Experimental Designs and Statistical Methods for Mapping Quantitative Trait Loci Underlying Triploid Endosperm Traits without Maternal Genetic Variation.

Many endosperm traits are related to grain quality in cereal crops. Endosperm traits are mainly controlled by the endosperm genome but may be affected by the maternal genome. Studies have shown that maternal genotypic variation could greatly influence the estimation of the direct effects of quantitative trait loci (QTLs) underlying endosperm traits. In this paper, we propose methods of interval mapping of endosperm QTLs using seeds of F₂ or BC₁ (an equal mixture of F₁ × P₁ and F₁ × P₂ with F₁ as the female parent) derived from a cross between 2 pure lines (P₁ × P₂). The most significant advantage of our experimental designs is that the maternal effects do not contribute to the genetic variation of endosperm traits and therefore the direct effects of endosperm QTLs can be estimated without the influence of maternal effects. In addition, the experimental designs can greatly reduce environmental variation because a few F₁ plants grown in a small block of field will produce sufficient F₂ or BC₁ seeds for endosperm QTL analysis. Simulation studies show that the methods can efficiently detect endosperm QTLs and unbiasedly estimate their positions and effects. The BC₁ design is better than the F₂ design. [ABSTRACT FROM AUTHOR]