Marker-assisted introgression of trypanotolerance QTL in mice

Dissection of Host Susceptibility to Bacterial Infections and Its Toxins

Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies. Most of current animal models used in complex traits diseases genetic mapping have limited genetic diversity. This limitation impedes the ability to create incorporated network using genetic interactions, epigenetics, environmental factors, microbiota, and other phenotypes. A novel mouse genetic reference population for high-resolution mapping and subsequently identifying genes underlying the QTL, namely the Collaborative Cross (CC) mouse genetic reference population (GRP) was recently developed. In this chapter, we discuss a variety of approaches using CC mice for mapping genes underlying quantitative trait loci (QTL) to dissect the host response to polygenic traits, including infectious disease caused by bacterial agents and its toxins.

Evaluation of quantitative trait loci affecting intramuscular fat and reproductive traits in pigs using marker-assisted introgression

We investigated the effects of previously identified quantitative trait loci (QTL) in an experimental backcross (BC) between Chinese Meishan pigs and commercial Duroc pigs. We performed marker-assisted introgression of two QTL for intramuscular fat (IMF) content (IMF population) and three QTL for reproductive traits (reproduction population) from a donor Meishan pig into a recipient Duroc pig. At the fourth BC generation of the IMF population and third BC generation of the reproduction population, carrier animals were selected for the production of animals homozygous for the QTL. Our previous studies have shown that the presence of a Meishan allele on the IMF QTL is associated with low IMF values, and the Meishan allele on the reproductive QTL is associated with large litters. In this study, the presence of a Duroc allele at the IMF QTL on SSC9 resulted in a 0.27% increase in IMF (additive effect = 0.27 ± 0.08), whereas the presence of a Meishan allele at the IMF QTL on SSC7 resulted in a 0.34% increase in IMF (additive effect = -0.34 ± 0.09). The presence of the Meishan allele at the IMF QTL on SSC7 thus had the opposite effect to our previous studies, that is, increased IMF. In the reproduction population, we observed no differences between the genotypes of the three QTL in regard to number of corpora lutea or litter size. Marker-assisted introgression at these QTL is thus unlikely to result in an associated increase in litter size. These results show that it is possible to introgress alleles from other breeds into a selection population using molecular markers; any unexpected results might be associated with the genetic background.

Review: Genetics of helminth resistance in sheep

Karrow, N. A., Goliboski, K., Stonos, N., Schenkel, F. and Peregrine, A. 2014. Review: Genetics of helminth resistance in sheep. Can. J. Anim. Sci. 94: 1–9. Gastrointestinal helminth parasites are an important source of economic loss to sheep producers. A rapid increase in anthelmintic resistance has occurred around the globe; therefore, the industry is exploring alternative strategies such as genetic selection to control losses attributed to helminth infection. Since helminths have co-evolved with sheep for millions of years, natural selection for enhanced helminth resistance has occurred within certain breeds from various parts of the world. These breeds of sheep are being used to better understand the genetic aspects of helminth resistance. If the genetic variants that contribute to this phenotype can be identified, it may be possible to use selection strategies to introduce resistance alleles into other breeds or to increase their frequency within breeds. This review will provide an up-to-date overview of the pathology of helminth disease, the immune response to helminth infection, and the search for genes that confer helminth resistance.

Generation of a multi-locus chicken introgression line to study the effects of genetic interactions on metabolic phenotypes in chickens

Most biological traits are regulated by a complex interplay between genetic and environmental factors. By intercrossing divergent lines, it is possible to identify individual and interacting QTL involved in the genetic architecture of these traits. When the loci have been mapped, alternative strategies are needed for fine-mapping and studying the individual and interactive effects of the QTL in detail. We have previously identified, replicated, and fine mapped a four-locus QTL network that determines nearly half of the eightfold difference in body weight at 56 days of age between two divergently selected chicken lines. Here, we describe, to our knowledge, the first generation of a three-locus QTL introgression line in chickens. Recurrent marker-assisted backcrossing was used to simultaneously transfer QTL alleles from the low-weight selected line into the high-weight selected line. Three generations of backcrossing and one generation of intercrossing resulted in an introgression line where all three introgressed QTL and several unlinked and linked control-loci were segregating at nearly expected allele frequencies. We show how intensive selection can be applied using artificial insemination to rapidly generate a multi-locus introgression line and provide recommendations for future breeding of introgression lines. This confirmed introgression line will facilitate later detailed studies of the effects of genetic interactions on complex traits in this population, including growth, and body-composition traits.

