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.

Switchgrass (Panicum virgatum L.) is a widely adapted warm‐season perennial that has potential as a bioenergy feedstock. The objectives of this study were to estimate the effect of harvest date on switchgrass cultivars at two locations in the north central USA and to determine the relative importance of cultivar × environment interactions for agronomic and biofuel traits of switchgrass. Six switchgrass cultivars were grown in southern Wisconsin and eastern South Dakota for 4 yr and harvested each year at three harvest dates (August, September, and October). Cultivars differed widely in biomass yield, but interacted with all environmental factors. Biomass yield did not respond consistently to harvest date, varying with cultivar, location, and year. Despite these interactions, cultivar rankings for biomass yield was consistent across harvest dates and years, but not locations. There was some preferential adaptation to either Wisconsin or South Dakota, related to longitude of the original germplasm collection site, also reflected by ground cover data. Reduced stands and biomass yields for the August harvest date in later years suggested that harvests delayed to late summer or early autumn may be beneficial in the long term. Mean dry matter, forage fiber, and lignin concentrations also varied among cultivars, consistently across locations and years. These three traits all increased with later harvest consistently across locations and years, but inconsistently among cultivars. It should be possible, through selection and breeding, to develop switchgrass germplasm with increased fiber and decreased lignin and ash, increasing the availability of fermentable sugars and decreasing the unfermentable and/or incombustible residues.

Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatumL.), an emerging biofuel crop and dominant tallgrass species. We conducted quantitative trait locus (QTL) mapping across 10 sites, ranging from Texas to South Dakota. This analysis revealed that beneficial biomass (fitness) QTL generally incur minimal costs when transplanted to other field sites distributed over a large climatic gradient over the 2 y of our study. Therefore, locally advantageous alleles could potentially be combined across multiple loci through breeding to create high-yielding regionally adapted cultivars.

Prairie cordgrass (Spartina pectinata Link.) is tall, rhizomatous, and native to marshes, drainage ways, and moist prairies in North America. Our objectives were to determine genetic variation among cordgrass populations for biomass production, to describe the distribution of biomass among phytomers and between leaf and stem components of cordgrass, to compare biomass production and composition of cordgrass to switchgrass (Panicum virgatum L.), and to determine heritability for biomass production in switchgrass. Seven populations of cordgrass and ‘Cave‐In‐Rock’, ‘Summer’, and ‘Sunburst’ switchgrass were harvested in October in 2001 through 2004. Mean biomass production across years ranged from 5.1 to 7. 9 Mg ha−1 among cordgrass populations. Yields of cordgrass (6.0 Mg ha−1) were similar to Cave‐In‐Rock (6.8 Mg ha−1) for the first two years. However production in the fourth year was greater for cordgrass (6.8 Mg ha−1) than Cave‐In‐Rock (2.0 Mg ha−1). Two cordgrass populations produced more biomass (9.3 Mg ha−1) than Summer and Sunburst (4.8 Mg ha−1) in the fourth year. Leaf comprised 70% of the biomass of cordgrass, and differences occurred among phytomers for leaf and internode traits. Cellulose and hemicellulose concentrations were similar for cordgrass and switchgrass, but cordgrass had higher levels of total N and ash. Narrow‐sense heritability estimates for biomass production in Summer and Sunburst switchgrass were 0.6. Biomass production of native warm‐season grasses intended for biofuel purposes in the northern Great Plains may be enhanced by selecting among populations of cordgrass and among families within cultivars of switchgrass.

Silphium perfoliatum L. (cup plant, silphie) and S. integrifolium Michx. (rosinweed, silflower) are in the same subfamily and tribe as sunflower (Helianthus annuus L.). Silphium perfoliatum has been grown in many countries as a forage or bioenergy crop with forage quality approaching that of alfalfa (Medicago sativa L.) and biomass yield close to maize (Zea mays L.) in some environments. Silphium integrifolium has large seeds with taste and oil quality similar to traditional oilseed sunflower. Silphium species are all long‐lived, diploid perennials. Crops from this genus could improve the yield stability, soil, and biodiversity of agricultural landscapes because, in their wild state, they are deep rooted and support a wide diversity of pollinators. In contrast with premodern domestication, de novo domestication should be intentional and scientific. We have the luxury and obligation at this moment in history to expand the domestication ideotype from food and energy production to include (i) crop‐driven ecosystem services important for sustainability, (ii) genetic diversity to enable breeding progress for centuries, (iii) natural adaptations and microbiome associations conferring resource use efficiency and stress tolerance, and (iv) improving domestication theory itself by monitoring genetic and ecophysiological changes from predomestication baselines. Achieving these goals rapidly will require the use of next‐generation sequencing for marker development and an international, interdisciplinary team committed to collaboration and strategic planning.

