netgwas (version 0.0.1-1)

tetraPotato: tetraploid potato genotype data

Description

Tetraploid potato (Solanum tuberosum L.) genotype data.

Usage

data(tetraPotato)

Format

The format is a matrix containing 1972 single-nucleotide polymorphism (SNP) markers for 156 individuals.

Details

The full-sib mapping population MSL603 consists of 156 F1 plants resulting from a cross between female parent "Jacqueline Lee" and male parent "MSG227-2". The obtained genotype data contain 1972 SNP markers with five allele dosages. This genotype data can be used to construct linkage map for tetraploid potato (see below example).

References

1. Behrouzi, P., and Wit, E. C. (2017c). netgwas: An R Package for Network-Based Genome-Wide Association Studies. arXiv preprint, arXiv:1710.01236. 2. Massa, Alicia N., Norma C. Manrique-Carpintero, Joseph J. Coombs, Daniel G. Zarka, Anne E. Boone, William W. Kirk, Christine A. Hackett, Glenn J. Bryan, and David S. Douches. "Genetic linkage mapping of economically important traits in cultivated tetraploid potato (Solanum tuberosum L.)." G3: Genes, Genomes, Genetics 5, no. 11 (2015): 2357-2364.

Examples

# NOT RUN {
data(tetraPotato)
#Shuffle the order of markers
potato <- tetraPotato[ ,sample(1:ncol(tetraPotato), ncol(tetraPotato), replace=FALSE)] 
#Constructing linkage map for tetraploid potato
out <- netmap(potato, method="npn", cross.typ= "outbred"); out
potato.map <- out$map; potato.map
plot(out)
# }