Exploring Switchgrass Genetic Diversity with Multiple Reference Genomes
Jeremy Schmutz1,2* (firstname.lastname@example.org), John T. Lovell1,2, Jerry Jenkins1, Shengqiang Shu2, David Goodstein2, Jane Grimwood1, and Thomas E. Juenger3
1HudsonAlpha Institute for Biotechnology; 2Joint Genome Institute; and 3University of Texas–Austin
Overall, researchers are striving to improve bioenergy feedstock production by understanding the genetic basis of plant-environment interactions. This goal includes testing for climate adaptation, modeling beneficial and stressful biotic interactions, and exploring the mechanisms of abiotic stress responses. During their work (Lowry et al. 2019; Lovell et al. 2021; Napier et al. 2022), researchers discovered a massive amount of physiological and molecular variation in switchgrass. While this diversity is the raw material that allows breeders to improve feedstock production, making use of this variation is very challenging—the immense DNA differences between some switchgrass genotypes means that traditional methods to explore genetic diversity simply do not work. Under the work presented here, researchers are developing multiple genome resources that span this diversity to provide the foundation for molecular characterization of switchgrass biomass production, stress responses and biotic interactions.
A single haploid reference genome gives breeders the resources to connect alleles to traits; a significant step towards accelerating crop improvement. However, breeding programs often leverage highly diverged germplasm, which contain large-scale variants that are not readily identified by a single reference genome. For example, in switchgrass, the fast-growing southern lowland AP13 genotype (which serves as the reference genome; Lovell et al. 2021) is ~1 million years diverged from the cold-tolerant northern upland gene pool. To assist breeding and gene discovery efforts, researchers have developed 16 total reference genome haplotypes from eight outbred heterozygous genotypes that span the genetic diversity of switchgrass, including a new annotated, haplotype resolved AP13. These fully de novo chromosome-scale genomes include three northern uplands, three southern lowlands, and two spanning the latitudinal range of the newly discovered coastal ecotype. Here, researchers present the progress on these genomes and an analysis of structural variation, including the presence of a putative minor chromosome that appears to segregate in coastal switchgrass populations. These variants can serve as a priori targets for ongoing molecular breeding efforts to make switchgrass a more economically and ecologically sustainable biofuel feedstock.
Lowry, D. B., et al. 2019. “QTL x Environment Interactions Underlie Adaptive Divergence in Switchgrass Across a Large Latitudinal Gradient.” Proceedings of the National Academy of Sciences, U. S. 116(26).
Lovell, J. T., et al. 2021. “Genomic Mechanisms of Climate Adaptation in Polyploid Bioenergy Switchgrass.” Nature 590, 438– DOI: https://doi.org/10.1038/s41586-020-03127-1.
Napier, J., et al. 2022. “A Generalist-Specialist Tradeoff Between Switchgrass Cytotypes Impacts Climate Adaptation and the Geographic Range.” Proceedings of the National Academy of Sciences, U.S. 119(15), e2118879119. DOI: https://doi.org/10.1073/pnas.2118879119.
This research was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0021126. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No DE-AC02-05CH1123.