中国农业科学院 作物科学研究所
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

 

Genetic model 2 used in simulations

 

1. Introduction

The second genome consisted of three chromosomes, each with 100 cM in length and 11 evenly distributed markers. Three QTL (represented by QB1 to QB3;) contributed to the expression of a quantitative trait of interest. QB1 is located at 35 cM on chromosome 1, QB2 at 53 cM on chromosome 2, and QB3 at 22 cM on chromosome 3. For this genome, we considered two genetic models corresponding to Set I ( =0.375, =0.375 and H =0.6) and Set III (=0 , =0.375 and H =0.3) of Boer et al. (2002), respectively. Considering that the indicator variable has value 0.5 for homozygous marker type, and -0.5 for heterozygous marker type in Boer et al. (2002), the additive and epistatic effects used in our simulation study were respectively half and quarter of those in Boer et al. (2002), so as to achieve the same additive and epistatic variances. One hundred backcross populations each of 200 individuals were simulated for this genome.

For more details see Boer MP, Ter Braak CJF, Jansen RC (2002) A penalized likelihood method for mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 162:951-960.

 

2. Input file for Windows QTL IciMapping (Boer2002.qtl)

 

3. 100 backcross populations for Windows QTL Cartographer (Boer2002CIM)

 

4. 100 backcross populations for Empiricam Bayesian Model (Boer2002BAYES)

 

5. 100 backcross populations for Windows QTL IciMapping (Boer2002ICIM)

 

6. Results from ICIM