SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.)

Although yield trials for switchgrass (Panicum virgatum L.), a potentially high value biofuel feedstock crop, are currently underway throughout North America, the genetic tools for crop improvement in this species are still in the early stages of development. Identification of high-density molecular markers, such as single nucleotide polymorphisms (SNPs), that are amenable to high-throughput genotyping approaches, is the first step in a quantitative genetics study of this model biofuel crop species. We generated and sequenced expressed sequence tag (EST) libraries from thirteen diverse switchgrass cultivars representing both upland and lowland ecotypes, as well as tetraploid and octoploid genomes. We followed this with reduced genomic library preparation and massively parallel sequencing of the same samples using the Illumina Genome Analyzer technology platform. EST libraries were used to generate unigene clusters and establish a gene-space reference sequence, thus providing a framework for assembly of the short sequence reads. SNPs were identified utilizing these scaffolds. We used a custom software program for alignment and SNP detection and identified over 149,000 SNPs across the 13 short-read sequencing libraries (SRSLs). Approximately 25,000 additional SNPs were identified from the entire EST collection available for the species. This sequencing effort generated data that are suitable for marker development and for estimation of population genetic parameters, such as nucleotide diversity and linkage disequilibrium. Based on these data, we assessed the feasibility of genome wide association mapping and genomic selection applications in switchgrass. Overall, the SNP markers discovered in this study will help facilitate quantitative genetics experiments and greatly enhance breeding efforts that target improvement of key biofuel traits and development of new switchgrass cultivars.

Has selection for improved agronomic traits made reed canarygrass invasive?

Plant breeders have played an essential role in improving agricultural crops, and their efforts will be critical to meet the increasing demand for cellulosic bioenergy feedstocks. However, a major concern is the potential development of novel invasive species that result from breeders' efforts to improve agronomic traits in a crop. We use reed canarygrass as a case study to evaluate the potential of plant breeding to give rise to invasive species. Reed canarygrass has been improved by breeders for use as a forage crop, but it is unclear whether breeding efforts have given rise to more vigorous populations of the species. We evaluated cultivars, European wild, and North American invader populations in upland and wetland environments to identify differences in vigor between the groups of populations. While cultivars were among the most vigorous populations in an agricultural environment (upland soils with nitrogen addition), there were no differences in above- or below-ground production between any populations in wetland environments. These results suggest that breeding has only marginally increased vigor in upland environments and that these gains are not maintained in wetland environments. Breeding focuses on selection for improvements of a specific target population of environments, and stability across a wide range of environments has proved elusive for even the most intensively bred crops. We conclude that breeding efforts are not responsible for wetland invasion by reed canarygrass and offer guidelines that will help reduce the possibility of breeding programs releasing cultivars that will become invasive.

Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences

Switchgrass (Panicum virgatum), a central and Eastern USA native, is highly valued as a component in tallgrass prairie and savanna restoration and conservation projects and a potential bioenergy feedstock. The purpose of this study was to identify regional diversity, gene pools, and centers-of-diversity of switchgrass to gain an understanding of its post-glacial evolution and to identify both the geographic range and potential overlap between functional gene pools. We sampled a total of 384 genotypes from 49 accessions that included the three main taxonomic groups of switchgrass (lowland 4x, upland 4x, and upland 8x) along with one accession possessing an intermediate phenotype. We identified primary centers of diversity for switchgrass in the eastern and western Gulf Coast regions. Migration, drift, and selection have led to adaptive radiation in switchgrass, creating regional gene pools within each of the main taxa. We estimate that both upland-lowland divergence and 4x-to-8x polyploidization within switchgrass began approximately 1.5-1 M ybp and that subsequent ice age cycles have resulted in gene flow between ecotype lineages and between ploidy levels. Gene flow has resulted in "hot spots" of genetic diversity in the southeastern USA and along the Atlantic Seaboard.

