Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon

Justin N. Vaughn; Sandra E. Branham; Brian Abernathy; Amanda M. Hulse-Kemp; Adam R. Rivers; Amnon Levi; William P. Wechter

doi:10.1038/s41467-022-35621-7

Nature Communications (Dec 2022)

Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon

Justin N. Vaughn,
Sandra E. Branham,
Brian Abernathy,
Amanda M. Hulse-Kemp,
Adam R. Rivers,
Amnon Levi,
William P. Wechter

Affiliations

Justin N. Vaughn: Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of Agriculture
Sandra E. Branham: Plant and Environmental Sciences Department, Coastal Research and Education Center, Clemson University
Brian Abernathy: Department of Crop and Soil Sciences, University of Georgia
Amanda M. Hulse-Kemp: Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of Agriculture
Adam R. Rivers: Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of Agriculture
Amnon Levi: US Vegetable Laboratory, The Agricultural Research Service of U.S. Department of Agriculture
William P. Wechter: Plant and Environmental Sciences Department, Coastal Research and Education Center, Clemson University

DOI: https://doi.org/10.1038/s41467-022-35621-7
Journal volume & issue: Vol. 13, no. 1
pp. 1 – 14

Abstract

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The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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