The theory and associated selection methods of classical quantitative genetics are based on the multifactorial or polygene hypothesis. Major genes or quantitative trait loci (QTL) in mod quantitative genetics based on amajor gene plus polygenesgenetic system have been paid much attention in genetic studies. However, it remains unclear how the numerous minor genes act, although the polygene theory has sustained genetic improvement in plants and animals for more than a hundred years. In the present study, we identified a novel minor gene, BnSOT-like1 (BnaA09g53490D), which is a sulfotransferase (SOT) gene catalyzing the formation of the core glucosinolate (GSL) structure in Brassica napus. This gene has been occasionally found during investigations of plant height-related genes, but has not been identified by QTL mapping because of its small phenotypic effects on GSL content. The overexpression of BnSOT-like1 up-regulated the expression of aliphatic GSL-associated genes, leading to a high seed aliphatic GSL content, and the overexpression of the allelic gene Bnsot-like1 did not increase seed GSL content. These findings suggest that the SOT gene has a marked effect on a quantitative trait from a reverse genetics standpoint, but a minor effect on the quantitative trait in its natural biological state. Because of the redundancy of GSL biosynthetic genes in the allotetraploid species B. napus, mutations of a single functional gene in the pathway will not result in significant phenotypic changes, and that the genes in biosynthetic pathways such as BnSOT-like1 in our study have minor effects and may be called polygenes in contrast to the reported three regulatory genes (BnHAG1s) which strongly affect GSL content in B. napus. The present study has shed light on a minor gene for a quantitative trait.