Multiple-Interval Mapping for Quantitative Trait Loci Controlling Endosperm Traits

Abstract

Endosperm traits are trisomic inheritant and are of great economic importance because they are usually directly related to grain quality. Mapping for quantitative trait loci (QTL) underlying endosperm traits can provide an efficient way to genetically improve grain quality. As the traditional QTL mapping methods (diploid methods) are usually designed for traits under diploid control, they are not the ideal approaches to map endosperm traits because they ignore the triploid nature of endosperm. In this article, a statistical method considering the triploid nature of endosperm (triploid method) is developed on the basis of multipleinterval mapping (MIM) to map for the underlying QTL. The proposed triploid MIM method is derived to broadly use the marker information either from only the maternal plants or from both the maternal plants and their embryos in the backcross and F 2 populations for mapping endosperm traits. Due to the use of multiple intervals simultaneously to take multiple QTL into account, the triploid MIM method can provide better detection power and estimation precision, and as shown in this article it is capable of analyzing and searching for epistatic QTL directly as compared to the traditional diploid methods and current triploid methods using only one (or two) interval(s). Several important issues in endosperm trait mapping, such as the relation and differences between the diploid and triploid methods, variance components of genetic variation, and the problems if effects are present and ignored, are also addressed. Simulations are performed to further explore these issues, to investigate the relative efficiency of different experimental designs, and to evaluate the performance of the proposed and current methods in mapping endosperm traits. The MIM-based triploid method can provide a powerful tool to estimate the genetic architecture of endosperm traits and to assist the marker-assisted selection for the improvement of grain quality in crop science. The triploid MIM FORTRAN program for mapping endosperm traits is available on the worldwide web (http:/ /www.stat.sinica.edu.tw/chkao/). C EREAL grains of many crops, such as rice, wheat, grains. The genetic improvement targeting these endobarley, and corn, are major food and nutritious sperm traits can provide an efficient way to enhance resources for human, animal feeds, and industrial prodthe grain quality, and it has attracted a lot of attention ucts. To enhance the yield and quality of grains, the in plant breeding (Sadimantara et al. 1997 and Zhu 2002). Genetically, the trisomic endosperm repThe cereal grains are generally composed of diploid (emresents the next generation and has a more complex bryo) and triploid (endosperm) tissues due to double genetic mechanism than the diploid tissues. For these fertilization. During the process of double fertilization, reasons, the approach of genetic analysis to endosperm one of the two sperm cells fuses with the egg cell to traits is different from that to traits under diploid conproduce a diploi...

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