A sorghum pangenome reference improves global crop trait discovery
Geoffrey P. Morris, Avril M. Harder, Adam Healey, Chloee M. McLaughlin, Joanna L. Rifkin, Clara Cruet-Burgos, Jerry W. Jenkins, Shengqiang Shu, John J Spiekerman, Carl VanGessel, Erica Agnew, Alain Audebert, Kerrie Barry, Ivan Baxter, Grégory Beurier, Lori Beth Boston, Richard Boyles, S. A. Brady, Victoria Bunting, Jacqueline M. Chaparro, Chaney Courtney, Joseph Sékou B. Dembele, Santosh Deshpande, Cyril Diatta, Nathaniel Eck, Andrea L. Eveland, Jacques M. Faye, Dave Flowers, Daniel Foncéka, Boubacar Gano, Marie De Gracia Coquerel, David Goodstein, Jane Grimwood, Matthew E. Hudson, Jana Kholová, Katherine Johnson, Kristen K. Johnson, Dorota Kawa, Mamoutou Kouressy, Stephen Kresovich, Scott Lee, Peggy G. Lemaux, Robert G. Lowery, Delphine Luquet, Fanna Maina, Sujan Mamidi, McKay John K., Todd P. Michael, Taye Tadesse Mindaye, John E. Mullet, Philip Ozersky, Christopher Plott, Jessica E. Prenni, Gaël Pressoir, Jean-François Rami, Trevor W. Rife, Jocelyn Saxton, Bassirou Sine, Avinash Sreedasyam, Jayson Talag, Niaba Témé, Mitchell R. Tuinstra, Vincent Vadez, John P. Vogel, Rachel Walstead, Jianan Wang, Jenell Webber, Melissa Williams, Yuxing Xu, Todd C. Mockler, Jesse R. Lasky, Brian R. Rice, Jeremy Schmutz, Nadia Shakoor, John T. Lovell
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 sorghum2–5, 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. A pangenome reference for the phenotypically diverse crop sorghum aims to help accelerate future efforts to breed crops that are better adapted to changing environments.