Resistance of Closely Mown Fine Fescue and Bentgrass Species to Snow Mold Pathogens

Creeping bentgrass (Agrostis stolonifera) is the primary species used on golf courses in temperate regions but requires prophylactic fungicide treatment to prevent snow mold diseases. We hypothesized that fine fescues (Festuca spp.) and colonial bentgrass (A. capillaris) have superior resistance to snow mold diseases compared with creeping bentgrass. Our objective was to compare the resistance of fine fescues, colonial bentgrass, and creeping bentgrass to snow mold diseases caused by Microdochium nivale and Typhula spp. Field plots were established in two separate years on fairways of three golf courses in Wisconsin to encompass the geographic distribution of snow mold pathogens. The experimental design was a split-split-split plot arrangement with three replications. Whole plots were pathogen species, host genus were subplots, host cultivars were sub-subplots, and inoculated versus noninoculated treatments were sub-sub-subplots. Plots were visually evaluated each spring for disease, turf quality, and Poa annua infestation. Data were analyzed using planned contrasts. Inoculation effects depended on pathogen type and location. Creeping bentgrass always had the most snow mold damage. Fine fescues had less snow mold damage than colonial bentgrass except for one year-location but did not provide acceptable year-long turf quality due to P. annua invasion.

Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars

Switchgrass (Panicum virgatum L.) is an important crop for bioenergy feedstock development. Switchgrass has two main ecotypes: the lowland ecotype being exclusively tetraploid (2n = 4x = 36) and the upland ecotype being mainly tetraploid and octaploid (2n = 8x = 72). Because there is a significant difference in ploidy, morphology, growth pattern, and zone of adaptation between and within the upland and lowland ecotypes, it is important to discriminate switchgrass plants belonging to different genetic pools. We used 55 simple sequence repeats (SSR) loci and six chloroplast sequences to identify patterns of variation between and within 18 switchgrass cultivars representing seven lowland and 11 upland cultivars from different geographic regions and of varying ploidy levels. We report consistent discrimination of switchgrass cultivars into ecotype membership and demonstrate unambiguous molecular differentiation among switchgrass ploidy levels using genetic markers. Also, SSR and chloroplast markers identified genetic pools related to the geographic origin of the 18 cultivars with respect to ecotype, ploidy, and geographical, and cultivar sources. SSR loci were highly informative for cultivar fingerprinting and to classify plants of unknown origin. This classification system is the first step toward developing switchgrass complementary gene pools that can be expected to provide a significant heterotic increase in biomass yield.

Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production

Switchgrass (Panicum virgatum L.) and reed canarygrass (Phalaris arundinacea L.) were pretreated under ambient temperature and pressure with sulfuric acid and calcium hydroxide in separate experiments. Chemical loadings from 0 to 100g (kg DM)(-1) and durations of anaerobic storage from 0 to 180days were investigated by way of a central composite design at two moisture contents (40% or 60% w.b.). Pretreated and untreated samples were fermented to ethanol by Saccharomyces cerevisiae D5A in the presence of a commercially available cellulase (Celluclast 1.5L) and beta-glucosidase (Novozyme 188). Xylose levels were also measured following fermentation because xylose is not metabolized by S. cerevisiae. After sulfuric acid pretreatment and anaerobic storage, conversion of cell wall glucose to ethanol for reed canarygrass ranged from 22% to 83% whereas switchgrass conversions ranged from 16% to 46%. Pretreatment duration had a positive effect on conversion but was mitigated with increased chemical loadings. Conversions after calcium hydroxide pretreatment and anaerobic storage ranged from 21% to 55% and 18% to 54% for reed canarygrass and switchgrass, respectively. The efficacy of lime pretreatment was found to be highly dependent on moisture content. Moreover, pretreatment duration was only found to be significant for reed canarygrass. Although significant levels of acetate and lactate were observed in the biomass after storage, S. cerevisiae was not found to be inhibited at a 10% solids loading.

Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production

Switchgrass (Panicum virgatum L.) and reed canarygrass (Phalaris arundinacea L.) were pretreated under ambient temperature and pressure with sulfuric acid and calcium hydroxide in separate experiments. Chemical loadings from 0 to 100g (kg DM)(-1) and durations of anaerobic storage from 0 to 180days were investigated by way of a central composite design at two moisture contents (40% or 60% w.b.). Pretreated and untreated samples were fermented to ethanol by Saccharomyces cerevisiae D5A in the presence of a commercially available cellulase (Celluclast 1.5L) and beta-glucosidase (Novozyme 188). Xylose levels were also measured following fermentation because xylose is not metabolized by S. cerevisiae. After sulfuric acid pretreatment and anaerobic storage, conversion of cell wall glucose to ethanol for reed canarygrass ranged from 22% to 83% whereas switchgrass conversions ranged from 16% to 46%. Pretreatment duration had a positive effect on conversion but was mitigated with increased chemical loadings. Conversions after calcium hydroxide pretreatment and anaerobic storage ranged from 21% to 55% and 18% to 54% for reed canarygrass and switchgrass, respectively. The efficacy of lime pretreatment was found to be highly dependent on moisture content. Moreover, pretreatment duration was only found to be significant for reed canarygrass. Although significant levels of acetate and lactate were observed in the biomass after storage, S. cerevisiae was not found to be inhibited at a 10% solids loading.