duction of a bioenergy crop, such as switchgrass (De La Torre Ugarte et al., 2003). Switchgrass (Panicum virgatum L.) has potential as feedstock forProper management of genetically diverse cultivars a cellulose-based biofuels industry in temperate steppe regions of the northern Great Plains. Therefore, our objectives were to determine:for sustainable biomass production has recently been (i) patterns of biomass accumulation and optimum harvest times for described for various regions of North America that an early maturing cultivar, Dacotah (origin 46؇ N, 100؇ W), and a receive average annual precipitation in excess of 500 later maturing cultivar, Cave-In-Rock (origin 37؇ N, 88؇ W), in central mm. In Iowa and Nebraska, optimum biomass yields South Dakota (44؇ N, 100؇ W) and (ii) if variation in patterns of for Cave-In-Rock switchgrass were obtained when harbiomass accumulation were associated with variation in patterns of vested at the stage of panicles fully emerged through precipitation. Dacotah and Cave-In-Rock were no-till planted near postanthesis and fertilized with 120 kg N ha Ϫ1 (Vogel Pierre, SD, on 6 Dec. 1999. Harvest dates were once per year during

Development of switchgrass (Panicum virgatum L.) as a dedicated biomass crop for conversion to energy requires substantial increases in biomass yield. Most efforts to breed for increased biomass yield are based on some form of indirect selection. The objective of this paper is to evaluate and compare the expected efficiency of several indirect measures of breeding value for improving sward-plot biomass yield of switchgrass. Sward-plot biomass yield, row-plot biomass, and spaced-plant biomass were measured on 144 half-sib families or their maternal parents from the WS4U-C2 breeding population of upland switchgrass. Heading date was also scored on row plots and anthesis date was scored on spaced plants. Use of any of these indirect selection criteria was expected to be less efficient than direct selection for biomass yield measured on sward plots, when expressed as genetic gain per year. Combining any of these indirect selection criteria with half-sib family selection for biomass yield resulted in increases in efficiency of 14 to 36%, but this could only be achieved at a very large cost of measuring phenotype on literally thousands of plants that would eventually have no chance of being selected because they were derived from inferior families. Genomic prediction methods offered the best solution to increase breeding efficiency by reducing average cycle time, increasing selection intensity, and placing selection pressure on all additive genetic variance within the population. Use of genomic selection methods is expected to double or triple genetic gains over field-based half-sib family selection.

Biomass production potential in switchgrass (Panicum virgatum L.) populations is inversely related to latitude of origin. However, phenological adaptation limits the latitudinal range from which to select populations for breeding for biomass in the northern Great Plains. Objectives of this study were to compare patterns of biomass partitioning, determine importance of tiller density and size, and identify morphological traits as potential selection criteria for two cultivars, Summer (origin 40° 42′ N, 95° 52′ W) and Sunburst (origin 42° 42′ N, 96° 41′ W), of comparable phenology. Summer (12.6 Mg ha−1) produced 20% more vegetative biomass than Sunburst and had higher percent reproductive tillers (62% vs. 40%) and more phytomers tiller−1 (7.9 vs. 6.4). Sunburst had more tillers m−2 (677 vs. 530). Cultivars did not differ for seed biomass (311 kg ha−1), but seeds of Sunburst (1.8 mg seed−1) were 90% heavier than seeds of Summer. Vegetative biomass decreased acropetally among phytomers. Reproductive tillers per m2 and seed mass per panicle were accurate predictors of vegetative and seed biomass, respectively. Frequency of reproductive tillers, number of phytomers per tiller, and rate of phytomer development morphologically differentiated Summer and Sunburst and were potential selection criteria for improving biomass yield within a maturity class of switchgrass adapted to the northern Great Plains.