An Efficient Hierarchical Generalized Linear Mixed Model for Mapping QTL of Ordinal Traits in Crop Cultivars

<div><p>Many important phenotypic traits in plants are ordinal. However, relatively little is known about the methodologies for ordinal trait association studies. In this study, we proposed a hierarchical generalized linear mixed model for mapping quantitative trait locus (QTL) of ordinal traits in crop cultivars. In this model, all the main-effect QTL and QTL-by-environment interaction were treated as random, while population mean, environmental effect and population structure were fixed. In the estimation of parameters, the pseudo data normal approximation of likelihood function and empirical Bayes approach were adopted. A series of Monte Carlo simulation experiments were performed to confirm the reliability of new method. The result showed that new method works well with satisfactory statistical power and precision. The new method was also adopted to dissect the genetic basis of soybean alkaline-salt tolerance in 257 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 6 main-effect QTL and 3 QTL-by-environment interactions were identified.</p> </div

Effect of the number of founders on association mapping for ordinal traits.

<p>Effect of the number of founders on association mapping for ordinal traits.</p

Association mapping for ordinal alkaline-salt tolerance in 257 soybean cultivars.

<p>MQ: main-effect QTL; QE: QTL-by-environment interaction. ^*similar results for continuous ATI and STI were derived from <b>Zhang</b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059541#pone.0059541-Zhang4" target="_blank">[<b>33</b>]</a> by enriched compression mixed linear model (ECMLM).</p><p>and epistatic association mapping (EAM) approaches. ^†Year, i.e., 2009 and 2010. ^$Probability of null hypothesis in the test of independence between the tolerance and marker.</p

Effect of sample size on association mapping for ordinal traits.

<p>Effect of sample size on association mapping for ordinal traits.</p

Frequency distribution for soybean alkaline-salt tolerance grade in 2009 (left) and 2010 (right).

<p>Frequency distribution for soybean alkaline-salt tolerance grade in 2009 (left) and 2010 (right).</p

Prediction for potential candidate genes that are homologous to alkaline-salt tolerance genes in <i>Arabidopsis thaliana.</i>

<p>Prediction for potential candidate genes that are homologous to alkaline-salt tolerance genes in <i>Arabidopsis thaliana.</i></p

Simulated parameters in all simulated experiments (3 alleles for marker and QTL, and 3 chromosomes).

<p>Simulated parameters in all simulated experiments (3 alleles for marker and QTL, and 3 chromosomes).</p

Effect of phenotypic distribution on association mapping for ordinal traits.

<p>Effect of phenotypic distribution on association mapping for ordinal traits.</p

Comparison of new method with single-QTL-based method and Chi-squared test.

<p>Comparison of new method with single-QTL-based method and Chi-squared test.</p

Effect of the number of categories on association mapping for ordinal traits.

<p>Effect of the number of categories on association mapping for ordinal traits.</p