-theoretic gene-gene and gene-environment interaction analysis of quantitative traits

BackgroundThe purpose of this research was to develop a novel information theoretic method and an efficient algorithm for analyzing the gene-gene (GGI) and gene-environmental interactions (GEI) associated with quantitative traits (QT). The method is built on two information-theoretic metrics, the k-way interaction information (KWII) and phenotype-associated information (PAI). The PAI is a novel information theoretic metric that is obtained from the total information correlation (TCI) information theoretic metric by removing the contributions for inter-variable dependencies (resulting from factors such as linkage disequilibrium and common sources of environmental pollutants).ResultsThe KWII and the PAI were critically evaluated and incorporated within an algorithm called CHORUS for analyzing QT. The combinations with the highest values of KWII and PAI identified each known GEI associated with the QT in the simulated data sets. The CHORUS algorithm was tested using the simulated GAW15 data set and two real GGI data sets from QTL mapping studies of high-density lipoprotein levels/atherosclerotic lesion size and ultra-violet light-induced immunosuppression. The KWII and PAI were found to have excellent sensitivity for identifying the key GEI simulated to affect the two quantitative trait variables in the GAW15 data set. In addition, both metrics showed strong concordance with the results of the two different QTL mapping data sets.ConclusionThe KWII and PAI are promising metrics for analyzing the GEI of QT.

Highly variable SSR markers suitable for rice genotyping using agarose gels

Simple sequence repeats (SSR) are the DNA markers of choice for genetic analysis in rice (Oryza sativa L.) due to their abundance, high polymorphism and simple assays using agarose gel electrophoresis. In an attempt to find most variable SSR loci for the agarose gel system, the relationship between SSR length and level of polymorphism was evaluated in a set of eight diverse rice genotypes using 201 random SSR loci of different repeat motifs and lengths, representing both genic and intergenic sequences from the 12 rice chromosomes. There was a positive correlation between SSR length and average number of alleles per locus but linearity of this relationship was limited to the SSR length range of 10–70 bp. The highest level of polymorphism was in the SSR length range of 51–70 bp, beyond which there was stabilization and then decline of polymorphism in SSRs longer than 70 bp. Proportion of polymorphic loci in the different SSR length groups also followed similar pattern with even sharper decline of polymorphism in the highest size range. Here we describe a genome wide set of 436 validated highly variable SSR (HvSSR) markers with repeat lengths of 51–70 bp for their consistent amplification and high polymorphism. In the parental lines of three different mapping populations, the HvSSR loci showed more than twice the level of polymorphism than random SSR markers with average repeat length of 34 bp, and therefore are suitable for QTL mapping and fingerprinting studies in rice employing agarose gels.

Computing power of quantitative trait locus association mapping for haploid loci

BackgroundStatistical power calculations are a critical part of any study design for gene mapping. Most calculations assume that the locus of interest is biallelic. However, there are common situations in human genetics such as X-linked loci in males where the locus is haploid. The purpose of this work is to mathematically derive the biometric model for haploid loci, and to compute power for QTL mapping when the loci are haploid.ResultsWe have derived the biometric model for power calculations for haploid loci and have developed software to perform these calculations. We have verified our calculations with independent mathematical methods.ConclusionOur results fill a need in power calculations for QTL mapping studies. Furthermore, failure to appropriately model haploid loci may cause underestimation of power.

Characterization of polymorphic microsatellite loci in cultivated and wildPanax ginseng

Ginseng (Panax ginseng) is one of the most important herbal remedies used in East Asia. The present study investigated six polymorphic microsatellite markers (PG29, PG281, PG287, PG668, PG1319, and PG1481) in samples of cultivated and wildP. ginseng collected in Korea. Total allelic number observed in this study was 27 (average allelic numbers per locus: 4.5). All examined loci exhibited deviation from the Hardy-Weinberg equilibrium and deficiency of heterozygosity in both cultivated and wild groups. Although the wild ginseng group exhibited slightly more polymorphic behavior (mean PIC=0.392, GD=0.454 and Hobs=0.129), compared with the cultivated group (mean PIC=0.383, GD=0.438 and Hobs=0.105), no significant differences of allele frequencies and genotype distributions were revealed. By combined analysis of six loci in 100 cultivated ginsengs, 71 different types were observed. The analyzed microsatellite loci in this study will be helpful for understanding genetic variation, QTL mapping and phylogenic studies inPanax species.

