A sorghum pangenome reference improves global crop trait discovery

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops<sup>1</sup>, like that of the grain and bioenergy crop sorghum<sup>2-5</sup>, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets<sup>6</sup>. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

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Publication Details

Journal
Nature
Published
2026-03-11
DOI
https://doi.org/10.1038/s41586-026-10229-9
Citations
2
Primary Topic
Cassava research and cyanide
Type
article
Field-Weighted Citation Impact
62.68
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article

A sorghum pangenome reference improves global crop trait discovery

Bassirou Sine, Richard Elmer Boyles, Taye Tadesse Mindaye, Geoffrey P. Morris et al.
2 citations
Nature
Cassava research and cyanide
62.68
article

A sorghum pangenome reference improves global crop trait discovery

Bassirou Sine, Richard Elmer Boyles, Taye Tadesse Mindaye, Geoffrey P. Morris, Dave Flowers, Avinash Sreedasyam, Jacques M. Faye, Brian R. Rice, Melissa Williams, Carl VanGessel, Matthew E. Hudson, John E. Mullet, Scott Lee, Jayson Talag, Chaney Courtney, Delphine Luquet, David Goodstein, Santosh Deshpande, Daniel Foncéka, Peggy G. Lemaux, Erica Agnew, Cyril Diatta, Kristen Johnson, Todd C. Mockler, Rachel Walstead, John J Spiekerman, Stephen Kresovich, Robert G. Lowery, Marie De Gracia Coquerel, Andrea L. Eveland, Jacqueline M. Chaparro, S. A. Brady, Trevor W. Rife, Avril M. Harder, Fanna Maina, Jesse R. Lasky, Katherine Johnson, Todd P. Michael, Jenell Webber, Boubacar Gano, Christopher Plott, Mamoutou Kouressy, McKay John K., Sujan Mamidi, Niaba Témé, Chloee M. McLaughlin, Philip Ozersky, Jessica E. Prenni, Jana Kholová, Vincent Vadez, Grégory Beurier, Dorota Kawa, Gaël Pressoir, Ivan Baxter, Joanna L. Rifkin, Adam Healey, Victoria Bunting, Nadia Shakoor, Nathaniel Eck, Joseph Sékou B. Dembele, Alain Audebert, Jean-François Rami, Jocelyn Saxton, Clara Cruet-Burgos, John T. Lovell, Jianan Wang, Kerrie Barry, Jane Grimwood, Mitchell R. Tuinstra, Yuxing Xu, Jerry W. Jenkins, John P. Vogel, Lori Beth Boston, Shengqiang Shu, Jeremy Schmutz
article en
2 citations

Abstract

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops<sup>1</sup>, like that of the grain and bioenergy crop sorghum<sup>2-5</sup>, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets<sup>6</sup>. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

Nature
University of Nebraska–Lincoln (US), University of Southern California (US), Salk Institute for Biological Studies (US), Pennsylvania State University (US), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR), Howard Hughes Medical Institute (US), University of Arizona (US), Lawrence Berkeley National Laboratory (US), Botanic Gardens Conservation International (GB), University of Illinois Urbana-Champaign (US), Utrecht University (NL), Joint Genome Institute (US), Université de Montpellier (FR), Hainan University (CN), Purdue University West Lafayette (US), Donald Danforth Plant Science Center (US), Center for Plant Conservation (US), University of California San Diego (US), 490 BioTech (United States) (US), University of Haiti (HT), Institut National de la Recherche Agronomique du Niger (NE), Institut d'Économie Rurale (ML), Innovative Genomics Institute (US), Université des Sciences, des Techniques et des Technologies de Bamako (ML), Diversité, adaptation et développement des plantes (FR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (FR), Institut Agro Montpelier (FR), HudsonAlpha Institute for Biotechnology (US), Institut Sénégalais de Recherches Agricoles (SN), International Crops Research Institute for the Semi-Arid Tropics (IN), Institut de Recherche pour le Développement (FR), Ethiopian Institute of Agricultural Research (ET), Clemson University (US), University of California, Davis (US), Texas A&M University (US), Colorado State University (US), University of California, Berkeley (US)
Zero hunger
Openalex Percentile: Top 0%
Cassava research and cyanide
62.68
DOIOpen Access PDFOpenAlex
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