Protein variation in strains of mice differing in body size

Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P < 0.05) were identified across the three lines. With GS, 70 selected regions were identified. Empirical thresholds for local allele frequency changes were determined from gene dropping, and differed considerably between GS (0.167-0.198) and BLUP (0.105-0.126). Between lines, the genomic regions with large changes in allele frequencies showed limited overlap. Our results show that GS applies selection pressure much more locally than BLUP, resulting in larger allele frequency changes. With these results, novel insights into the nature of selection on quantitative traits have been gained and important questions regarding the long-term impact of GS are raised. The rapid changes to a part of the genetic architecture, while another part may not be selected, at least in the short term, require careful consideration, especially when selection occurs before phenotypes are observed.

Promises and limitations of hitchhiking mapping

Building the connection between genetic and phenotypic variation is an important 'work in progress', and one that will enable proactive diagnosis and treatment in medicine, promote development of environment-targeted varieties in agriculture, and clarify the limits of species adaptation to changing environments in conservation. Quantitative trait loci (QTL) mapping and genome wide association (GWA) studies have recently been allied to an additional focus on 'hitchhiking' (HH) mapping--using changes in allele frequency due to artificial or natural selection. This older technique has been popularized by the falling costs of high throughput sequencing. Initial HH-resequensing experiments seem to have found many thousands of polymorphisms responding to selection. We argue that this interpretation appears too optimistic, and that the data might in fact be more consistent with dozens, rather than thousands, of loci under selection. We propose several developments required for sensible data analyses that will fully realize the great power of the HH technique, and outline ways of moving forward.

Genome-enabled hitchhiking mapping identifies QTLs for stress resistance in natural Drosophila

Identification of genes underlying complex traits is an important problem. Quantitative trait loci (QTL) are mapped using marker-trait co-segregation in large panels of recombinant genotypes. Most frequently, recombinant inbred lines derived from two isogenic parents are used. Segregation patterns are also studied in pedigrees from multiple families. Great advances have been made through creative use of these techniques, but narrow sampling and inadequate power represent strong limitations. Here, we propose an approach combining the strengths of both techniques. We established a mapping population from a sample of natural genotypes, and applied artificial selection for a complex character. Selection changed the frequencies of alleles in QTLs contributing to the selection response. We infer QTLs with dense genotyping microarrays by identifying blocks of linked markers undergoing selective changes in allele frequency. We demonstrated this approach with an experimental population composed from 20 isogenic strains. Selection for starvation survival was executed in three replicated populations with three control non-selected populations. Three individuals per population were genotyped using Affymetrix GeneChips. Two regions of the genome, one each on the left arms of the second and third chromosomes, showed significant divergence between control and selected populations. For the former region, we inferred allele frequencies in selected and control populations by pyrosequencing. We conclude that the allele frequency difference, averaging approximately 40% between selected and control lines, contributed to selection response. Our approach can contribute to the fine scale decomposition of the genetics of direct and indirect selection responses, and genotype by environment interactions.

Variation in IL-1beta gene expression is a major determinant of genetic differences in arthritis aggressivity in mice

In humans and in animal models, susceptibility to arthritis is under complex genetic control, reflecting influences on the immunological processes that initiate autoimmunity and on subsequent inflammatory mechanisms in the joints. The effector phases are conveniently modeled by the K/BxN serum transfer system, a robust model well suited for genetic analysis where arthritis is initiated by pathogenic Ig. Here, we mapped the genetic loci distinguishing the high-responder BALB/c vs. low-responder SJL strains. After computational modeling of potential breeding schemes, we adapted a stepwise selective breeding strategy, with a whole-genome scan performed on a limited number of animals. Several genomic regions proved significantly associated with high sensitivity to arthritis. One of these regions, on distal chr2, was centered on the interleukin 1 gene family. Quantitation of transcripts of the Il1a and Il1b candidate genes revealed a 10-fold greater induction of Il1b mRNA in BALB/c than in SJL splenocytes after injection of LPS, whereas Il1a showed much less difference. The differential activity of the Il1b gene was associated with a particular sequence haplotype of noncoding polymorphisms. The BALB/c haplotype was found in 75% of wild-derived strains but was rare among conventional inbred strains (4/33 tested, one of which is DBA/1, the prototype arthritis-susceptible strain) and was associated with vigorous Il1b responses in a panel of inbred strains. Inbred strains carrying this allele were far more responsive to serum-transferred arthritis, confirming its broad importance in controlling arthritis severity.

