Designing and modeling high-throughput phenotyping data in quantitative genetics

Quantitative genetics aims to bridge the genome to phenome gap. The advent of high-throughput genotyping technologies has accelerated the progress of genome to phenome mapping, but a challenge remains in phenotyping. Various high-throughput phenotyping (HTP) platforms have been developed recently to obtain economically important phenotypes in an automated fashion with less human labor and reduced costs. However, the effective way of designing HTP has not been investigated thoroughly. In addition, high-dimensional HTP data bring up a big challenge for statistical analysis by increasing computational demands. A new strategy for modeling high-dimensional HTP data and elucidating the interrelationships among these phenotypes are needed. Previous studies used pedigree-based connectetdness statistics to study the design of phenotyping. The availability of genetic markers provides a new opportunity to evaluate connectedness based on genomic data, which can serve as a means to design HTP. This dissertation first discusses the utility of connectedness spanning in three studies. In the first study, I introduced genomic connectedness and compared it with traditional pedigree-based connectedness. The relationship between genomic connectedness and prediction accuracy based on cross-validation was investigated in the second study. The third study introduced a user-friendly connectedness R package, which provides a suite of functions to evaluate the extent of connectedness. In the last study, I proposed a new statistical approach to model high-dimensional HTP data by leveraging the combination of confirmatory factor analysis and Bayesian network. Collectively, the results from the first three studies suggested the potential usefulness of applying genomic connectedness to design HTP. The statistical approach I introduced in the last study provides a new avenue to model high-dimensional HTP data holistically to further help us understand the interrelationships among phenotypes derived from HTP.