Genotypic variability in mineral composition of switchgrass

Switchgrass (Panicum virgatum L.) is a warm season perennial grass with great potential as an energy crop in the USA. It is widely adapted to many regions of the country, produces large amounts of biomass, serves as a useful forage grass, and provides ecosystem services that benefit soil and water quality and wildlife. Biological and thermochemical technologies are being developed to convert herbaceous biomass, including switchgrass, to energy. The objective of this research was to determine the effect of genotype and production environment on the concentration of minerals that affect the suitability of switchgrass for thermochemical conversion and to quantify the amount of potassium (K) and phosphorus (P) removed from the production system by harvest of the aboveground biomass, a measure of the sustainability of the practice. Straw dry biomass contained from 1.3 to 6.4 kg Mg(-1) and from 6.2 to 15.8 kg Mg(-1) of P and K, respectively. Variability in aluminum (Al), calcium (Ca), chloride (Cl), K, P, silicon (Si), and sulfur (S) concentrations across locations was relatively high, ranging from twofold (Al) to eightfold (Cl). Location had a strong impact on mineral concentrations among switchgrass genotypes evaluated in this study. Latitude of origin impacted the Cl and Si concentrations measured in plant tissues, but none of the other minerals analyzed in this study. Upland and lowland cytotypes explained some of the observed differences, but populationxlocation interactions were the primary source of variability in the concentration of these minerals.

Season and bedding impacts on ammonia emissions from tie-stall dairy barns

Federal and state regulations are being promulgated under the Clean Air Act to reduce hazardous air emissions from livestock operations. Few data are available on emissions from livestock facilities in the USA and the management practices that may minimize emissions. The objective of this study was to measure seasonal and bedding impacts on ammonia emissions from tie-stall dairy barns located in central Wisconsin. Four chambers each housed four Holstein dairy heifers (approximately 17 mo of age; body weights, 427-522 kg) for three 28-d trial periods corresponding to winter, summer, and fall. A 4x4 Latin Square statistical design was used to evaluate four bedding types (manure solids, chopped newspaper, pine shavings, and chopped wheat straw) in each chamber for a 4-d ammonia monitoring period. Average ammonia-N emissions (g heifer(-1) d(-1)) during summer (20.4) and fall (21.0) were similar and twice the emissions recorded during winter (10.1). Ammonia-N emissions accounted for approximately 4 to 7% of consumed feed N, 4 to 10% of excreted N, and 9 to 20% of manure ammonical N. Cooler nighttime temperatures did not result in lower ammonia emissions than daytime temperatures. Ammonia emissions (g heifer(-1) d(-1)) from chambers that contained manure solids (20.0), newspaper (18.9), and straw (18.9) were similar and significantly greater than emissions using pine shavings (15.2). Chamber N balances, or percent difference between the inputs feed N and bedding N, and the outputs manure N, body weight N, and ammonia N were 105, 90, and 89% for the winter, summer, and fall trials, respectively. Relatively high chamber N balances and favorable comparisons of study data with published values of ammonia emissions, feed N intake, and manure N excretion provided confidence in the accuracy of the study results.

Mapping QTL for dollar spot resistance in creeping bentgrass (Agrostis stolonifera L.)

