This repository contains essential data to support the findings presented in the forthcoming publication titled "Linkage Mapping of Root Shape Traits Associated with Market Class in Two Biparental Carrot Populations." It includes VCF files for two distinct carrot biparental populations, as well as R code for filtering, constructing linkage maps, and conducting QTL analysis. Furthermore, the repository hosts phenotypic data gathered from these two biparental populations during the years 2020 and 2021. Two carrot genetic maps, one for each population, have been made available alongside their respective phenotypic data. The provided R code contains absolute working directory paths that may not function as intended on your system. The primary purpose of sharing this code is to offer readers insight into the techniques employed in this study. You may need to adapt the directory paths to suit your specific setup. To assist readers in understanding the logical sequence of steps involved in our linkage mapping project, the R code scripts have been sequentially numbered from 0 to 10. For more info contact: vegaalfaro@wisc.edu.