Chromosome-wise dissection of the genome of the extremely big mouse line DU6i

Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci

The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F₂-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.

A comprehensive linkage map and QTL map for carcass traits in a cross between Giant Grey and New Zealand White rabbits

BACKGROUND

Genomic resources for the rabbit are still limited compared to many other livestock species. The genomic sequence as well as linkage maps have gaps that hamper their use in rabbit genome research. Therefore, the aims of this study were the improvement of existing linkage maps and the mapping of quantitative trait loci (QTL) for carcass and meat quality traits. The study was performed in a F2 population of an initial cross between Giant Grey (GG) and New Zealand White (NZW) rabbits. The population consisted of 363 F2 animals derived from 9 F1 bucks and 33 F1 does. 186 microsatellite and three SNP markers were informative for mapping.

RESULTS

Out of 189 markers, which could be assigned to linkage groups, 110 markers were genetically mapped for the first time. The average marker distance was 7.8 cM. The map across all autosomes reached a total length of 1419 cM. The maternal linkage map was 1.4 times longer than the paternal. All linkage groups could be anchored to chromosomes. On the basis of the generated genetic map, we identified a highly significant QTL (genome-wide significance p < 0.01) for different carcass weights on chromosome 7 with a peak position at 91 cM (157 Mb), a significant QTL (p < 0.05) for bone mass on chromosome 9 at 61 cM (65 Mb), and another one for drip loss on chromosome 12 at 94 cM (128 Mb). Additional suggestive QTL were found on almost all chromosomes. Several genomic loci affecting the fore, intermediate and hind parts of the carcass were identified. The identified QTL explain between 2.5 to 14.6% of the phenotypic variance in the F2 population.

CONCLUSIONS

The results present the most comprehensive genetic map and the first genome-wide QTL mapping study for carcass and meat quality traits in rabbits. The identified QTL, in particular the major QTL on chromosome 7, provide starting points for fine mapping and candidate gene search. The data contribute to linking physical and genetic information in the rabbit genome.

Genomic imprinting and genetic effects on muscle traits in mice

BACKGROUND

Genomic imprinting refers to parent-of-origin dependent gene expression caused by differential DNA methylation of the paternally and maternally derived alleles. Imprinting is increasingly recognized as an important source of variation in complex traits, however, its role in explaining variation in muscle and physiological traits, especially those of commercial value, is largely unknown compared with genetic effects.

RESULTS

We investigated both genetic and genomic imprinting effects on key muscle traits in mice from the Berlin Muscle Mouse population, a key model system to study muscle traits. Using a genome scan, we first identified loci with either imprinting or genetic effects on phenotypic variation. Next, we established the proportion of phenotypic variation explained by additive, dominance and imprinted QTL and characterized the patterns of effects. In total, we identified nine QTL, two of which show large imprinting effects on glycogen content and potential, and body weight. Surprisingly, all imprinting patterns were of the bipolar type, in which the two heterozygotes are different from each other but the homozygotes are not. Most QTL had pleiotropic effects and explained up to 40% of phenotypic variance, with individual imprinted loci accounting for 4-5% of variation alone.

CONCLUSION

Surprisingly, variation in glycogen content and potential was only modulated by imprinting effects. Further, in contrast to general assumptions, our results show that genomic imprinting can impact physiological traits measured at adult stages and that the expression does not have to follow the patterns of paternal or maternal expression commonly ascribed to imprinting effects.

A unique genetic defect on chromosome 3 is responsible for juvenile obesity in the Berlin Fat Mouse

OBJECTIVE

This study aimed at the mapping and estimation of genetic and sex effects contributing to the obese phenotype of the Berlin Fat Mouse Inbred line 860 (BFMI860). This mouse line is predisposed for juvenile obesity. BFMI860 mice accumulate 24% total fat mass at 10 weeks of age under a standard maintenance diet.

DESIGN

A total of 471 mice of a (BFMI860 x C57BL/6NCrl) F₂ intercross population were fed a standard maintenance diet and were analysed for body composition at 10 weeks when they finished their rapid growth phase.

RESULTS

The most striking result was the identification of a novel obesity locus on chromosome 3 (Chr 3) at 40 Mb, explaining 39% of the variance of total fat mass in the F₂ population under a standard diet. This locus was named jObes1 (juvenile obesity 1). The BFMI860 allele effect was recessive. Males and females homozygous at jObes1 had on average 3.0 and 3.3 g more total fat mass at 10 weeks than the other two genotype classes, respectively. The effect was evident in all white adipose tissues, brown adipose tissue and also in liver. The position of the Chr 3 effect is syntenic to an obesity locus in humans. Additional loci for total fat mass and different white adipose tissue weights with minor effects were detected on mouse Chr 5 and 6. Another locus on Chr 4 had influence especially on liver weight. Many loci including jObes1 affected males and females to a different extent.