A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution

BackgroundGenomic resources for the majority of free-living vertebrates of ecological and evolutionary importance are scarce. Therefore, linkage maps with high-density genome coverage are needed for progress in genomics of wild species. The Siberian jay (Perisoreus infaustus; Corvidae) is a passerine bird which has been subject to lots of research in the areas of ecology and evolutionary biology. Knowledge of its genome structure and organization is required to advance our understanding of the genetic basis of ecologically important traits in this species, as well as to provide insights into avian genome evolution.ResultsWe describe the first genetic linkage map of Siberian jay constructed using 117 microsatellites and a mapping pedigree of 349 animals representing five families from a natural population breeding in western Finland from the years 1975 to 2006. Markers were resolved into nine autosomal and a Z-chromosome-specific linkage group, 10 markers remaining unlinked. The best-position map with the most likely positions of all significantly linked loci had a total sex-average size of 862.8 cM, with an average interval distance of 9.69 cM. The female map covered 988.4 cM, whereas the male map covered only 774 cM. The Z-chromosome linkage group comprised six markers, three pseudoautosomal and three sex-specific loci, and spanned 10.6 cM in females and 48.9 cM in males. Eighty-one of the mapped loci could be ordered on a framework map with odds of >1000:1 covering a total size of 809.6 cM in females and 694.2 cM in males. Significant sex specific distortions towards reduced male recombination rates were revealed in the entire best-position map as well as within two autosomal linkage groups. Comparative mapping between Siberian jay and chicken anchored 22 homologous loci on 6 different linkage groups corresponding to chicken chromosomes Gga1, 2, 3, 4, 5, and Z. Quite a few cases of intra-chromosomal rearrangements within the autosomes and three cases of inter-chromosomal rearrangement between the Siberian jay autosomal linkage groups (LG1, LG2 and LG3) and the chicken sex chromosome GgaZ were observed, suggesting a conserved synteny, but changes in marker order, within autosomes during about 100 million years of avian evolution.ConclusionThe constructed linkage map represents a valuable resource for intraspecific genomics of Siberian jay, as well as for avian comparative genomic studies. Apart from providing novel insights into sex-specific recombination rates and patterns, the described maps – from a previously genomically uncharacterized superfamily (Corvidae) of passerine birds – provide new insights into avian genome evolution. In combination with high-resolution data on quantitative trait variability from the study population, they also provide a foundation for QTL-mapping studies.

Erratum to Genetic and metabolic aspects of androstenone and skatole deposition in pig adipose tissue: A review

High levels of androstenone and skatole in fat tissues are considered the primary causes of boar taint, an unpleasant odour and flavour of the meat from non-castrated male pigs. The aim of this article is to review our current knowledge of the biology and genetic control of the accumulation of androstenone and skatole in fat tissue. Two QTL mapping studies have shown the complexity of the genetic control of these traits. During the last ten years, several authors have taken a more physiological approach to investigate the involvement of genes controlling the metabolism of androstenone and skatole. Although some authors have claimed the identification of candidate genes, it is more appropriate to talk about target genes. This suggests that genes affecting androstenone and skatole levels will have to be sought for among specific or non-specific transcription factors interacting with these target genes.

Fine mapping quantitative trait loci for feed intake and feed efficiency in beef cattle1

Feed intake and feed efficiency are economically important traits in beef cattle because feed is the greatest variable cost in production. Feed efficiency can be measured as feed conversion ratio (FCR, intake per unit gain) or residual feed intake (RFI, measured as DMI corrected for BW and growth rate, and sometimes a measure of body composition, usually carcass fatness, RFI(bf)). The goal of this study was to fine map QTL for these traits in beef cattle using 2,194 markers on 24 autosomes. The animals used were from 20 half-sib families originating from Angus, Charolais, and University of Alberta Hybrid bulls. A mixed model with random sire and fixed QTL effect nested within sire was used to test each location (cM) along the chromosomes. Threshold levels were determined at the chromosome and genome levels using 20,000 permutations. In total, 4 QTL exceeded the genome-wise threshold of P < 0.001, 3 exceeded at P < 0.01, 17 at P < 0.05, and 30 achieved significance at the chromosome-wise threshold level (at least P < 0.05). No QTL were detected on BTA 8, 16, and 27 above the 5% chromosome-wise significance threshold for any of the traits. Nineteen chromosomes contained RFI QTL significant at the chromosome-wise level. The RFI(bf) QTL results were generally similar to those of RFI, the positions being similar, but occasionally differing in the level of significance. Compared with RFI, fewer QTL were detected for both FCR and DMI, 12 and 4 QTL, respectively, at the genome-wise thresholds. Some chromosomes contained FCR QTL, but not RFI QTL, but all DMI QTL were on chromosomes where RFI QTL were detected. The most significant QTL for RFI was located on BTA 3 at 82 cM (P = 7.60 x 10(-5)), for FCR on BTA 24 at 59 cM (P = 0.0002), and for DMI on BTA 7 at 54 cM (P = 1.38 x 10(-5)). The RFI QTL that showed the most consistent results with previous RFI QTL mapping studies were on BTA 1, 7, 18, and 19. The identification of these QTL provides a starting point to identify genes affecting feed intake and efficiency for use in marker-assisted selection and management.

