Arvid R. Boe

Abstract Long-term climate change and periodic environmental extremes threaten food and fuel security 1 and global crop productivity 2–4 . Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience 5 , these approaches require sufficient knowledge of the genes that underlie productivity and adaptation 6 —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 virgatum L.), 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.

Breeding to improve biomass production of switchgrass ( Panicum virgatum L.) and big bluestem ( Andropogon gerardii Vitman) for conversion to bioenergy began in 1992. The purpose of this study was (i) to develop a platform for uniform regional testing of cultivars and experimental populations for these species, and (ii) to estimate the gains made by breeding during 1992 to 2012. A total of 25 switchgrass populations and 16 big bluestem populations were planted in uniform regional trials at 13 locations in 2012 and 2014. The reference region was USDA Hardiness Zones 3 through 6 in the humid temperate United States. Significant progress toward increased biomass yield was made in big bluestem and within upland‐ecotype populations, lowland‐ecotype populations, and hybrid‐derived populations of switchgrass. Four mechanisms of increasing biomass yield were documented: (i) increased biomass yield per se, (ii) later flowering to extend the growing season, (iii) combined later flowering from the lowland ecotype with survivorship of the upland ecotype in hybrid‐derived populations, and (iv) increased survivorship of late‐flowering lowland populations in hardiness zones that represent an expansion of their natural adaption zone. Switchgrass exhibited all four mechanisms in one or more improved populations, whereas improved populations of big bluestem were likely influenced by two of the four mechanisms. The uniform testing program was successful at documenting increases in biomass yield, identifying the mechanisms for increased yield, and determining adaptation characteristics and limitations of improved populations.

Switchgrass ( Panicum virgatum L.) is undergoing development as a biomass crop to support conversion of cellulosic biomass to energy. To avoid the competition of biomass with food or feed crops, most commercialization proposals suggest that switchgrass should be grown exclusively on marginal lands that are not fit for food or feed production. The objective of this study was to investigate the potential for cultivar × environment interactions that would affect the methods and approaches for breeding and evaluating switchgrass cultivars, including both upland and lowland types, for high‐input versus low‐input types of environments. Biomass yield was measured on 14 cultivars that were present in 28 replicated field experiments representing seven regions, ranging from 75 to 100° W and spanning USDA Hardiness Zones 4 through 7. Region was the most important environmental factor interacting with cultivars, supporting the idea that the north‐central and northeastern United States should have independent switchgrass breeding programs. Cultivars interacted with soil phosphorus concentration in New Jersey and with depth of the A and B horizons in New York and showed mild interactions with rate of nitrogen fertilizer at several locations. Cultivar rank correlation coefficients between the two rates of nitrogen fertilization (100 vs. 0 kg N ha −1 ) ranged from 0.23 to 0.88, suggesting a possible benefit to breeding and selection without applied nitrogen fertilizer.