Improving power of genome-wide association studies via transforming ordinal phenotypes into continuous phenotypes

Abstract

Introduction: Ordinal traits are important complex traits in crops, while genome-wide association study (GWAS) is a widely-used method in their gene mining. Presently, GWAS of continuous quantitative traits (C-GWAS) and single-locus association analysis method of ordinal traits are the main methods used for ordinal traits. However, the detection power of these two methods is low.

Methods: To address this issue, we proposed a new method, named MTOTC, in which hierarchical data of ordinal traits are transformed into continuous phenotypic data (CPData).

Results: Then, FASTmrMLM, one C-GWAS method, was used to conduct GWAS for CPData. The results from the simulation studies showed that, MTOTC+FASTmrMLM for ordinal traits was better than the classical methods when there were four and fewer hierarchical levels. In addition, when MTOTC was combined with FASTmrEMMA, mrMLM, ISIS EM-BLASSO, pLARmEB, and pKWmEB, relatively high power and low false positive rate in QTN detection were observed as well. Subsequently, MTOTC was applied to analyze the hierarchical data of soybean salt-alkali tolerance. It was revealed that more significant QTNs were detected when MTOTC was combined with any of the above six C-GWAs.

Discussion: Accordingly, the new method increases the choices of the GWAS methods for ordinal traits and helps to mine the genes for ordinal traits in resource populations.

Keywords: genome-wide association study; hierarchical data; ordinal trait; salt-alkali tolerance; soybean.