Exploratory Marker Data Analysis

Abstract

Genetic data sets available to breeders are increasing in size, both in numbers of markers and in numbers of breeding individuals or lines genotyped. The scale of the data sets requires breeders to use software to perform quality control checks, visualize, and manipulate data. Breeders will often want to combine genetic marker data with physical or linkage map information, phenotypic data, and pedigree information. In this chapter we demonstrate the use of base R and the synbreed package of R to process an example data set from a maritime pine breeding population. The synbreed package defines the gpData object class, which can hold phenotypes, genotypes, pedigree, and genetic map information. This package is particularly useful to streamline data manipulation and analyses that combine genotype and phenotype data. Readers should be aware that algorithm and software developments for genomic data are areas of active research, more efficient and powerful methods are constantly being developed.