A sorghum pangenome reference improves global crop trait discovery

Morris, G P and Harder, A M and Healey, A L and McLaughlin, C M and Rifkin, J L and Cruet-Burgos, C and Jenkins, J W and Shu, S and Spiekerman, J J and VanGessel, C J and Agnew, E and Audebert, A and Barry, K and Baxter, I and Beurier, G and Boston, L B and Boyles, R E and Brady, S M and Bunting, V and Chaparro, J M and Courtney, C and Dembele, J S B and Deshpande, S P and Diatta, C and Eck, N and Eveland, A L and Faye, J M and Flowers, D and Fonceka, D and Gano, B and Coquerel, M G and Goodstein, D and Grimwood, J and Hudson, M E and Kholova, J and Johnson, K and Johnson, K K and Kawa, D and Kouressy, M and Kresovich, S and Lee, S and Lemaux, P G and Lowery, R and Luquet, D and Maina, F and Mamidi, S and McKay, J K and Michael, T P and Mindaye, T T and Mullet, J and Ozersky, P and Plott, C and Prenni, J E and Pressoir, G and Rami, J F and Rife, T W and Saxton, J and Sine, B and Sreedasyam, A and Talag, J and Teme, N and Tuinstra, M R and Vadez, V and Vogel, J P and Walstead, R and Wang, J and Webber, J and Williams, M and Xu, Y and Mockler, T C and Lasky, J R and Rice, B R and Schmutz, J and Shakoor, N and Lovell, J T (2026) A sorghum pangenome reference improves global crop trait discovery. Nature. pp. 1-21. ISSN 0028-0836

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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 crops1, like that of the grain and bioenergy crop sorghum2,3,4,5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets6. 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.

Item Type:	Article
Divisions:	Global Research Program - Accelerated Crop Improvement
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Agricultural genetics, Biofuels, Evolutionary genetics, Genome informatics, Plant breeding
Subjects:	Others > Biofuels Others > Plant Breeding Mandate crops > Sorghum Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	29 Apr 2026 08:34
Last Modified:	29 Apr 2026 08:34
URI:	http://oar.icrisat.org/id/eprint/13612
Official URL:	https://www.nature.com/articles/s41586-026-10229-9
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	The work (proposals: 503014, 504730, 2015; Award DOIs: 10.46936/10. 25585/60001093, 10.46936/10.25585/60001224, 10.46936/10.25585/60001015) conducted by the US DOE Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US DOE operated under contract number DE-AC02-05CH11231. This work was also supported by Gates Foundation projects: ‘Green Evolution—Accelerating Dryland Cereals Improvement for Africa’ (INV-053669), the ‘Sorghum Genomics Toolbox: TERRA Partnership (OPP1129603)’, and ‘Mining useful alleles for climate change adaptation from CGIAR gene banks’. The information presented herein was funded in part by the Advanced Research Projects Agency-Energy (ARPA-E), US Department of Energy, under Award Numbers DE-AR0000594. S.M.B., D.K. and T.T. acknowledge support from NIOO via grant OPP1082853 ‘RSM Systems Biology for Sorghum’. J.T.L. was supported by the Center for Bioenergy Innovation (US DOE, Office of Science, Biological and Environmental Research under contract number ERKP886). P.G.L. was supported by the US Cooperative Extension Service through the Division of Agriculture and Natural Resources of the University of California and DOE Grant DE-SC0014081. J.E.M. was supported by the Great Lakes Bioenergy Research Center (DOE BER Office of Science Grant/Award: DE-SC0018409). M.E.H. is supported by the DOE Center for Advanced Bioenergy and Bioproducts Innovation (US DOE, Office of Science, Biological and Environmental Research Program under Award Number DE-SC0018420). This study is made possible by the support of the American People provided to the Feed the Future Innovation Lab for Collaborative Research on Sorghum and Millet through the United States Agency for International Development (USAID) under associate award no. AID-OAAA13-00047, ‘Feed the Future Innovation Lab for Genomics-Assisted Sorghum Breeding’ and ‘Feed the Future Innovation Lab for Crop Improvement’. The contents are the sole responsibility of the authors and do not necessarily reflect the views of USAID or the US Government. We dedicate this work to the memory of Todd C. Mockler, a founding contributor to the sorghum pangenome effort. We honour his vision by advancing this work and building on the groundwork he helped establish. His loss is felt deeply, and his legacy lives on through the data, tools and collaborations he inspired.
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