Genomic Prediction Using Canopy Coverage Image and Genotypic Information in Soybean via a Hybrid Model.

Abstract

Prediction techniques are important in plant breeding as they provide a tool for selection that is more efficient and economical than traditional phenotypic and pedigree based selection. The conventional genomic prediction models include molecular marker information to predict the phenotype. With the development of new phenomics techniques we have the opportunity to collect image data on the plants, and extend the traditional genomic prediction models where we incorporate diverse set of information collected on the plants. In our research, we developed a hybrid matrix model that incorporates molecular marker and canopy coverage information as a weighted linear combination to predict grain yield for the soybean nested association mapping (SoyNAM) panel. To obtain the testing and training sets, we clustered the individuals based on their marker and canopy information using 2 different clustering techniques, and we compared 5 different cross-validation schemes. The results showed that the predictive ability of the models was the highest when both the canopy and marker information was included, and it was the lowest when only the canopy information was included.

Code and data availability

The paper's canopy coverage and phenotypic/genotypic measurements derive from the publicly available SoyNAM population dataset hosted at SoyBase, which the authors explicitly identify as the data source for their study. No author analysis code, scripts, or trained models are mentioned with any availability statement,so