Serious limitations of the QTL/microarray approach for QTL gene discovery

BACKGROUND

It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL). However, the effectiveness of this approach has not been assessed.

RESULTS

Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Three studies led to the identification of an underlying QTL gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD) regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of QTL regulated in cis (cis eQTL) showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP).

CONCLUSIONS

The literature shows limited successes from the QTL/microarray approach to identify QTL genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select cis-eQTL over trans-eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false cis-eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes that were not tested. Together, our results explain the tendency to report QTL candidates as differentially expressed and indicate that the utility of the QTL/microarray as currently implemented is limited. Alternatives are proposed that make use of microarray data from multiple experiments to overcome the outlined limitations.

Quantitative trait loci for resistance to Heligmosomoides bakeri and associated immunological and pathological traits in mice: comparison of loci on chromosomes 5, 8 and 11 in F2 and F6/7 inter-cross lines of mice

A comparison of F2 and F6/7 inter-cross lines of mice, derived from CBA and SWR parental strains, has provided strong evidence for several previously undetected quantitative trait loci (QTL) for resistance to Heligmosomoides bakeri. Five QTL affecting average faecal egg counts and/or worm burdens in week 6 were detected on mouse chromosomes 5 (Hbnr9 and Hbnr10), 8 (Hbnr11) and 11 (Hbnr13 and Hbnr14). Three QTL for faecal egg counts in weeks 4 and 6 were found on both chromosomes 5 (Hbnr9) and 11 (Hbnr13 and Hbnr14). Two QTL for the mucosal mast cell protease 1 (MCPT1) response were located on chromosomes 8 (Hbnr11) and 11 (Hbnr13), two for the IgG1 antibody response to adult worms on chromosomes 5 (Hbnr10) and 8 (Hbnr11), two for PCV in week 6 on chromosomes 5 (Hbnr9) and 11 (Hbnr13), and two for the granulomatous response on chromosome 8 (Hbnr12) and 11 (Hbnr15). Our data emphasize that the control of resistance to H. bakeri is multigenic, and regulated by genes within QTL regions that have a complex range of hierarchical relationships.

Introgression of a major QTL from an inferior into a superior population using genomic selection

BACKGROUND

Selection schemes aiming at introgressing genetic material from a donor into a recipient line may be performed by backcross-breeding programs combined with selection to preserve the favourable characteristics of the donor population. This stochastic simulation study investigated whether genomic selection can be effective in preserving a major quantitative trait locus (QTL) allele from a donor line during the backcrossing phase.

METHODS

In a simulation study, two fish populations were generated: a recipient line selected for a production trait and a donor line characterized by an enhanced level of disease resistance. Both traits were polygenic, but one major QTL affecting disease resistance was segregating only within the donor line. Backcrossing was combined with three types of selection (for total merit index) among the crossbred individuals: classical selection, genomic selection using genome-wide dense marker maps, and gene-assisted genomic selection. It was assumed that production could be observed directly on the selection candidates, while disease resistance had to be inferred from tested sibs of the selection candidates.

RESULTS

Classical selection was inefficient in preserving the target QTL through the backcrossing phase. In contrast, genomic selection (without specific knowledge of the target QTL) was usually effective in preserving the target QTL, and had higher genetic response to selection, especially for disease resistance. Compared with pure genomic selection, gene-assisted selection had an advantage with respect to disease resistance (28-40% increase in genetic gain) and acted as an extra precaution against loss of the target QTL. However, for total merit index the advantage of gene-assisted genomic selection over genomic selection was lower (4-5% increase in genetic gain).

CONCLUSION

Substantial differences between introgression programs using classical and genomic selection were observed, and the former was generally inferior with respect to both genetic gain and the ability to preserve the target QTL. Combining genomic selection with gene-assisted selection for the target QTL acted as an extra precaution against loss of the target QTL and gave additional genetic gain for disease resistance. However, the effect on total merit index was limited.

