Functional principal component based time-series genome-wide association in sorghum

Abstract

The phenotypes of plants develop over time and change in response to the environment. New engineering and computer vision technologies track phenotypic change over time. Identifying genetic loci regulating differences in the pattern of phenotypic change remains challenging. In this study we used functional principal component analysis (FPCA) to achieve this aim. Time-series phenotype data was collected from a sorghum diversity panel using a number of technologies including RGB and hyperspectral imaging. Imaging lasted for thirty-seven days centered on reproductive transition. A new higher density SNP set was generated for the same population. Several genes known to controlling trait variation in sorghum have been cloned and characterized. These genes were not confidently identified in genome-wide association analyses at single time points. However, FPCA successfully identified the same known and characterized genes. FPCA analyses partitioned the role these genes play in controlling phenotype. Partitioning was consistent with the known molecular function of the individual cloned genes. FPCA-based genome-wide association studies can enable robust time-series mapping analyses in a wide range of contexts. Time-series analysis can increase the accuracy and power of quantitative genetic analyses.

Plant phenotyping relevance

時系列画像から得た植物表現型をFPCAで解析し、表現型変化のパターンを定量化して遺伝子座同定に用いる計算手法が研究の中心である。

Code and data availability

The supplied blocks describe time-series phenotyping (RGB/hyperspectral imaging, FPCA-based GWAS) of a sorghum diversity panel, but contain no data or code availability statement, no public repository deposit, and no author-provided URL for phenotype datasets, images, analysis code, or models. Only a supplementary file

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