# Inbred Based Populations

#### Statistical Genetics Lab
Department of Genetics
Luiz de Queiroz College of Agriculture
University of São Paulo

#### 2025-05-16

Access the complete version of this vignette here

To have access to all example datasets. Install `onemap` from GitHub and run the following command:

    #install.packages("devtools") ## if you do not have it installed
    devtools::install_github("cristianetaniguti/onemap")

Starting in version 2.0-0, `OneMap` can also deal with inbred-based populations, that is, populations that have homozygous parental lines in the genealogy (F2s, backcrosses, and RILs). As a consequence, linkage phases do not need to be estimated. Since version 2.3.0, phases are estimated for F2 populations to properly generate progeny haplotypes not only the recombination fraction.

In this vignette, we explain how to proceed with the analysis in an F2 population. The same procedure can be used for backcrosses and RILs as well, and therefore users should not have any difficulty in analyzing their data. However, there are a number of differences from genetic mapping in outcrossing species; please read the proper vignette.

If you are not familiar with `R`, we recommend first the reading of vignette Introduction to R. You do not need to be an expert in R to build your linkage map, but some concepts are necessary and will help you through the process.

The software has been available on CRAN since 2007 (OneMap on CRAN) and has undergone several updates, adding new features and optimization up to version 3.2.0 in 2024. Future updates will focus solely on maintaining accessibility and functionality. New feature development and optimization efforts are now being directed toward the MAPpoly and MAPpoly2 packages.

MAPpoly is a more robust package designed for constructing linkage maps in polyploid species. Its optimized algorithms also provide improved efficiency for diploid species compared to OneMap. Therefore, we recommend using MAPpoly instead of OneMap in the following scenarios for diploid species:

- When working with only biallelic markers (e.g., SNPs).
- For outcrossing full-sib (F1), F2, or backcross populations.
- For datasets with a large number of markers (>5,000).
- For multi-population datasets (e.g., progeny from multiple parents; see MAPpoly2).

However, OneMap remains the best choice if you have:

- Populations derived from recombinant inbred lines (RILs).
- Datasets with multiallelic or dominant markers.

For guidance on best practices in building linkage maps while accounting for genotyping errors, please refer to Taniguti et. al 2023.