Breeding for Biomass Yield in Switchgrass Using Surrogate Measures of Yield

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

Selection for Biomass Yield in Upland, Lowland, and Hybrid Switchgrass

Switchgrass (Panicum virgatum L.) is a candidate for cellulosic bioenergy feedstock development in many parts of North America, Europe, and Asia. Breeding for increased biomass yield is a viable and desirable research objective to improve both economic and energy yields per hectare. The objectives of this study were to estimate progress from (i) selection for biomass yield in upland switchgrass, (ii) selection for winter survival, biomass yield, and biomass quality in lowland switchgrass, and (iii) advanced-generation heterosis effects in four upland × lowland hybrid switchgrass populations. Selection for increased biomass yield in upland switchgrass resulted in mean genetic gains for of 0.71 Mg ha-1 per cycle (8% per cycle = 4% yr-1) for biomass yield. Selection for increased biomass yield in lowland switchgrass resulted in mean genetic gains of 0.89 Mg ha-1 (18% = 1% yr-1) for biomass yield. Mean high-parent heterosis between upland and lowland ecotypes was 3.57 Mg ha-1 (43%). These gains in biomass yield resulted in significant increases in ethanol production for a fermentation platform or high heating value for a combustion platform. Biomass yield is a moderately heritable trait in switchgrass and it can be readily improved in both upland and lowland populations using conventional breeding methods

Switchgrass

Switchgrass (Panicum virgatum L.) is a tall, erect, warm-season perennial native to the tall grass prairie, oak savanna, and associated ecosystems of North America. It can be found in prairies, open woodlands, and brackish marshes east of the Rocky Mountains and generally south of 55° north latitude (Hitchcock 1951; Stubbendieck et al. 1991). Less than 1% of these ecosystems exist today, but these prairie and savanna remnants have served as in situ gene banks, preserving a vast amount of genetic diversity within switchgrass and many other plant species. Switchgrass has a diversity of uses as well, including pasture, hay production, biomass for energy production, soil and water conservation, carbon sequestration, and wildlife habitat

Population genetic structure of N. American and European \u3ci\u3ePhalaris arundinacea\u3c/i\u3e L. as inferred from inter-simple sequence repeat markers

Phalaris arundinacea L. (reed canarygrass) has become one of the most aggressive invaders of North American wetlands. P. arundinacea is native to temperate N. America, Europe, and Asia, but repeated introductions of European genotypes to N. America, recent range expansions, and the planting of forage and ornamental cultivars complicate the resolution of its demographic history. Molecular tools can help to unravel the demographic and invasion history of populations of invasive species. In this study, inter-simple sequence repeat markers were used to analyze the population genetic structure of European and N. American populations of reed canary grass as well as forage and ornamental cultivars. We found that P. arundinacea harbors a high amount of genetic diversity with most of the diversity located within, as opposed to among, populations. Cluster analyses suggested that current populations are admixtures of two formerly distinct genetic groups

Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for \u3ci\u3eIn Vitro\u3c/i\u3e Dry Matter Digestibility

Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four loci in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. This study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality

Genetic Diversity, Plant Adaptation Regions, and Gene Pools for Switchgrass

Switchgrass (Panicum virgatum L.) is a perennial grass native to the North American tallgrass prairie and broadly adapted to the central and eastern USA. Transfer of germplasm throughout this region creates the potential of contaminating local gene pools with genes that are not native to a locale. The objective of this study was to identify structural patterns and spatial variation for molecular markers of switchgrass populations from the northern and central USA. Forty six prairie-remnant populations and 11 cultivars were analyzed for random amplified polymorphic DNA (RAPD) markers. Although there was significant population differentiation, little of this variation was associated with geographic regions. A small amount of population differentiation was associated with hardiness zones and ecoregions, suggesting that a recent proposal to use these two criteria for defining plant adaptation regions has merit for defining gene pools and seed-transfer zones of switchgrass. Cultivars of switchgrass cannot be differentiated from prairie-remnant populations in the northern and central USA on the basis of RAPD markers, indicating that they are still highly representative of natural germplasm. Seed sources of switchgrass can be moved considerable distance within hardiness zones and ecoregions without causing significant contamination, pollution, swamping, or erosion of local gene pools

Biofuels, Bioenergy, and Bioproducts from Sustainable Agricultural and Forest Crops

This issue of BioEnergy Research highlights the Short Rotation Crops International Conference held in Bloomington, Minnesota in August 2008. This is the first special issue of BioEnergy Research, with several additional special issues planned in the next year, focused on the three U.S. Department of Energy Bioenergy Research Centers (Great Lakes Bioenergy Research Center, BioEnergy Science Center, and Joint BioEnergy Institute), and emerging technologies for biodiesel production. The purpose of these special issues is to highlight emerging research efforts in the areas of biomass, biofuels, and bioenergy. The Short Rotation Crops International Conference represented a unique opportunity for communication and interaction between researchers working on herbaceous and woody bioenergy feedstocks, one that we hope will continue to stimulate new interactions and creative solutions for bioenergy and bioproducts. We invite other groups to submit ideas for future special issues to one of the three co-Editors-in-Chief of BioEnergy Research

Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass

Citation: Grabowski, Paul P., Geoffrey P. Morris, Michael D. Casler, and Justin O. Borevitz. “Population Genomic Variation Reveals Roles of History, Adaptation and Ploidy in Switchgrass.” Molecular Ecology 23, no. 16 (2014): 4059–73. https://doi.org/10.1111/mec.12845.Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass

Biofuels, Bioenergy, and Bioproducts from Sustainable Agricultural and Forest Crops

This issue of BioEnergy Research highlights the Short Rotation Crops International Conference held in Bloomington, Minnesota in August 2008. This is the first special issue of BioEnergy Research, with several additional special issues planned in the next year, focused on the three U.S. Department of Energy Bioenergy Research Centers (Great Lakes Bioenergy Research Center, BioEnergy Science Center, and Joint BioEnergy Institute), and emerging technologies for biodiesel production. The purpose of these special issues is to highlight emerging research efforts in the areas of biomass, biofuels, and bioenergy. The Short Rotation Crops International Conference represented a unique opportunity for communication and interaction between researchers working on herbaceous and woody bioenergy feedstocks, one that we hope will continue to stimulate new interactions and creative solutions for bioenergy and bioproducts. We invite other groups to submit ideas for future special issues to one of the three co-Editors-in-Chief of BioEnergy Research

Participatory Development of a Forage Grass Cultivar

Perennial forage grasses exist in both nature and agriculture as a highly heterogeneous mixture of genotypes. Extreme environments, fluctuating environments, and severe managements can impose selection pressures that will result in loss of unadapted genotypes. Mortality of unadapted genotypes leads to dominance of fewer highly adapted genotypes which may be useful as superior germplasm in other similar environments