I develop a test of pleiotropy vs. separate QTL for multiparental populations. It extends the two-parent cross methods of Jiang and Zeng (1995) by surmounting two challenges in the multiparental population setting. First, my test accommodates more than two founder alleles. Second, my test incorporates multivariate polygenic random effects to allow for complicated pedigrees. Additionally, my test uses parametric bootstrap methods to get p-values. After discussing methods development in Chapter 2, I demonstrate my test in analyses of data from Diversity Outbred mice in Chapter 3. I organize Chapter 3 as three vignettes. Each allows us to study properties and applications of the test. First, I perform a comparative study of my pleiotropy test with linear regression-based mediation analysis in the context of dissecting an expression trait hotspot. Second, I examine the test's power through a study of local expression QTL. Lastly, I apply the test to inform gut microbiome studies. In Chapter 4, I present a tutorial on the software package qtl2pleio. qtl2pleio is a R package that implements my test and related analyses and visualizations. I offer concluding thoughts and discuss future research in Chapter 5.