maize: Simulated maize data

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

This is a simulated dataset of a maize breeding program. Data comprises 1250 doubled haploid (DH) lines that were genotyped with 1117 polymorphic SNP markers and phenotyped in a testcross with a single tester for one quantitative trait. All individuals are labeled with a unique ID, starting from 11360 to 12609. Markers are distributed along all 10 chromosomes of maize. Pedigree information starts with basis population and is available up to 15 generations. The 1250 lines belong to 25 full sib families with 50 individuals in each family. In the simulation of true breeding values (TBV), 1000 biallelic quantitative trait loci (QTL) with equal and additive (no dominance or epistasis) effects were generated. True breeding values for individuals were calculated according to

TBV=∑ QTL(k)

where QTL(k) is the effect of the k-th QTL. Phenotypic values were simulated according to

trait=tbv+e

where e = N(0,sigma2). The value for sigma2 was chosen in a way that a given plot heritability of h2=0.197 is realized. Note that true breeding values for 1250 phenotyped lines are stored as tbv in covar of gpData object. Reported phenotypic values of lines are adjusted values testcross means for yield [dt/ha] evaluated in 3 locations.

Usage

data(maize)

Format

Object of class gpData

Examples

## Not run: 
library(synbreed)
data(maize)
summary(maize)                                       

## End(Not run)

synbreed documentation built on March 12, 2021, 3:01 a.m.