Phansak et al. (2016) mated 48 high protein soybean accessions in seven MGs (000 to IV) to a matching MG high yield cultivar of ordinary protein content. From these matings, they genrated 48 populations that each had about 220 F2 plants. They measured the seed protein (and oil) contents of F3 seed produced by each of the 220 F2 plants of a given mating, but only. Only 44 genotypes of the 220 phenotypes were genotyped - these were the 22 F2 plants with lowest F2.3 seed protein content and the 22 F2 plant with the highest F2.3 seed protein content. This procedure, known as selective genotyping was used to survey the 48 high protein accessions for the existnce of QTLs controlling seed protein (and oil) content. 

The software known as R/qtl was ideal for a QTL analysis of selectively genoytped populations and Phansak et al. (2016) have provided SoyBase readers with the *.csv files (phenotype and genotype data) and the matchiing *.txt files (R/qtl program code) for each of the 48 populations, plus three populations sets involving pooling of the identical parental matings discovered in this research.

If a SoyBase reader is interested in how the software known as R/qtl was used for phenotypic and genotypic error-checking and then for QTL analysis of seed protein and seed oli content, you need to first install R on your computer and then install R/qtl. Instructions for installing R and R/qtl are available at SoyBase (http://soybase.org/projects/SoyBase.D2016.01.php  ). Thereafter, you can simply follow the instructions in the R/qtl *.txt file to conduct a QTL analysis of the matching population *.csv file. 

Jim Specht
April 2016