Clinical chemistry of congenic mice with quantitative trait loci for predicted responses to Trypanosoma congolense infection

Trypanosoma congolense is a protozoan parasite that causes severe diseases in livestock. Three major quantative trait loci (QTL), Tir1, Tir2, and Tir3, control the survival time of mice after infection with T. congolense. Congenic mice carrying the C57BL/6 resistance alleles on the A/J background were developed for each of these loci. The congenic mice were used to physically map the regions containing the QTL gene(s) and to investigate the physiological effect of each locus. Clinical chemistry data for infected A/J, C57BL/6, and BALB/c mice were obtained for 15 analytes at five time points. Congenic mice were assessed for survival, parasitemia, and anemia as well as seven clinical-chemical analytes. The survival times were significantly increased in the Tir1 and Tir2 mice but not Tir3 congenic mice. The survival time of the parental inbred mice correlated negatively with parasitemia but positively with alanine aminotransferase activities in serum, suggesting that inflammatory reactions in the liver had a beneficial effect possibly associated with reduced parasitemia. However, there was no difference in parasitemia or liver enzyme activities of Tir1 and Tir2 congenic mice relative to their controls, showing that survival, parasitemia, and degree of liver damage are not associated with each other, despite the correlation in the parental lines. These data suggest that the congenic loci affect survival but do not affect control of parasite number. They may therefore act by limiting the pathological consequences of T. congolense infection.

Heligmosomoides bakeri: a model for exploring the biology and genetics of resistance to chronic gastrointestinal nematode infections

The intestinal nematode Heligmosomoides bakeri has undergone 2 name changes during the last 4 decades. Originally, the name conferred on the organism in the early 20th century was Nematospiroides dubius, but this was dropped in favour of Heligmosomoides polygyrus, and then more recently H. bakeri, to distinguish it from a closely related parasite commonly found in wood mice in Europe. H. bakeri typically causes long-lasting infections in mice and in this respect it has been an invaluable laboratory model of chronic intestinal nematode infections. Resistance to H. bakeri is a dominant trait and is controlled by genes both within and outside the MHC. More recently, a significant QTL has been identified on chromosome 1, although the identity of the underlying genes is not yet known. Other QTL for resistance traits and for the accompanying immune responses were also defined, indicating that resistance to H. bakeri is a highly polygenic phenomenon. Hence marker-assisted breeding programmes aiming to improve resistance to GI nematodes in breeds of domestic livestock will need to be highly selective, focussing on genes that confer the greatest proportion of overall genetic resistance, whilst leaving livestock well-equipped genetically to cope with other types of pathogens and preserving important production traits.

A systematic strategy for the discovery of candidate genes responsible for phenotypic variation

It is increasingly common to combine genome-wide expression data with quantitative trait mapping data to aid in the search for sequence polymorphisms responsible for phenotypic variation. By joining these complex but different data types at the level of the biological pathway, we can take advantage of existing biological knowledge to systematically identify possible mechanisms of genotype-phenotype interaction. With the development of web services and workflows, this process can be made rapid and systematic. Our methodology was applied to a use case of resistance to African trypanosomiasis in mice. Workflows developed in this investigation, including a guide to loading and executing them with example data, are available at http://www.myexperiment.org/users/43/workflows .

Incorporating desirable genetic characteristics from an inferior into a superior population using genomic selection

Resistance to specific diseases may be improved by crossing a recipient line with a donor line (a distantly related strain) that is characterized by the desirable trait. However, considerable losses in the total merit index are expected when crossing recipient and donor lines. Repeated backcrossing with the recipient line will improve total merit index, but usually at the expense of the newly introgressed disease resistance, especially if this is due to polygenic effects rather than to a known single major QTL. This study investigates the possibilities for a more detailed introgression program based on marker-trait associations using dense marker genotyping and genomic selection. Compared with classical selection, genomic selection increased genetic gain, with the largest effect on low heritability traits and on traits not recorded on selection candidates (due to within-family selection). Further, within a wide range of economic weights and initial differences in the total merit index between donor and recipient lines, genomic selection produced backcrossed lines that were similar or better than the purebred lines within three to five generations. When using classical selection in backcrossing schemes, the long-term genetic contribution of the donor line was low. Hence, such selection schemes would usually perform similarly to simple purebreeding selection schemes.