Dollar spot caused by Sclerotinia homoeocarpa F. T. Bennett is the most economically important turf disease on golf courses in North America. Dollar spot resistance in a creeping bentgrass cultivar would greatly reduce the frequency, costs, and environmental impacts of fungicide application. Little work has been done to understand the genetics of resistance to dollar spot in creeping bentgrass. Therefore, QTL analysis was used to determine the location, number and effects of genomic regions associated with dollar spot resistance in the field. To meet this objective, field inoculations using a single isolate were performed over 2 years and multiple locations using progeny of a full sib mapping population '549 x 372'. Dollar spot resistance seems to be inherited quantitatively and broad sense heritability for resistance was estimated to be 0.88. We have detected one QTL with large effect on linkage group 7.1 with LOD values ranging from 3.4 to 8.6 and explaining 14-36% of the phenotypic variance. Several smaller effect QTL specific to rating dates, locations and years were also detected. The association of the tightly linked markers with the LG 7.1 QTL based on 106 progeny was further examined by single marker analysis on all 697 progeny. The high significance of the QTL on LG 7.1 at a sample size of 697 (P < 0.0001), along with its consistency across locations, years and ratings dates, indicated that it was stable over environments. Markers tightly linked to the QTL can be utilized for marker-assisted selection in future bentgrass breeding programs.

Cell wall composition of smooth bromegrass plants selected for divergent fiber concentration

Neutral detergent fiber (NDF) is considered the single best laboratory predictor of voluntary intake by ruminant livestock, creating interest in using NDF as a selection criterion in forage breeding programs. Because genetic reductions in NDF lead to increases in dry matter digestibility but not to changes in digestibility of the NDF fraction, we postulated that low-NDF plants do not have altered compositions of their cell walls. We tested this hypothesis using clones of smooth bromegrass (Bromus inermis Leyss.) with divergent NDF concentrations. High-NDF and low-NDF plants did not differ in cell wall concentrations or in the concentrations of any cell wall component (fucose, arabinose, rhamnose, galactose, glucose, xylose, mannose, uronic acids, and lignin). Instead, low-NDF plants had a cell wall that was more susceptible to solubilization in neutral detergent solution, suggesting that their cell walls were less well-developed as compared to high-NDF plants. NDF should not be used as a substitute for cell wall concentration in forage plants.

Genetic modification of lignin concentration affects fitness of perennial herbaceous plants

Populations of four perennial herbaceous species that were genetically modified for altered lignin content (or associated forage digestibility) by conventional plant breeding were evaluated for two agricultural fitness traits, plant survival and plant biomass, in three Northcentral USA environments for more than 4 years. Reduced lignin concentration or increased digestibility resulted in increased winter mortality in two of four species and reduced biomass in one species. Results from other experiment indicate that these apparent genetic correlations may be ephemeral, suggesting that selection for fitness can be successful within high-digestibility or low-lignin germplasm. Results indicate that perennial plants genetically engineered with altered lignin concentration or composition for use in livestock, pulp and paper, or bioenergy production should be evaluated for fitness in field environments prior to use in agriculture.

Host Range and Alternate Host of a Puccinia coronata Population from Smooth Brome Grass

A rust fungus was observed on smooth brome grass (Bromus inermis Leyss.) leaves growing in the fields of the University of Wisconsin (UW) Agricultural Research Station at Arlington, WI. The population (WPc-95A) was classified as Puccinia coronata Corda. Reports of P. coronata on B. inermis are rare, so a study of the pathogen host range, alternate host, and morphology of urediniospores and teliospores was undertaken. Fourteen grass species representing 10 genera were inoculated with P. coronata WPc-95A, which was maintained with repeated inoculations on B. inermis cv. PL-BDR1. Seventy-two 30-day-old seedlings of B. inermis were inoculated with urediniospores of the fungus. Infection type, pustule density, and disease incidence were recorded 15 days after inoculation. The same grass cultivars were also inoculated with aecio-spores collected from Rhamnus cathartica L. located on the UW campus. To test for host specificity, urediniospores produced on aeciospore-susceptible grass species were used to reinoculate plants of B. inermis and the host species from which the urediniospores were derived. B. inermis, B. riparius Rehm., Festuca pratensis Huds., and Lolium perenne L. were susceptible to P. coronata WPc-95A. The two Bromus spp. had the highest disease incidence. R. cathartica was found to be an alternate host of P. coronata WPc-95A, as it is for P. coronata isolates found on F. pratensis. However, cross-inoculations with urediniospores from R. cathartica-derived aeciospore infections indicated that only urediniospores of B. inermis origin were capable of infecting B. inermis. Thus, P. coronata WPc-95A appears to belong to a forma speciales previously undescribed in North America.

