Designing a QTL Mapping Study for Implementation in the Realized Collaborative Cross Genetic Reference Population

Abstract

The Collaborative Cross (CC) mouse resource is a next‐generation mouse genetic reference population (GRP) designed for high‐resolution mapping of quantitative trait loci (QTL) of large effect affecting complex traits during health and disease. The CC resource consists of a set of 72 recombinant inbred lines (RILs) generated by reciprocal crossing of five classical and three wild‐derived mouse founder strains. Complex traits are controlled by variations within multiple genes and environmental factors, and their mutual interactions. These traits are observed at multiple levels of the animals’ systems, including metabolism, body weight, immune profile, and susceptibility or resistance to the development and progress of infectious or chronic diseases. Herein, we present general guidelines for design of QTL mapping experiments using the CC resource—along with full step‐by‐step protocols and methods that were implemented in our lab for the phenotypic and genotypic characterization of the different CC lines—for mapping the genes underlying host response to infectious and chronic diseases. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: CC lines for whole body mass index (BMI) Basic Protocol 2: A detailed assessment of the power to detect effect sizes based on the number of lines used, and the number of replicates per line Basic Protocol 3: Obtaining power for QTL with given target effect by interpolating in Table 1 of Keele et al. (2019)

Studying the pharmacogenomic effect of cranberry extract on reducing body weight using collaborative cross mice

“…The present study was undertaken to challenge this assumption by using a genotyped and defined population of CC mouse lines previously shown to allow the determination of the heritability of a test trait employing a relatively low number of mice lines. 25,39 Polyphenol-rich cranberry extract was used as a source of food supplement because it holds the premise to influence obesity in a limited study. For example, in one study it was found that the multi-component polyphenol-rich extract obtained from cranberries could have a beneficial effect on the prevention or treatment of obesity via the inhibition of adipogenesis, lipid accumulation, and reactive oxygen species (ROS) production in adipocytes without affecting their viability.…”

“…The biological replica (number of mice per line and sex) used in this study was an excellent resource, which allowed performing a strong statistical analysis and calculating heritability and genetic covariance, and met the requirements as suggested earlier. 25,39 We anticipate that by increasing the number of assessed CC lines (30 lines and up) with an appropriate number of mice per line, 17 and by using the multi-trait and the multilocus analytical methods developed specifically for this genetically highly diverse reference population, 41 we will be able to map a genetic quantitative trait loci (QTL) with unprecedented precision to allow identification of genes associated with the ability of a particular food supplement to function in reducing weight. Because most mouse genes have orthologous genes in humans, we may be able to personalize the use of food supplements to function in reducing BW in humans.…”

Morphine analgesia in male inbred genetic diversity mice recapitulates the among‐individual variance in response to morphine in humans

“…The relationship of Tenm4 mutations and morphine tolerance may be worth researching in future investigations. However, owing to the limited number of GD strains used in this study, the QTL analysis is not obviously significant 34,35 . To confirm the exact role of these genetic loci in individual differences in morphine analgesia, much work remains to be done and more strains of GD mice need to be tested following this preliminary work.…”

“…However, owing to the limited number of GD strains used in this study, the QTL analysis is not obviously significant. 34,35 To confirm the exact role of these genetic loci in individual differences in morphine analgesia, much work remains to be done and more strains of GD mice need to be tested following this preliminary work. Meanwhile, GD mice may play an increasingly important role as a new resource in the study of individual differences in drug responses.…”

Alcohol Sensitivity as an Endophenotype of Alcohol Use Disorder: Exploring Its Translational Utility between Rodents and Humans

“…There are several types of highly recombinant populations that can be used for rodent QTL studies that have gained traction in recent years due to advances in genotyping technology and statistical techniques [ 90 ]. They include heterogeneous stocks (such as the heterogeneous stock (HS) rat and mouse populations), hybrid diversity panels (such as the Hybrid Rat Diversity Panel (HRDP) and Hybrid Mouse Diversity Panel (HMDP)), recombinant inbred (RI) strains (such as the BXD, LXS, and CC panels), and commercially available outbred stocks (such as CFW mice and Sprague Dawley rats) [ 62 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 ]. Heterogeneous stocks and commercially available outbred populations are generally created by semi-random breeding strategies that maximize genetic diversity while maintaining favorable minor allele frequencies (e.g., >10%).…”