Identifying footprints of directional and balancing selection in marine and freshwater three‐spined stickleback (Gasterosteus aculeatus) populations

Natural selection is expected to leave an imprint on the neutral polymorphisms at the adjacent genomic regions of a selected gene. While directional selection tends to reduce within-population genetic diversity and increase among-population differentiation, the reverse is expected under balancing selection. To identify targets of natural selection in the three-spined stickleback (Gasterosteus aculeatus) genome, 103 microsatellite and two indel markers including expressed sequence tags (EST) and quantitative trait loci (QTL)-associated loci, were genotyped in four freshwater and three marine populations. The results indicated that a high proportion of loci (14.7%) might be affected by balancing selection and a lower proportion (2.8%) by directional selection. The strongest signatures of directional selection were detected in a microsatellite locus and two indel markers located in the intronic regions of the Eda-gene coding for the number of lateral plates. Yet, other microsatellite loci previously found to be informative in QTL-mapping studies revealed no signatures of selection. Two novel microsatellite loci (Stn12 and Stn90) located in chromosomes I and VIII, respectively, showed signals of directional selection and might be linked to genomic regions containing gene(s) important for adaptive divergence. Although the coverage of the total genomic content was relatively low, the predominance of balancing selection signals is in agreement with the contention that balancing, rather than directional selection is the predominant mode of selection in the wild.

A preliminary microsatellite genetic map of the ostrich (Struthio camelus)

Molecular genetic maps can provide information for the identification and localization of major genes associated with quantitative traits. However, there are currently no published genetic linkage maps for any ratites. Herein, a preliminary genetic map of ostrich was developed using a two-generation ostrich reference family by linkage analysis of 104 polymorphic microsatellite markers, including 40 novel markers reported in this study. A total of 35 microsatellite markers were placed into 13 linkage groups. Five linkage groups are composed of three or more loci, whereas the remaining eight groups each contained two markers. The sex-averaged map spans 365.4 cM. The marker interval of each linkage group ranges from 5.3 to 25.4 cM, and the average interval distance is 16.61 cM. The male map covers 342.7 cM, with an average intermarker distance of 15.58 cM, whereas the female map is 456.7 cM, with the average intermarker spacing of 20.76 cM. In order to screen the orthologous loci between ostrich and chicken, all of the flanking sequences of the 104 polymorphic loci, nine monomorphic loci and a further 12 reported microsatellite loci for ostrich were screened against the chicken genomic sequence using the BLAST algorithm (Altschul et al., 1990), and corresponding orthologs were found for 13 sequences. The microsatellite loci and genetic map developed in this study will be useful for QTL mapping, population genetics and phylogenetic studies in the ratite. In addition, the 13 orthologous loci identified in this study will be advantageous to the construction of a comparative genetic map between chicken and ostrich.

Combining quantitative trait loci analyses and microarray data: An empirical likelihood approach

Selective transcriptional profiling is an attractive approach for alleviating the high cost of genetical genomics research as it requires only a subset of individuals in the QTL mapping study for microarray experiments. Current statistical methods for this approach are based on parametric models that might not be appropriate for all experiments. To provide a nonparametric method for analyzing data obtained in selective transcriptional profiling studies, an empirical-likelihood-based inference is derived for multi-sample comparisons when information is available on surrogate variables. The results show that when testing for the association between the transcriptional abundance of a given gene and a known QTL, using relatively inexpensive trait data on extra individuals significantly improves the power for the proposed test.

Genetic and metabolic aspects of androstenone and skatole deposition in pig adipose tissue: A review (Open Access publication)

High levels of androstenone and skatole in fat tissues are considered the primary causes of boar taint, an unpleasant odour and flavour of the meat from non-castrated male pigs. The aim of this article is to review our current knowledge of the biology and genetic control of the accumulation of androstenone and skatole in fat tissue. Two QTL mapping studies have shown the complexity of the genetic control of these traits. During the last ten years, several authors have taken a more physiological approach to investigate the involvement of genes controlling the metabolism of androstenone and skatole. Although some authors have claimed the identification of candidate genes, it is more appropriate to talk about target genes. This suggests that genes affecting androstenone and skatole levels will have to be sought for among specific or non-specific transcription factors interacting with these target genes.