Detection of quantitative trait loci from frequency changes of marker alleles under selection

A method was developed to estimate effects of quantitative trait loci (QTL) by maximum likelihood using information from changes of gene frequency at marker loci under selection, assuming an additive model of complete linkage between markers and QTL. The method was applied to data from 16 molecular and coat colour marker loci in mouse lines derived from the F2 of two inbred strains which were divergently selected on 6-week weight for 21 generations. In 4 regions of the genome, marker allele frequencies were more extreme than could be explained by sampling, implying selection at nearby QTL. An effect of about 0.5 standard deviations was located on chromosome 11, and accounted for nearly 10% of the genetic variance in the base population. QTL with effects as small as 0.2 phenotypic standard deviations could be detected. For typing of a given number of individuals, the power of detection of QTL is very high compared to, for example, analysis of an F2 population. The joint effects of linkage and selection were investigated by Monte Carlo simulation. Marker gene frequencies change little as a consequence of selection at a QTL unless the marker and QTL are less than about 20 cM apart.

Identification of ornithine decarboxylase as a trait gene for growth in replicated mouse lines divergently selected for lean body mass

Studies of lines of mice selected for body mass have shown that there is a significant genetic component affecting this trait although the nature of the genes involved remains to be elucidated. Using replicate lines of mice, our studies have shown that two different variants of the mouse ornithine decarboxylase (ODCase) gene have been selected in replicate lines of mice selected for high and low lean body mass respectively. One variant is associated with an increased peak of ODCase activity in embryos (10-13 days of gestation) in all high mass lines and with a restriction fragment length polymorphism of the expressed gene. The increased ODCase activity coincides with increased ODCase mRNA levels in the high mass selected lines. These results provide evidence implicating ornithine decarboxylase as a major factor in cell growth, and as a candidate 'trait gene'.

Physiological variation of mouse haemoglobins

Polymorphism at Hbb (haemoglobin beta-chain) is widespread in natural populations of the house mouse, Mus musculus, and appears to be maintained by natural selection. This report is an attempt to correlate genotypic fluctuations at Hbb with a most important physiological attribute of haemoglobin, its oxygen carrying capacity. Oxygen affinity has been studied and P50 values have been measured in 12 inbred strains as well as wild-caught mice from Skokholm island. The mean P50 of each inbred strain is a constant characteristic, although there is high within-strain variation and the oxygen affinity of the blood of an individual can fluctuate considerably from week to week. The causes of this variation remain obscure but neither within-strain nor between-strain differences are correlated with known modulators of oxygen binding. In general, the blood of mice of inbred strains as well as wild-caught mice that are homozygous for Hbbd tends to have a higher oxygen affinity than that from comparable animals homozygous for Hbbs, but it seems likely that the oxygen dissociation properties of haemoglobin are not the only ones important in determining differential survival of a particular Hbb type under varying environmental stress.

H-2-associated differences in replicated strains of mice divergently selected for body weight

A random-bred strain (Q) was established and divided into six replicates. Each replicate was divergently selected for 6-week weight (for over 30 generations) and each had an unselected control. We have investigated the H-2 haplotype of individual mice of the 18 selected Q strains to determine whether selection for size had also selected for H-2 or H-2-linked genes. From the results it appeared that only the H2b and H-2q haplotypes were present in the foundation stock. A large number of individuals of the six small sublines were of H-2b haplotype, while the majority of those of the six large sublines were of the H-2q haplotype. Individuals in the six control strains were H-2b, H-2q or both (i.e., H-2 heterozygotes and/or H-2 recombinants). These results suggest that control of body size is associated with H-2 or an H-2-linked gene(s).

