PT  - JOURNAL ARTICLE
AU  - Frederick J. Boehm
AU  - Elissa J. Chesler
AU  - Brian S. Yandell
AU  - Karl W. Broman
TI  - Testing pleiotropy vs. separate QTL in multiparental populations
AID  - 10.1101/550939
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 550939
4099  - http://biorxiv.org/content/early/2019/02/15/550939.short
4100  - http://biorxiv.org/content/early/2019/02/15/550939.full
AB  - The high mapping resolution of multiparental populations, combined with technology to measure tens of thousands of phenotypes, presents a need for quantitative methods to enhance understanding of the genetic architecture of complex traits. When multiple traits map to a common genomic region, knowledge of the number of distinct loci provides important insight into the underlying mechanism and can assist planning for subsequent experiments. We extend the method of Jiang and Zeng (1995), for testing pleiotropy with a pair of traits, to the case of more than two alleles. We also incorporate polygenic random effects to account for population structure. We use a parametric bootstrap to determine statistical significance. We apply our methods to a behavioral genetics data set from Diversity Outbred mice, where we find evidence for presence of two distinct loci in a 2.5 cM region. Our methods have been incorporated into the R package qtl2pleio.