A major QTL affects temperature sensitive adult lethality and inbreeding depression in life span in Drosophila melanogaster

BackgroundThe study of inbreeding depression has major relevance for many disciplines, including conservation genetics and evolutionary biology. Still, the molecular genetic basis of this phenomenon remains poorly characterised, as knowledge on the mechanistic causes of inbreeding depression and the molecular properties of genes that give rise to or modulate its deleterious effects is lacking. These questions warrant the detailed study of genetic loci giving rise to inbreeding depression. However, the complex and polygenic nature of general inbreeding depression makes this a daunting task. Study of inbreeding effects in specific traits, such as age-specific mortality and life span, provide a good starting point, as a limited set of genes is expected to be involved.ResultsHere we report on a QTL mapping study on inbreeding related and temperature sensitive lethality in male Drosophila melanogaster. The inbreeding effect was expressed at moderately high temperature, and manifested itself as severe premature mortality in males, but not in females. We used a North Carolina crossing design 3 to estimate average dominance ratio and heritability. We found the genetic basis of the lethal effect to be relatively simple, being due mainly to a single recessive QTL on the left arm of chromosome 2. This locus colocalised with a QTL that conditioned variation in female life span, acting as an overdominant locus for this trait. Male life span was additionally affected by variation at the X-chromosome.ConclusionThis demonstrates that analysis of large conditional lethal effects is a viable strategy for delineating genes which are sensitive to inbreeding depression.

Association mapping of leaf traits, flowering time, and phytate content inBrassica rapa

Association mapping was used to investigate the genetic basis of variation within Brassica rapa, which is an important vegetable and oil crop. We analyzed the variation of phytate and phosphate levels in seeds and leaves and additional developmental and morphological traits in a set of diverse B. rapa accessions and tested association of these traits with AFLP markers. The analysis of population structure revealed four subgroups in the population. Trait values differed between these subgroups, thus defining associations between population structure and trait values, even for traits such as phytate and phosphate levels. Marker-trait associations were investigated both with and without taking population structure into account. One hundred and seventy markers were found to be associated with the observed traits without correction for population structure. Association analysis with correction for population structure led to the identification of 27 markers, 6 of which had known map positions; 3 of these were confirmed in additional QTL mapping studies.

Mapping of quantitative trait loci controlling tick [Riphicephalus (Boophilus) microplus] resistance on bovine chromosomes 5, 7 and 14

Differences in domestication and selection processes have contributed to considerable phenotypic and genotypic differences between Bos taurus and Bos indicus cattle breeds. Of particular interest in tropical and subtropical production environments are those genetic differences between subspecies that underlie the phenotypic extremes in tolerance and susceptibility to parasite infection. In general, B. taurus cattle are more susceptible to ectoparasites than B. indicus cattle in tropical environments, and much of this difference is under genetic control. To identify genomic regions involved in tick resistance, we developed a B. taurus x B. indicus F(2) experimental population to map quantitative trait loci (QTL) for resistance to the Riphicephalus (Boophilus) microplus tick. About 300 individuals were measured for parasite load in two seasons (rainy and dry) and genotyped for 23 microsatellite markers covering chromosomes 5, 7 and 14. We mapped a suggestive chromosome-wide QTL for tick load in the rainy season (P < 0.05) on chromosome 5. For the dry season, suggestive (P < 0.10) chromosome-wide QTL were mapped on chromosomes 7 and 14. The additive effect of the QTL on chromosome 14 corresponds to 3.18% of the total observed phenotypic variance. Our QTL-mapping study has identified different genomic regions controlling tick resistance; these QTL were dependent upon the season in which the ticks were counted, suggesting that the QTL in question may depend on environmental factors.

Molecular barley breeding

Breeding progress in barley yield in the UK is being sustained at a rate in the order of 1% per annum against a background of declining seed sales. Commercial barley breeders are largely concentrating upon the elite local gene pool but with genotypic evidence suggesting that there is still considerable variation between current recommended cultivars, even those produced as half-sibs by the same breeder. Marker Assisted Selection (MAS) protocols could be substituted for conventional selection for a number of major-gene targets but, in the majority of cases, conventional selection is more resource efficient. Results from current QTL mapping studies have not yet identified sufficiently robust and validated targets for UK barley breeders to adopt MAS to assist in the selection of complex traits such as yield and malting quality. Results from multiple population mapping amongst the elite gene pool being utilised by breeders and from association studies of elite germplasm tested as part of the UK recommended list trial process do, however, show some promise.