Penstemon Mitchell (Plantaginaceae) is one of the largest, most diverse plant genera in North America. Their unique diversity, paired with their drought-tolerance and overall hardiness, give Penstemon a vast amount of potential in the landscaping industry—especially in the more arid western United States where they naturally thrive. In order to develop Penstemon lines for more widespread commercial and private landscaping use, we must improve our understanding of the vast genetic diversity of the genus on a molecular level. In this study we utilize genome reduction and barcoding to optimize 454-pyrosequencing in four target species of Penstemon (P. cyananthus, P. davidsonii, P. dissectus and P. fruticosus). Sequencing and assembly produced contigs representing an average of 0.5% of the Penstemon species. From the sequence, SNP information and microsatellite markers were extracted. One hundred and thirty-three interspecific microsatellite markers were discovered, of which 50 met desired primer parameters, and were of high quality with readable bands on 3% Metaphor gels. Of the microsatellite markers, 82% were polymorphic with an average heterozygosity value of 0.51. An average of one SNP in 2,890 bp per species was found within the individual species assemblies and one SNP in 97 bp were found between any two supposed homologous sequences of the four species. An average of 21.5% of the assembled contigs were associated with putative genes involved in cellular components, biological processes, and molecular functions. On average 19.7% of the assembled contigs were identified as repetitive elements of which LTRs, DNA transposons and other unclassified repeats, were discovered. Our study demonstrates the effectiveness of using the GR-RSC technique to selectively reduce the genome size to putative homologous sequence in different species of Penstemon. It has also enabled us the ability to gain greater insights into microsatellite, SNP, putative gene and repetitive element content in the Penstemon genome which provide essential tools for further genetic work including plant breeding and phylogenetics.

Discoveries revolving around false hellebore (Veratrum californicum Durand) have caused a paradigm shift in treatment from eradication to harvest and preservation. Test plots set in place 18 years ago to analyze the effectiveness of eradication treatments (tilling, herbicide, mow, and remow) give us a better idea of how false hellebore communities might respond to disturbances caused by harvest. We focused mainly on the tilling, mow, and remow treatments because of similarities to harvest techniques.We found that mow and remow treatments have little effect on the population of false hellebore in the wild. Tilling treatments were effective in reducing the population dramatically; however some recovery in numbers has taken place. Tilled plots showed a significant decrease in mid seral plant populations, and a significant increase in early seral populations. Tilled treatments were also opened up to intermediately desirable and undesirable plants. Mow and remow treatments reacted similarly to each other, with mow treatments showing decreases in mid seral species and with both treatments showing neither an increase nor a decrease in the other seral stages. Mow and remow plots showed a decrease in desirable plants, but an increase in intermediately desirable plants and no increase in undesirable plants. Greenhouse experiments were unsuccessful due to phenological disruptions caused by removal from the native habitat as well as climate and temperature differences.

Two plazas at Cobá, Mexico, may have been the place of market activity during the classic Maya period. The intense decomposition in the warm, moist soils of the Yucatan Peninsula precludes the identification of organic artifacts in archaeological contexts, but phosphorus and trace elements accumulation in soils may provide evidence of marketing activities. The spatial patterns of P and trace element concentrations were used to elucidate the types of ancient Maya activities that took place in those plazas. Phosphorus concentrations are highly correlated (p-value <0.01) with Fe, Mn, and Zn levels in both Plaza B and D. Although the soil geochemistry of Plaza B does not show a marketplace pattern in comparison with previous studies, the elemental concentrations and distributions within Plaza D join other lines of evidence to support the premise that marketplace activities took place at that location. Soil samples were analyzed using DTPA extraction, Mehlich II, Olsen, and Portable X-Ray Fluorescence (PXRF). Experiments were performed to study the suitability of PXRF for field studies. Aspects that were studied include granule size, soil moisture content, protective plastic films that could interfere with the X-Ray signal when placing the samples on top of the analyzer, and a comparison of certified soil standards to the PXRF elemental concentration readings. The results suggest that a field laboratory could be set up to air-dry and sieve soil samples to a minimum mesh size of #10 (> 2 mm).