Contributions of experimental mouse models to the understanding of African trypanosomiasis

African trypanosomiasis is the collective name for a wide variety of trypanosome infections that affect humans and livestock. In recent years, experimental mice infection models have provided new insights into both human and animal trypanosomiasis. Mouse models seem to be a valuable and versatile tool in trypanosomiasis-associated pathology and immunology research and highlight the variety shown by African trypanosomiases. Indeed, inbred mouse strains have enabled the study of genetic determinants of susceptibility and of the roles of anti-parasite antibodies, inflammatory mediators and anti-inflammatory mediators for each trypanosome species. Remarkable advances relating to the encephalitic stage of sleeping sickness have also been achieved thanks to murine models. The different contributions of murine models to the African trypanosomiases knowledge are presented here. Future search directions are finally proposed, with respect to mouse model opportunities and limitations.

Biphasic survival analysis of trypanotolerance QTL in mice

A marker-assisted introgression (MAI) experiment was conducted to transfer trypanotolerance quantitative trait loci (QTL) from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. The objective was to assess the effect of three previously identified chromosomal regions on mouse chromosomes 1 (MMU1), 5 (MMU5) and 17 (MMU17) in different genetic backgrounds on the survival pattern following infection with Trypanosoma congolense. An exploratory data analysis revealed a biphasic pattern of time to death, with highly distinct early and late mortality phases. In this paper, we present survival analysis methods that account for the biphasic mortality pattern and results of reanalyzing the data from the MAI experiment. The analysis with a Weibull mixture model confirmed the biphasic pattern of time to death. Mortality phase, an unobserved variable, appears to be an important factor influencing survival time and is modeled as a binary outcome variable using logistic regression analysis. Accounting for this biphasic pattern in the analysis reveals that a previously observed sex effect on average survival is rather an effect on proportion of mice in the two mortality phases. The C57BL/6 (donor) QTL alleles on MMU1 and MMU17 act dominantly in the late mortality phase while the A/J (recipient) QTL allele on MMU17 acts dominantly in the early mortality phase. From this study, we found clear evidence for a biphasic survival pattern and provided models for its analysis. These models can also be used when studying defense mechanisms against other pathogens. Finally, these approaches provide further information on the nature of gene actions.

Combined detection and introgression of quantitative trait loci underlying desirable traits

This study presents a new method that combines QTL mapping and gene introgression. The effectiveness of this method for simultaneous detection and introgression of a desirable QTL from a donor line into a recipient line was evaluated by simulation. For evaluation, we used the fourth backcross generation of 2 inbred lines. The difference between the 2 lines for the trait of interest was described entirely by 1 QTL, with the donor line carrying the superior allele. Nine scenarios, combinations of 3 heritabilities (h(2) = 0.10, 0.05, or 0.01) and 3 population sizes (N = 100, 500, or 1,000) were considered in the simulation. Selection of parents for the next backcross was based solely upon the estimated probability of carrying the superior allele after a QTL analysis. Estimates of the QTL location and allele substitution effect in most scenarios were comparable to the true values. However (with either small h(2) or N) the QTL allele substitution effect was underestimated, and location was also biased. The SE of the estimates decreased with increasing N. The retained donor chromosome segment and linkage drag were close to the expected values from other published work. In general, combined detection and introgression of genes underlying desirable traits not only saves at least 1 generation, but also it ensures that the desirable QTL is introgressed where its function is simultaneously tested in a planned environment and recipient genome structure.

A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis

It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit declaration of experimental methods. In this article, we highlight the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes. We show how automated approaches provide a systematic means to investigate genotype-phenotype correlations. This methodology was applied to a use case of resistance to African trypanosomiasis in the mouse. Pathways represented in the results identified Daxx as one of the candidate genes within the Tir1 QTL region. Subsequent re-sequencing in Daxx identified a deletion of an amino acid, identified in susceptible mouse strains, in the Daxx-p53 protein-binding region. This supports recent experimental evidence that apoptosis could be playing a role in the trypanosomiasis resistance phenotype. Workflows developed in this investigation, including a guide to loading and executing them with example data, are available at http://workflows.mygrid.org.uk/repository/myGrid/PaulFisher/.