maize: Simulated maize data

In synbreedData: Data for the Synbreed Package

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)

Example output

object of class 'gpData' 
covar 
	 No. of individuals 1610 
	         phenotyped 1250 
	          genotyped 1250 
pheno 
	 No. of traits:		   1 

    IDTrait     
 Min.   :120.7  
 1st Qu.:142.8  
 Median :148.9  
 Mean   :148.9  
 3rd Qu.:154.9  
 Max.   :181.8  

geno 
	 No. of markers 1117 
	 genotypes 0 1 
	 frequencies 0.339995 0.660005 
	 NA's 0.000 %
map 
	 No. of mapped markers  1117 
	 No. of chromosomes     10 

	 markers per chromosome 
	
  1   2   3   4   5   6   7   8   9  10 
 76  96  99 122  85 106 154 130 121 128 

pedigree 
Number of 
	 individuals  1610 
	 Par 1        219 
	 Par 2        221 
	 generations  15 

synbreedData documentation built on May 1, 2019, 6:51 p.m.