Research Article

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

Published: October 21, 2015
Genet. Mol. Res. 14 (4) : 13003-13012 DOI: 10.4238/2015.October.21.21

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 and 30% (at least >10%) for practical marker-assisted breeding.

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 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.

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