Categorization of Quantitative Trait Loci by Their Functional Roles: QTL Analysis for Chemical Concentration in Seed Grains

Quantitative trait loci (QTL) with different bio-functional roles may occur simultaneously in QTL analysis. Categorizing these QTL by their functional roles is imperative for choosing markers suitable for marker-assisted selection and gene searching. The feasibility of the QTL categorization is discussed in the context of QTL analysis for chemical concentration in seed grains. Our simulated QTL analysis under simple, hypothetical histo-developmental and genetic models shows that, based on the concentration scores taken by conventional methods such as near-infrared transmittance spectroscopy (called score C), a gene can be detected as a QTL even though it has no role in the synthesis or storage of the objective chemical. Such QTL, called nominal QTL, will not be useful as a target of marker-assisted selection for a high chemical harvest. When QTL patterns obtained with score C are compared with those obtained with a modified score, score C x grain weight (called score D), nominal QTL can be distinguished and QTL can be categorized into two groups of functional categories, that is, QTL that control the size of tissues and QTL that control the rate of chemical synthesis. When QTL patterns are evaluated across multiple chemicals, QTL in each group can be distinguished by their functional charges.