Elucidating the patterns of pleiotropy and its biological relevance in maize.

Autor: Khaipho-Burch M; Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York., Ferebee T; Department of Computational Biology, Cornell University, Ithaca, New York., Giri A; Institute for Genomic Diversity, Cornell University, Ithaca, New York., Ramstein G; Institute for Genomic Diversity, Cornell University, Ithaca, New York.; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark., Monier B; Institute for Genomic Diversity, Cornell University, Ithaca, New York., Yi E; Institute for Genomic Diversity, Cornell University, Ithaca, New York., Romay MC; Institute for Genomic Diversity, Cornell University, Ithaca, New York., Buckler ES; Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York.; Institute for Genomic Diversity, Cornell University, Ithaca, New York.; USDA-ARS, Ithaca, New York, United States of America.
Jazyk: angličtina
Zdroj: PLoS genetics [PLoS Genet] 2023 Mar 21; Vol. 19 (3), pp. e1010664. Date of Electronic Publication: 2023 Mar 21 (Print Publication: 2023).
DOI: 10.1371/journal.pgen.1010664
Abstrakt: 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 biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using 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 assess 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.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)
Databáze: MEDLINE
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