Quantitative trait loci(QTL) mapping is an important tool in sweetpotato research, contributing to the understanding of genetic architecture of various traits, including dry matter, nematode resistance, and flesh color. Early QTL work was carried out by using marker information alone via single marker analysis (SMA), or based on parent-specific linkage map using interval mapping (IM), composite interval mapping (CIM), and multiple interval mapping (MIM). Initially developed for inbred diploid species populations, these methods did not fully consider the complex autopolyploid, outcrossing nature of sweetpotato. Technological and methodological advances made it possible to obtain integrated, fully phased genetic maps for the crop. A random-effect MIM approach that leverages identity-by-descent based on QTL genotype conditional probabilities has been employed since with increasing power and resolution. To illustrate QTL identification in sweetpotato, we used publicly available data from ‘Beauregard’ × ‘Tanzania’ full-sib family ($$N = 315$$
N
=
315
) evaluated for flesh color in Peru. Several methods were able to detect two QTL on chromosomes 3 and 12 each for this trait in the same genomic regions. Despite the importance of such methods, there is need to extend existing models to account for multi-trait or multi-environment data and to evaluate their application in genomic-enabled prediction.