CONCLUSION

The major locus on Chr 3 for juvenile obesity and its interaction with sex is unique and makes the BFMI860 mice an interesting resource for the discovery of novel genetic factors predisposing obesity, which might also contribute to obesity in humans. The results suggested that metabolic and regulatory pathways differed between the sexes.

Taste solution consumption by FHH-Chr nBN consomic rats

There has been extensive work to elucidate the behavioral and physiological mechanisms responsible for taste preferences of the rat but little attempt to delineate the underlying genetic architecture. Here, we exploit the FHH-Chr n(BN)/Mcwi consomic rat strain set to identify chromosomes carrying genes responsible for taste preferences. We screened the parental Fawn Hooded Hypertensive (FHH) and Brown Norway (BN) strains and 22 FHH-Chr n(BN) consomic strains, with 96-h 2-bottle tests, involving a choice between water and each of the following 16 solutions: 10 mM NaCl, 237 mM NaCl, 32 mM CaCl(2), 1 mM saccharin, 100 mM NH(4)Cl, 32 mM sucrose, 100 mM KCl, 4% ethanol, 1 mM HCl, 10 mM monosodium glutamate, 1 mM citric acid, 32 microM quinine hydrochloride, 1% corn oil, 32 microM denatonium, 1% Polycose, and 1 microM capsaicin. Depending on the taste solution involved, between 1 and 16 chromosomes were implicated in the response. Few of these chromosomes carried genes believed to mediate taste transduction in the mouse, and many chromosomes with no candidate taste genes were revealed. The genetic architecture of taste preferences is considerably more complex than has heretofore been acknowledged.

Genetic factors on mouse chromosome 18 affecting susceptibility to testicular germ cell tumors and permissiveness to embryonic stem cell derivation

Despite strong heritability, little is known about the genetic control of susceptibility to testicular germ cell tumors (TGCT) in humans or mice. Although the mouse model of spontaneous TGCTs has been extensively studied, conventional linkage analysis has failed to locate the factors that control teratocarcinogenesis in the susceptible 129 family of inbred strains. As an alternative approach, we used both chromosome substitution strains (CSS) to identify individual chromosomes that harbor susceptibility genes and a panel of congenic strains derived from a selected CSS to determine the number and location of susceptibility variants on the substituted chromosome. We showed that 129-Chr 18(MOLF) males are resistant to spontaneous TGCTs and that at least four genetic variants control susceptibility in males with this substituted chromosome. In addition, early embryonic cells from this strain fail to establish embryonic stem cell lines as efficiently as those from the parental 129/Sv strain. For the first time, 129-derived genetic variants that control TGCT susceptibility and fundamental aspects of embryonic stem cell biology have been localized in a genetic context in which the genes can be identified and functionally characterized.

QTL for body composition on chromosome 7 detected using a chromosome substitution mouse strain

OBJECTIVE

Previous studies in mice have detected quantitative trait loci (QTLs) on chromosome 7 that affect body composition. As a step toward identifying the responsible genes, we compared a chromosome 7 substitution strain C57BL/6J-Chr7(129S1/SvImJ)/Na (CSS-7) to its host (C57BL/6J) strain.

METHODS AND PROCEDURES

Fourteen-week-old mice were measured for body size (weight, length), organ weight (brain, heart, liver, kidneys, and spleen), body and bone composition (fat and lean weight; bone area, mineral content, and density), and individual adipose depot weights (gonadal, retroperitoneal, mesenteric, inguinal, and subscapular). Differences between the CSS-7 strain and the host strain were interpreted as evidence for the presence of one or more QTLs on chromosome 7.

RESULTS

Using this criterion, we detected QTLs for body weight, bone area, bone mineral content, brain, and heart weight, most adipose depot weights and some indices of fatness. A few strain differences were more pronounced in males (e.g., most adiposity measures) and others were more pronounced in females (e.g., bone area). QTLs for body length, lean weight, bone mineral density, and kidney, spleen, and liver weight were not detected.

DISCUSSION

This study found several associations that suggest one or more QTLs specific to the weight of select tissues and organs exist on mouse chromosome 7. Because these loci are detectable on a fixed and uniform genetic background, they are reasonable targets for high-resolution mapping and gene identification using a congenic approach.

