Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment interactions (GxE). Therefore, uncovering the genetic and GxE effects on organismal homeostasis can be used to pinpoint the mechanisms underlying complex diseases. Given the limitations and challenges inherent in human genetic studies, genetic reference populations (GRPs) have become an invaluable tool for genetic mapping because they can mirror human genetic heterogeneity. Among these populations, the BXD GRP is one of the biggest mouse GRPs derived from a cross of the C57BL/6J and DBA/2J strains. In this thesis, I used systems genetics approaches to reveal the effects of diet, genes, and GxE on metabolic health and gut inflammation in BXD mice fed a standard chow or high-fat diet (HFD). All findings stemming from the BXDs were corroborated in datasets from unrelated mouse GRPs and from human populations. In Chapter 2, I applied a continuous metric - a metabolic health score (MHS) - to monitor overall metabolic health in BXD mice. The equivalent human MHS calculated in human UK Biobank (UKBB) confirmed that it can be a predictor of subsequent metabolic diseases and their related phenotypes. To understand the molecular mechanisms underlying the MHS, liver molecular signatures and plasma lipid biomarkers associated with the MHS in BXDs were identified, such as decreased cholesterol and FA metabolism, adipogenesis, and mTORC1 signalling. I also performed quantitative trait locus (QTL) analyses to explore the genetics and GxE effects on the MHS in BXD mice and found three MHS-associated genetic loci, which were validated in unrelated mouse populations. Emerging evidence shows the crucial roles of the gastro-intestinal tract in mediating organismal homeostasis. Therefore, in Chapter 3, I utilized the colon transcriptome of BXD mice to explore the diet, genetics, and GxE effect on intestinal homeostasis. Particularly, a subset of BXD strains exhibited an inflammatory bowel disease (IBD)-like transcriptome signature upon HFD. IBD-related gene expression modules in HFD-fed mice were then identified based on IBD signatures in mice and human. To understand the mechanisms underlying gut inflammation induced by dietary challenges, I employed transcription factor enrichment analyses and module QTL mapping to uncover the cis-regulatory elements and genetic loci regulating the expression of IBD-related modules. In particular, I found three transcription factors, STAT2, SMAD3, and REL, that might mediate the gene expression of genes involved in gut inflammation and one suggestive QTL of one IBD-related module was also identified which regulates HFD-driven intestinal inflammation in BXD mice. Collectively, I found potential genetic regulators that can control metabolic health and intestinal inflammation upon feeding with a HFD, which were confirmed in human datasets, e.g., the UKBB. These findings may lead to a better understanding of how a chronic unhealthy diet may gradually lead to complex diseases and serves as a source of potential biomarkers and gene targets to diagnose and treat early manifestations of metabolic diseases.