The control of body size in mouse chimaeras

Aggregation chimaeras were made from embryos of strains of mice selected for large and small body size and of unselected controls. The strains were combined in pairs marked by albino coat colour and by allo-zyme variants at the Gpi-1 locus. The proportion of cells derived from each component was scored visually in the coat melanocytes and by electrophoresis in ten other organs or tissues (blood, liver, lung, spleen, spinal cord, brain, pituitary, kidney, adrenal and testis). The object was to find out how body weight is related to cell proportions in the body as a whole and in the separate organs. Individuals varied widely in their mean cell proportions but there were significant differences between organs within individuals. Body weight was linearly related to the mean cell proportions which accounted for most, or possibly all, of the chimaeric variance of body weight. No one of the organs studied could be identified as being solely responsible for growth control, or as having a predominant influence on growth. The weights of some organs were probably influenced to a small extent by their own cell proportions independently of the individual's mean, but the differences of body weight were too great to be accounted for by the summation of localized effects on organs. The mean cell proportion, averaged over individuals, was close to 50%, proving that there was no tendency for cells from the larger component to outgrow those from the smaller. It is concluded that growth control must be systemic, but it was not possible to decide whether the systemic effect comes from some particular organ not studied, or is in some undefined way the consequence of the cell proportions in the body as a whole. There was some evidence, though it was inconclusive, that chimaeras show ‘heterosis’ for body weight.

Heterogeneous heterozygosities in Mus musculus populations

Both chance and adaptation have effects in determining the genetical constitution of local populations of any organism, but opinions differ widely over their relative importance. This study describes the frequencies of electrophoretically detected alleles at 22 loci in 1538 house mice ( Mus musculus L.) from 27 population samples collected from the Faroe, Shetland and Orkney archipelagoes; the mainland of Great Britain plus three small off-shore islands; and a sub-Antarctic island (Macquarie) lying between Australia and the Antarctic Continent. Neither the average heterozygosities nor the distribution of allele frequencies in the different populations showed any discernible pattern, but at least three loci ( Hbb , Es -2, Dip -1) underwent seasonal changes in frequency which could only be due to selection. Moreover the overall variances of allele frequencies were significantly heterogeneous ( P ≈ 0.001), suggesting that different factors affect different loci. The key to understanding this apparent randomness of frequencies is recognizing that selection pressures are non-constant, and particular traits may affect fitness only spasmodically. The occurrence and frequency of an allele in any population may reflect only chance historical factors, but the trait(s) affected by it is potentially subject to selection at any time. For example, the proportion of heterozygotes at the Hbb locus in one population (Skokholm) living entirely independent of man, increased in five summers out of six. Winter death in mice is colddependent, and the exceptional summer followed a particularly mild winter when the usual decrease in heterozygotes did not take place. An r -selected species like the house mouse is more likely to reveal the interplay of genetical chance and purpose than a numerically less volatile one in which short-term genetical adjustment will be relatively uncommon.

The effect of selection on the standardized variance of gene frequency

The effect of directional and heterotic selection on the standardized variance of gene frequency (f=σ q (2) /¯q(1-¯q)) has been examined. It has been found that heterotic selection always results in f values lower than those expected due to drift alone. Additive directional selection can result in low f values, but values larger than those expected due to drift will be observed under additive selection with low initial gene frequency, or when the populations have been separated for a very long period of time in which case f expected due to drift is quite high (around 0.7 or greater). The effect of selection on f is unlikely to be detected if the observed value of f is less than 0.1.

The genetic relationship between the Hbb locus and body size in a population of mice divergently selected for six-week body weight

Both pleiotropy and linkage were examined as possible explanations for the fixation of the Hbb3 allele in the six Large lines of a population of mice divergently selected for six-week body weight (six replicates in each direction and six controls). A survey of over 1200 individuals in the lines still segregating at the Hbb locus excluded pleiotropy as a possible explanation. The results showed a nonsignificant effect of haemoglobin genotype on body weight. The linkage relationship of the Hbb locus was examined using a backcross mating system. The Hbb3 c+ region (chromosome 7) of a Large line was backcrossed into its corresponding Small line (Hbb4 c). The resultant difference in body weight between the two segregants (Hbb8 c+ [Hbb4 c; Hbb4 c/Hbb4 c) was measured. The results suggested linkage as the most plausible explanation for the fixation of the Hbb4 allele in the six Large lines.