Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests

Genetic identification of Ly75 as a novel quantitative trait gene for resistance to obesity in mice

Identification of causal quantitative trait genes (QTGs) governing obesity is challenging. We previously revealed that the lymphocyte antigen 75 (Ly75) gene with an immune function is a putative QTG for Pbwg1.5, a quantitative trait locus (QTL) for resistance to obesity found from wild mice (Mus musculus castaneus). The objective of this study was to identify a true QTG for Pbwg1.5 by a combined approach of a quantitative complementation test, qualitative phenotypic analyses and causal analysis using segregating populations. In a four-way cross population among an Ly75 knockout strain, a subcongenic strain carrying Pbwg1.5 and their background strains, the quantitative complementation test showed genetic evidence that the Ly75 locus is identical to Pbwg1.5. Qualitative phenotypic analyses in two intercross populations between knockout and background strains and between subcongenic and background strains suggested that Ly75 may have pleiotropic effects on weights of white fat pads and organs. Causal analysis in the intercross population between knockout and background strains revealed that only variation in fat pad weight is caused by the genotypic difference via the difference in liver Ly75 expression. The results showed that Ly75 is a true Pbwg1.5 QTG for resistance to obesity. The finding provides a novel insight for obesity biology.

Adiposity QTL Adip20 decomposes into at least four loci when dissected using congenic strains

An average mouse in midlife weighs between 25 and 30 g, with about a gram of tissue in the largest adipose depot (gonadal), and the weight of this depot differs between inbred strains. Specifically, C57BL/6ByJ mice have heavier gonadal depots on average than do 129P3/J mice. To understand the genetic contributions to this trait, we mapped several quantitative trait loci (QTLs) for gonadal depot weight in an F2 intercross population. Our goal here was to fine-map one of these QTLs, Adip20 (formerly Adip5), on mouse chromosome 9. To that end, we analyzed the weight of the gonadal adipose depot from newly created congenic strains. Results from the sequential comparison method indicated at least four rather than one QTL; two of the QTLs were less than 0.5 Mb apart, with opposing directions of allelic effect. Different types of evidence (missense and regulatory genetic variation, human adiposity/body mass index orthologues, and differential gene expression) implicated numerous candidate genes from the four QTL regions. These results highlight the value of mouse congenic strains and the value of this sequential method to dissect challenging genetic architecture.

A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis

Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.