Long-term climate change and periodic environmental extremes threaten food and fuel security¹and global crop productivity^2–4. 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.

Switchgrass (Panicum virgatum) has been identified as a promising cellulosic biofuel crop in the United States. Construction of a genetic linkage map is fundamental for switchgrass molecular breeding and the elucidation of its genetic mechanisms for economically important traits. In this study, a novel population consisting of 139 selfed progeny of a northern lowland genotype, NL 94 LYE 16X13, was used to construct a linkage map. A total of 2493 simple sequence repeat markers were screened for polymorphism. Of 506 polymorphic loci, 80.8% showed a goodness-of-fit of 1:2:1 segregation ratio. Among 469 linked loci on the framework map, 241 coupling vs. 228 repulsion phase linkages were detected that conformed to a 1:1 ratio, confirming disomic inheritance. A total of 499 loci were mapped to 18 linkage groups (LG), of which the cumulative length was 2085.2 cM, with an average marker interval of 4.2 cM. Nine homeologous LG pairs were identified based on multi-allele markers and comparative genomic analysis. Two clusters of segregation-distorted loci were identified on LG 5b and 9b, respectively. Comparative analysis indicated a one-to-one relationship between nine switchgrass homeologous groups and nine foxtail millet (Setaria italica) chromosomes, suggesting strong homology between the two species. The linkage map derived from selfing a heterozygous parent, instead of two separate maps usually constructed for a cross-fertilized species, provides a new genetic framework to facilitate genomics research, quantitative trait locus (QTL) mapping, and marker-assisted breeding.

Construction economics of plant roots exhibit predictable relationships with root growth, death, and nutrient uptake strategies. Plant taxa with inexpensively constructed roots tend to more precisely explore nutrient hotspots than do those with costly constructed roots but at the price of more frequent tissue turnover. This trade-off underlies an acquisitive to conservative continuum in resource investment, described as the “root economics spectrum (RES).” Yet the adaptive role and genetic basis of RES remain largely unclear. Different ecotypes of switchgrass (Panicum virgatum) display root features exemplifying the RES, with costly constructed roots in southern lowland and inexpensively constructed roots in northern upland ecotypes. We used an outbred genetic mapping population derived from lowland and upland switchgrass ecotypes to examine the genetic architecture of the RES. We found that absorptive roots (distal first and second orders) were often “deciduous” in winter. The percentage of overwintering absorptive roots was decreased by northern upland alleles compared with southern lowland alleles, suggesting a locally-adapted conservative strategy in warmer and acquisitive strategy in colder regions. Relative turnover of absorptive roots was genetically negatively correlated with their biomass investment per unit root length, suggesting that the key trade-off in framing RES is genetically facilitated. We also detected strong genetic correlations among root morphology, root productivity, and shoot size. Overall, our results reveal the genetic architecture of multiple traits that likely impacts the evolution of RES and plant aboveground–belowground organization. In practice, we provide genetic evidence that increasing switchgrass yield for bioenergy does not directly conflict with enhancing its root-derived carbon sequestration. Significance Plants have evolved diverse root form and function across the Earth’s environment, yet only certain types of trait combinations have proved evolutionarily viable. Using a genetic mapping population of the native perennial switchgrass, our study demonstrates multiple genetic linkages among root morphology, growth, and turnover. Switching alleles derived from southern-origin ecotypes to alleles from northern-origin ecotypes increases root turnover but reduces tissue investment in root length construction. The genetic trade-off between construction and turnover likely facilitates the local adaptation of root strategy along the warm to cold climatic gradients of the species range. In practice, our study provides the genetic evidence that increasing switchgrass yield for bioenergy does not directly conflict with enhancing its root-derived carbon sequestration.

Common bermudagrass has been widely used as a major warm‐season turf, forage, and soil stabilization grass in the southern United States. However, codominant marker development, linkage, and quantitative trait loci (QTL) mapping resources are limited in the important taxon. Accordingly, the objectives of this study were to develop simple sequence repeat (SSR) markers, construct a genetic map, and identify genomic regions associated with establishment rate. Five genomic SSR libraries were constructed, sequenced, and used in the development of 1003 validated SSR primer pairs (PPs). A linkage map was constructed using a first‐generation selfed population derived from a genotype A12359 (2 n = 4 x = 36). A total of 249 polymorphic SSR PPs were mapped to 18 linkage groups (LGs). The total length of the map is 1094.7 cM, with an average marker interval of 4.3 cM. Ninety‐eight out of 252 mapped loci (39%) were found to be distorted from the Mendelian 1:2:1 segregation ratio. Among the other 154 nondistorted loci, 88 coupling vs. 66 repulsion linkage phases were observed to confirm the allopolyploid origin of the parent. Ground coverage (GCR) phenotypic data in the establishment stage were collected in two replicated field trials. Quantitative trait loci mapping identified five genomic regions significantly related to the trait. The findings of this study provide valuable genetic tools and resources for genomic research, genetic improvement, and breeding new cultivars in the species.