Genetic regulation of hypothalamic cocaine and amphetamine-regulated transcript (CART) in BxD inbred mice

Cocaine and Amphetamine-Regulated Transcript (CART) peptides are implicated in a wide range of behaviors including in the reinforcing properties of psychostimulants, feeding and energy balance and stress and anxiety responses. We conducted a complex trait analysis to examine natural variation in the regulation of CART transcript abundance (CARTta) in the hypothalamus. CART transcript abundance was measured in total hypothalamic RNA from 26 BxD recombinant inbred (RI) mouse strains and in the C57BL/6 (B6) and DBA/2J (D2) progenitor strains. The strain distribution pattern for CARTta was continuous across the RI panel, which is consistent with this being a quantitative trait. Marker regression and interval mapping revealed significant quantitative trait loci (QTL) on mouse chromosome 4 (around 58.2 cM) and chromosome 11 (between 20-36 cM) that influence CARTta and account for 31% of the between strain variance in this phenotype. There are numerous candidate genes and QTL in these chromosomal regions that may indicate shared genetic regulation between CART expression and other neurobiological processes referable to known actions of this neuropeptide.

Differentially expressed genes in adipose tissues of high body weight-selected (obese) and unselected (lean) mouse lines

Recently, quantitative trait loci (QTLs) for body weight and obesity have been mapped in an intercross population between the high body weight-selected mouse line DU6i and the inbred line DBA/2. Most QTLs were highly significant, but had small effects only. Under the hypothesis that small-effect QTLs might result from changes in gene activity, our strategy to identify candidate genes for the observed effects was directed towards the identification of differentially expressed genes. Therefore, here we compare the transcription profile of about 11 000 genes in epididymal fat tissues of males of two high body weight-selected (DU6 and DU6i) and two unselected mouse lines (DUKs and DBA/2). For the hybridisation of GeneChips, we used pooled samples of 20 individual mice. By pair-wise comparisons between selected and unselected mouse lines, a set of 77 genes was identified representing genes whose level of expression differed between obese and lean mouse strains. According to the functional classification of genes, 69 differentially expressed genes were involved in regulatory and metabolic pathways, cell division, cell stability, or immune response, and thus might have an effect on body weight and fat accumulation. 14 out of these genes, occur in QTL regions for body weight or abdominal fat weight. Further analyses are necessary to discriminate between genes directly causing QTL effects and indirectly regulated differentially expressed genes.

Genetics of behavioural domains across the neuropsychiatric spectrum; of mice and men

Family and twin studies have revealed that genetic factors play a major role in psychiatric disorders, however, attempts to find susceptibility genes for these complex disorders have been largely unsuccessful. Therefore, new research strategies are required to tackle the complex interactions of genes, developmental, and environmental events. Here, we will address a behavioural domain concept that focuses on the genetics of behavioural domains relevant to both animal behaviour and across human psychiatric disorders. We believe that interspecies trait genetics rather than complex syndrome genetics will optimize genotype-phenotype relationships for psychiatric disorders and facilitate the identification of biological substrates underlying these disorders.

The mouse as a model for human biology: a resource guide for complex trait analysis

The mouse has been a powerful force in elucidating the genetic basis of human physiology and pathophysiology. From its beginnings as the model organism for cancer research and transplantation biology to the present, when dissection of the genetic basis of complex disease is at the forefront of genomics research, an enormous and remarkable mouse resource infrastructure has accumulated. This review summarizes those resources and provides practical guidelines for their use, particularly in the analysis of quantitative traits.

Complex genetic architecture revealed by analysis of high-density lipoprotein cholesterol in chromosome substitution strains and F2 crosses

Intercrosses between inbred lines provide a traditional approach to analysis of polygenic inheritance in model organisms. Chromosome substitution strains (CSSs) have been developed as an alternative to accelerate the pace of gene identification in quantitative trait mapping. We compared a classical intercross and three CSS intercrosses to examine the genetic architecture underlying plasma high-density lipoprotein cholesterol (HDL) levels in the C57BL/6J (B) and A/J (A) mouse strains. The B x A intercross revealed significant quantitative trait loci (QTL) for HDL on chromosomes 1, 4, 8, 15, 17, 18, and 19. A CSS survey revealed that many have significantly different HDL levels compared to the background strain B, including chromosomes with no significant QTL in the intercross and, in some cases (CSS-1, CSS-17), effects that are opposite to those observed in the B x A intercross population. Intercrosses between B and three CSSs (CSS-3, CSS-11, and CSS-8) revealed significant QTL but with some unexpected differences from the B x A intercross. Our inability to predict the results of CSS intercrosses suggests that additional complexity will be revealed by further crosses and that the CSS mapping strategy should be viewed as a complement to, rather than a replacement for, classical intercross mapping.