Elucidating the patterns of pleiotropy and its biological relevance in maize
Authors: Merritt Khaipho-Burch 1; Taylor Ferebee 2; Anju Giri 3; Guillaume Ramstein 3,4; Brandon Monier 3; Emily Yi 3; M. Cinta Romay 3; Edward Buckler 1,3,5
Affiliations: 1) Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY; 2) Department of Computational Biology, Cornell University, Ithaca, NY; 3) Institute for Genomic Diversity, Cornell University, Ithaca, NY; 4) Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark; 5) USDA-ARS; Ithaca, NY
Keywords: Complex traits
Pleiotropy has been shown to have effects on traits such as flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of true biological (or horizontal) pleiotropy across all maize phenotypes is largely unknown. Here we investigated the extent to which true biological pleiotropy impacts phenotypes within maize through GWAS summary statistics reanalyzed from previously published physiological, metabolic, and expression phenotypes across the Nested Association Mapping population (US-NAM) and Goodman Association Panel. Through phenotypic saturation of 120,625 traits in maize, we obtained over 480 million significant quantitative trait nucleotides and estimated how pleiotropic each region was in the genome. We then assessed the relationship between pleiotropy and numerous biological features such as gene expression, the prevalence of open chromatin, sequence conservation, and enrichment for gene ontology terms using random forest models. We find very little relationship between pleiotropy and these variables compared to permuted pleiotropy values. Thus, we hypothesize that biological pleiotropy is not a common phenomenon in maize; however, mediated or vertical pleiotropy may be. We suggest that natural selection on large standing natural variation in maize populations will remove deleterious or large-effect variants, leaving the prevalence of biological pleiotropy relatively low. We recommend that the maize and surrounding plant science community accurately describe the types of pleiotropy under investigation and robustly test hypotheses of pleiotropy before claiming its widespread prevalence and causality.