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen of a variety of grass genra and species, including Bromus tectorum, an exotic grass that has invaded many natural ecosystems of the U.S. Intermountain West. As a natural seed pathogen of B. tectorum, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing dormant B. tectorum seeds; however, few genetic resources exist for this fungus. Here, the genome assembly of a P. semeniperda isolate using 454 GS-FLX genomic and paired-end pyrosequencing techniques is presented. The total assembly is 32.5 Mb and contains 11,453 gene models greater than 24 amino acids. The assembly contains a variety of predicted genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, 454 sequence reads were used to identify single nucleotide polymorphisms between two isolates of P. semeniperda. In total, 20 SNP markers were developed for the purposes of recombination assesment of 600 individual P. semeniperda isolates representing 36 populations from throughout the U.S. Intermountain West. Although 17 of the fungal populations were fixed at all SNP loci, linkage disequilibrium was determined in the remaining 18 populations. This research demonstrates the effectiveness of the 454 GS-FLX sequencing technology, for de novo assembly and marker development of filamentous fungal genomes. Many features of the assembly match those of other Pyrenophora genomes including P. tritici-repentis and P. teres f. teres, which lend validity to our assembly. These findings present a significant resource for examining and furthering our understanding of P. semeniperda biology.

The Great Basin is North America's largest desert, encompassing 135 million acres. Grazing and other anthropogenic activities in the Great Basin have put heavy demands on the landscape over the last 150 years. Heavily grazed areas lack diversity which allows the spread of exotic weed species. Cheatgrass (Bromus tectorum L [Poaceae]) has invaded and shortened fire frequency intervals from historic 30—100 years to as few as three to five years. Post-fire reseeding of native species is requisite for restoration of highly invaded ecosystems thus, preventing complete conversion to exotic weeds. Most native shrubs and grasses are available for restoration projects, but native forbs are largely unavailable or expensive. This situation led to the creation of The Great Basin Native Plant Selection and Increase Project (GBNPSIP). In 2000 this project was initiated as a joint effort between the Bureau of Land Management, Forest Service Research, and the Utah Division of Wildlife Resources in an effort to make native seed more available and less expensive for landscape scale restoration projects. To meet restoration goals the GBNPSIP project promotes cultivation of native species to increase seed supplies. This research focuses on overcoming seed dormancy issues that have hindered cultivation through scarification and evaluating germination, establishment, and seed production in a cultural setting of four lupine species: hairy big leaf lupine, (Lupinus prunophilus M.E. Jones [Fabaceae]); silky lupine, (L. sericeus Pursh); silvery lupine, (L. argenteus Pursh); and longspur lupine, (L. arbustus Dougl. ex Lind) five scarification treatments were evaluated sulphuric acid and mechanical treatments significantly improved germination on three of the four species tested. All other treatments were unpredictable and not significant. No treatments significantly improved germination of L. arbustus and three of the five treatments significantly decreased seed germination from the control. Results demonstrate that scarification method, and exposure interval, differ in effectively increasing % germination among species. Germination, establishment, and seed production were evaluated using two planting methods for each species. Broadcast plots (covered) were covered with N-Sulate fabric™ and 5 cm (2 in) of sawdust. Control plots (uncovered) were drilled and left untreated. Germination was significantly improved for all four lupine species under treatment conditions. Lupinus prunophilus and L. sericeus exhibited the greatest improvement in germination when covered. Germination of L. argenteus and L. arbustus were also significantly improved (p<0.0001 and p=0.004, respectively) by the covered treatment. Higher germination in the covered treatment was mirrored in establishment for every species except L. arbustus. There is an advantage of using the covered treatment, but low yields make cultivation unprofitable.

Wyoming big sagebrush (Artemisia tridentata Nutt.) is an important native shrub in the Great Basin because of its wide distribution where it dominates over 60 million ha and provides essential habitat and forage for many varied species. The hand collection of sagebrush seed often results in seed scarcity and the available seed quantities are at times inadequate to revegetate large areas that have been disturbed, resulting in a demand for sagebrush seed. Study locations were selected near Scipio and Sahara sand dunes of Utah, and treatments were 1-) control, no treatment applied area left undisturbed 2-) general chemical strip thinning 3-) general chemical thinning of entire stand, 4-) general mechanical strip thinning, and 5-) general mechanical thinning of the entire stand. Significant differences among treatments in seed yields were collected in 2011 at Scipio but not at Sahara. At Scipio, the mechanical strip of competing sagebrush in 3m strips was the most effective of all treatment and produced 2.47kg/ha compared to 4.624kg/ha in the control, but the mechanical land area was only utilizing half the compared control area. The chemical treatments produced 1.819kg/ha and 1.31kg/ha. The percent of sagebrush mortality by each treatment determined the level of competition killed in treatment areas. All treatments at both locations killed at least 57% of the sagebrush. Chemical treatments had a consistent kill rate at both locations, although lower than anticipated, but mechanical kill was the highest at 93% in Scipio. Both mechanical and chemical treated plots had increased cover levels of cheatgrass when compared to the control plots.

