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.), a cross‐pollinated perennial, produces very little or no seed when self‐pollinated, indicating the presence of self‐incompatibility mechanisms. Knowledge of self‐incompatibility mechanisms is required to use germplasm effectively in a breeding program. The objective of this study was to characterize features of the incompatibility systems in switchgrass. Seed set and seed characteristics of reciprocal matings of tetraploid, octaploid, and tetraploid × octaploid plants were used as measures of incompatibility. Both bagged mutual pollination and manual emasculation and pollination methods were used to make crosses. The percentages of self‐compatibility in the tetraploid and octaploid parent plants were 0.35 and 1.39%, respectively. Prefertilization incompatibility in switchgrass is apparently under gametophytic control, since there were significant differences in percentage of compatible pollen as measured by percentage of total seed set between reciprocal matings within ploidy levels. Results indicated that the prefertilization incompatibility system in switchgrass is similar to the S‐Z incompatibility system found in other members of the Poaceae. A postfertilization incompatibility system also exists that inhibits intermatings among octaploid and tetraploid plants. In these interploidy crosses, two very distinctive types of abnormal seed were found. When the female parent was the tetraploid plant, the resulting seed was small and shriveled, while when the female parent was the octaploid, small seed with floury endosperm was obtained. These results are similar to those obtained for endosperm incompatibility due to the endosperm balance number system found in other species.

Population and specific hybrids were made between populations and genotypes of switchgrass, Panicum virgatum L., and their progeny were evaluated for heterosis in space‐transplanted field trials in eastern Nebraska for a 3‐yr period. ‘Kanlow’ (lowland tetraploid) × ‘Summer’ (upland tetraploid) hybrids exhibit midparent heterosis for second‐ and third‐year biomass yields for both population and individual plant hybrids. These data and previously reported molecular marker data indicate that lowland‐tetraploid and upland‐tetraploid switchgrasses represent different heterotic groups that can potentially be used to produce F1 hybrid cultivars. Hybrids produced from cultivars and experimental strains developed from upland‐octaploid germplasm originating from spatially separated western and eastern regions of the original tallgrass or an adjacent forested ecoregion did not exhibit heterosis for any trait evaluated. These results suggest that these upland populations evaluated were from the same or closely related large germplasm pools or heterotic groups. A method for developing F1 switchgrass hybrid cultivars utilizing the gametophytic self‐incompatibility mechanism of the species is described.

1966). Porter (1966) reported that the lowland plants in central Oklahoma were entirely tetraploid, whereas Switchgrass (Panicum virgatum L.) has two cytotypes or cytoplasm the upland plants were both hexaploids and octaploids. types, L and U, that are associated with the lowland and upland Barnett and Carver (1967) also reported the same ploidy ecotypes, respectively. The L cytotypes are tetraploids while the U cytotypes can be either tetraploids or octaploids. The objective of pattern in plants from Oklahoma and Kansas. The lowthis research was to characterize meiotic stability of reciprocal crosses land type has coarse and erect stems, glabrous leaves, of U and L plants as indicated by chromosome pairing at meiosis and and rust (Puccinia graminis Pers.:Pers.) resistance, and to determine the mode of inheritance of chloroplast DNA (cpDNA) grows as a 0.6-to 3.0-m-tall semi-bunchgrass. The upin the hybrids of these cytotypes. Morphological markers that characland type has fine and semi-decumbent stems, pubesterize the parents and hybrids also were investigated to confirm that cence in the upper surface of the leaf blade, short rhiprogeny were true hybrids. Reciprocal crosses were made between zomes which produce a sod, and less robust growth Kanlow (L tetraploid) and Summer (U tetraploid) plants. Pubescence with a height of 0.9 to 1.5 m (Porter, 1966; Barnett on the upper surface of the leaf blade, foliage color, and seed size and Carver, 1967). Recent analyses of lowland plants were evaluated as markers to verify hybridization. Meiotic pairing of confirms that they are tetraploid (2n ϭ 4x ϭ 36) while some of the hybrids was analyzed at the diakinesis stage of meiosis by means of immature anthers. The clone pRR12 from a spinach 1579

Controlled hybridizations of plants are necessary for genetic studies, including those that u.se molecular markers. A hybridization technique for grass species such as switchgrass, Panicum virgatum L., with indurate floral bracts has not been previously reported. The objective of this study was to develop a technique for emasculating and hybridizing switchgrass. Emasculations were successful when the top of the stigmas could be seen through the translucent tips of the iemma and palea. Panicle branches containing 25 to 50 fertile florets were emasculated at this stage after removing excess panicle branches. Both sessile staminate florets and the fertile florets of a spikelet were emasculated because removal of the sessile floret damaged the upper fertile floret. Emasculations and hybridization were completed before natural pollen shed, which occurs after 1000 h in the greenhouse. Panicle branches with emasculated rioters were covered with glassine bags. Anthers from florets of male parents at a similar stage of development were collected in petri dishes and shaken to induce pollen shed. Pollen in petri dishes was applied directly to stigmas of florets emasculated previously the same morning. The average percentage of crossability [(seed/floret emasculated and fertilized) 100] for crosses that produced seed was 27%, with a range of 4 to 86%. The procedure was successfully used to make controlled crosses in a greenhouse between plants of 'Summer', an upland tetraploid, and 'Kanlow', a lowland tetraploid switchgrass.