Inheritance of resistance in smooth bromegrass to the crown rust fungus

Common smooth bromegrass (Bromus inermis Leyss.) is octoploid, 2n = 8x = 56, with a genome structure of AAAAB1B1B2B2. Tetrasomic inheritance patterns have been observed in smooth bromegrass, but disomic inheritance is also expected from cytologic observations. Smooth bromegrass is susceptible to the crown rust fungus (Puccinia coronata Corda.). The objective of this study was to determine the inheritance of smooth bromegrass resistance to P. coronata. Seven smooth bromegrass clones, three susceptible and four resistant, were selfed and crossed in a diallel with bulked reciprocals. Inoculations were made with a population of P. coronata from PL-BDR1 smooth bromegrass. Resistance of smooth bromegrass to this population of P. coronata is complex. At least three genes appear to be involved in this host-pathogen interaction, one tetrasomic dominant gene which determines susceptibility (S) and two dominant genes (R1 and R2) that may be complementary and could be inherited either tetrasomically or disomically. Other genes may be involved in the smooth bromegrass-P. coronata interaction, possibly accounting for the lack of fit to expected ratios of some progeny. Heterogeneity for avirulence phenotype in the pathogen population may also have contributed to lack of fit of some progeny. Multiple resistance genes were detected because a pathogen population, likely consisting of genotypes with different genes for virulence, was used to challenge the host.

Performance of lactating dairy cows fed alfalfa silage or perennial ryegrass silage

The nutrient contents of perennial ryegrass (Lolium perenne L.) and alfalfa (Medicago sativa L.) are reasonably similar. Despite similarities, the lactation performance of dairy cows fed perennial ryegrass has not been compared with the lactation performance of dairy cows fed alfalfa. The present study was implemented to compare the performance of lactating cows fed alfalfa or perennial ryegrass silage. Alfalfa and perennial ryegrass were harvested at late bud and boot stages of maturity, respectively, and ensiled in separate 4.9- x 18.3-m concrete silos. The experimental silages were supplemented with a concentrate mix at 31.1% of dietary dry matter and fed to 18 multiparous Holstein cows in early lactation in a crossover experimental design with 28-d periods. Digestibility and rate of passage of experimental diets were also measured using rare earth markers. The perennial ryegrass contained 3.0 percentage units more neutral detergent fiber than did alfalfa, but in vitro digestibility of neutral detergent fiber was 8.8 percentage units higher for perennial ryegrass. In vitro digestibility of dry matter was also higher for perennial ryegrass. Cows fed alfalfa silage produced more milk (31.8 kg/d) than did cows fed perennial ryegrass silage (30.2 kg/d). Cows fed perennial ryegrass silage ate less feed (2.2 kg/d) than did cows fed alfalfa. Because dry matter intake was lower, diet digestibilities were higher, and rate of passage was slower, for cows consuming perennial ryegrass. Based on laboratory evaluations, perennial ryegrass silage has high nutritional quality, but performance of lactating cows indicated that the forage was suboptimal for supporting high milk production when compared with alfalfa. The perennial ryegrass silage was suboptimal because it did not stimulate high amounts of dry matter intake in lactating cows.

Genetic variation and covariation in a population of tetraploid Dactylis L. accessions

Efficient utilization of divergent germ plasm sources in breeding cultivated Dactylis glomerata L. ssp. glomerata Domin depends on knowledge of quantitative variation within and among accessions. This study was undertaken to quantify variation and covariation for forage yield, maturity, disease reaction, and ground cover within a population of tetraploid Dactylis accessions. Variation was observed among families within the population for each variable. Most genetic variation (73%-93% of the family sums of squares) was within country sources or within accessions. Thus, country boundaries, which are traditionally important factors used in defining limits of plant exploration expeditions, have limited expected use in targeting future exploration for specific sources of high yield, disease resistance, or ground cover. Maturity was the exception to this; late-maturing accessions were identified as originating exclusively from the USSR. Some relationships among traits, such as that for yield and disease reaction, differed for accessions and cultivars. Several accessions and families within accessions were identified to have performance superior to most or all cultivars included in this study. Existing germ plasm from several countries was identified to have potential in breeding orchardgrass, while that from other countries appeared to have little or no potential in supplying germ plasm for hay production in humid-temperate environments.