(1,3;1,4)-β- D-glucan (β-glucan) is a plant cell wall hemicellulose and a main component of endosperm cell walls. The Cellulose Synthase F family of genes is involved in the synthesis of β-glucan. In this study full-length genomic sequences of CslF6 were obtained from multiple Avena species. Three unique alleles were found in each A. sativa line. Comparisons of these alleles to diploid Avena species allowed for identification of the genomic origin of each allele. The A and D genome alleles had identical amino acid sequences while the C-genome had 13 different amino acids. Global expression of CslF6 was completed at three developmental time point and three tissue types. RNAseq technology was utilized to determine genome specific expression patterns. Differential expression of genome specific-copies of CslF6 was found at all time points tested. Lower levels of C-genome expression of CslF6 were associated with increased levels of B-glucan.

From quinua crop residue it is possible to obtain byproducts that can be used to feed small animals, especially guinea pigs. These byproducts can become an alternative feed to ameliorate food deficiencies generally present in the Altiplano. This study compared the effect of consumed quinua meal rations on guinea pig body weight increase and food and economic conversion. This project was developed in two phases: pre-experimental and experimental. In the first phase, genetic material appropriate for the project and the initial rations for consumption was acquired. The second phase included the experimental design where the treatments were developed. The study concluded that a diet of 30% of dry quinua residue completely substituted a diet of wheat meal. This study also presented information on a bactericidal effect of consumed quinua in the digestive tract, resulting in improved weight increase and feed conversion.

In the highlands, where regular agriculture and livestock are not viable, raising camelids is the only means of subsistence for rural families. While grazing during the dry season in the high Andean region, llamas face serious nutritional deficiencies due to limited forage availability. This study was done at the experimental station of the Benson Agriculture and Food Institute located in the community of Letanias which is in the municipality of Viacha. The objective was to determine the effect of food deprivation on the metabolic profile of blood plasma (concentration of urea-nitrogen, total protein, albumin, and creatinine) as well as the concentration of nitrogen in feces and urine of four and five year old llamas. These llamas were fed on a diet of 80% barley hay and 20% alfalfa hay during two periods of study (before and after food deprivation). Eight male Q’ara llamas were cannulated with a one meter tube in the jugular vein for blood sampling and trained to stay in metabolic cages. The study took place over a period of seven weeks, in which there was a four week period where food was reduced to 30%. The statistical analysis used was the paired t test. The results obtained were: urea-nitrogen concentration = 23.31 ± 8.73 mg/dl, total protein = 9.15 ± 1.50 mg/dl, albumin = 4.47 ± 0.41 mg/dl, and creatinine = 2.39 ± 0.49 mg/dl. The results for nitrogen concentration (%) in feces and urine were 1.61 ± 0.09 and 0.82 ± 0.15 respectively. The average weight loss for the animals was 13.25 kg. According to the results obtained in this study, the concentration of metabolites in blood plasma is within the range reported in other investigations. Statistical analysis indicates no significant differences (p<0.05) in the study periods before and after food deprivation for urea nitrogen, total protein, albumin, and nitrogen in the feces. In contrast, there was a significant difference (p<0.01) in plasma creatinine, nitrogen in the urine, and animal body weight.

With the objective to determine guinea pig digestibility of the nutritive components of Vicia villosa, red clover, and Lolium multiflorum in relation to alfalfa, the digestibility coefficients were evaluated for fiber, protein, dry matter, energy, and dry matter consumption in these three species in a completely random block design with four repetitions. The results showed that for alfalfa digestibility coefficients of 85.7% of the protein and 2806.6 kcal/kg of digestible energy, plus an economic substitution value (ESV) of fiber, protein, and energy of US$0.41 and $0.38/kg and US$0.009/1000 kcal, respectively. Lolium multiflorum had the highest tendency toward digestibility with 60.7% of fiber and the highest consumption with 81.3g. Finally, the dry matter had a digestibility of 77.9% for red clover and 75.6% for alfalfa.