Abstract
Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2–4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6—knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.
Highlights
Switchgrass (P. virgatum) is both a promising biofuel crop and an important component of the North American tallgrass prairie
Our deep PacBio long-read sequencing coupled with deep short-read polishing and bacterial artificial chromosome (BAC) clone validation produced a highly contiguous ‘v5’ AP13 genome assembly (Extended Data Fig. 1; data are available from Phytozome at https:// phytozome-next.jgi.doe.gov)
The genome assembly was co-linear with three sources of genetic information, despite being assembled independently from all three: the assembly of a close diploid relative (Panicum hallii), the marker order of a pseudo-F2 genetic map and the gene order of the alternative subgenome (Fig. 1a, Extended Data Fig. 1, Supplementary Data 2)
Summary
Relatedness and provides breeders with genetic diversity to target for switchgrass improvement in local environments. This overlap was especially strong within the two northern subpopulations (Midwest, odds = 11.5× and P < 1 × 10−15; Atlantic, odds = 17.8× and P < 1 × 10−15) (Fig. 3c), where we expected to see the strongest effect of selection on survival during cold winters. Consistent with adaptive roles for genomic introgressions in other systems[31,37], these findings suggest that introgression of putatively northern-adapted alleles from the Midwest into the Atlantic subpopulation could have facilitated the post-glacial colonization by switchgrass of colder habitats in the northeastern coastal region of the USA To test this hypothesis, we conducted redundancy analyses to relate the presence of introgression blocks with climatic, geographical and phenotypic factors. The N subgenome has accumulated heritable variation[49] that future breeding regimes can target to shape natural switchgrass populations and improve biofuel yield
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