Influence of various quantitative trait loci (QTL) mapping methods on the mapping accuracy under varying heritability levels

Abstract

ABSTRACT. The study of quantitative trait effects is of great significance for molecular marker-assisted breeding. The accuracy of quantitative trait loci (QTL) mapping is the key factor affecting marker-assisted breeding, and is extremely significant. The effect of different heritability rates (10, 30, 50, 70, and 90%) on the accuracy of QTL mapping of five recombinant inbred lines (RILs) were analyzed via computer simulation. RILs display additive and epistatic genetic effects. The QTLs were analyzed using four different mapping procedures: multiple QTL model (MQM), composite interval mapping (CIM), multiple interval mapping (MIMR), and inclusive composite interval mapping (ICIM). The results revealed an increase in the QTL mapping accuracy and QTL detection power, and a decrease in the QTL interval range with the increase in heritability; conversely, an irregular number of false positive QTLs were generated. CIM and MQM only screen the additive and dominant effects; MIMR and ICIM screen the additive, dominant, and epistatic effects. The highest QTL detection power obtained using MQM and CIM was only 75%, while MIMR and ICIM showed a detection power of 100%. At heritability rates of more than 50 and less than 10%, the detection powers of the MIMR and ICIM procedures were >95 13004 C.F. Su et al.©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 13003-13012 (2015) and <35%, respectively. QTL mapping has no significance at heritability rates <10%. The results of this study suggest that QTL mapping has significance at a heritability rate >30% (at least >10%) for practical marker-assisted breeding.

Factors influencing QTL mapping accuracy under complicated genetic models by computer simulation

“…Although heritability has a large influence on QTL mapping (Su et al, 2015), heritability determined by the specific quantitative trait itself cannot be altered; thus, researchers cannot increase QTL mapping accuracy by increasing heritability. The marker density of the genetic linkage map is currently thought to be one of most important factors affecting QTL mapping accuracy.…”