Statistical approaches in QTL mapping and molecular breeding for complex traits

Most of the important agronomic traits in crops, such as yield and quality, are complex traits affected by multiple genes with gene × gene interaction as well as gene × environment interaction. Understanding the genetic architecture of complex traits is a long-term task for quantitative geneticists and plant breeders who wish to design efficient breeding programs. Conventionally, the genetic properties of traits can be revealed by partitioning the total variation into variation components caused by specific genetic effects. With recent advances in molecular genotyping and high-throughput technology, the unraveling of the genetic architecture of complex traits by analyzing quantitative trait locus (QTL) has become possible. The improvement of complex traits has also been achieved by pyramiding individual QTL. In this review, we describe some statistical methods for QTL mapping that can be used to analyze QTL × QTL interaction and QTL × environment interaction, and discuss their applications in crop breeding for complex traits.