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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #396633

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: Elucidating the patterns of pleiotropy and its biological relevance in maize

item KHAIPHO-BURCH, MERRITT - Cornell University - New York
item FEREBEE, TAYLOR - Cornell University - New York
item GIRI, ANJU - Syngenta
item RAMSTEIN, GUILLAUME - Aarhuis University
item MONIER, BRANDON - Cornell University - New York
item YI, EMILY - Cornell University - New York
item ROMAY, MARIA - Cornell University - New York
item Buckler, Edward - Ed

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 7/21/2022
Publication Date: 7/21/2022
Citation: Khaipho-Burch, M., Ferebee, T., Giri, A., Ramstein, G., Monier, B., Yi, E., Romay, M.C., Buckler IV, E.S. 2022. Elucidating the patterns of pleiotropy and its biological relevance in maize. bioRxiv.

Interpretive Summary: In this paper we investigate the patterns and prevalence of pleiotropy - the genetic phenomenon where a single locus impacts two or more seemingly unrelated traits. Past studies on the prevalence of pleiotropy in maize have focused on small subsets of related traits and noted its broad implications on the genetic architecture of crop plants. Here, we discuss the limited patterns of pleiotropy and describe the mechanisms that control this genetic phenomenon in maize. Within this study we accomplished: 1. The curation and association of 120,597 previously published field, metabolite, and expression traits in two large maize community panels and resulting 480+ million significant quantitative trait nucleotides that will be publicly available to the community. 2. The delivery of the largest and most comprehensive descriptions of the patterns and prevalence of pleiotropy across multiple trait types. We find that pleiotropy is limited to a small number of traits and regions within the maize genome. 3. The demonstration that pleiotropic loci do not show a strong relationship with key biological features that control and regulate plant genome architecture.

Technical Abstract: Pleiotropy - when a single gene controls two or more seemingly unrelated traits - has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of true biological pleiotropy across all maize phenotypes is largely unknown. Here we investigate the extent to which biological pleiotropy impacts phenotypes within maize through GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56-32.3% of intervals show some degree of pleiotropy. We then assessed the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide- and large-effect variants, leaving the prevalence of detectable pleiotropy relatively low.