Evaluation of the OSU Ndvi Pocket Sensor

There are methods to increase nitrogen use efficiency through optical sensor based nitrogen application; however, the sensors are expensive and cost prohibitive to farmers in the developing world. This study evaluated a reduced cost prototype Normalized Difference Vegetative Index (NDVI) sensor to determine if it could be used with the same level of accuracy as a commercial sensor. The stability of the prototype sensor (Pocket Sensor) to maintain an accurate calibration over time, the effect of operator on sensor readings, and sensor performance in maize and wheat were assessed. Sensor stability was evaluated using turf grass canopies over a 6 month period, and the effect of operator was tested using wheat canopies in existing field experiments. Sensor performance in wheat and maize was also tested in existing field experiments at the International Maize and Wheat Improvement Center (CIMMYT), Ciudad Obregon, Mexico. The prototype sensors were highly correlated to the commercial GreenseekerTM sensor in turf grass, wheat, and maize canopies (r2>0.97, r2>0.95, and r2>0.91 , respectively). With adequate training there was no significant operator effect on sensor readings. The Pocket Sensors lacked some precision in comparison to the commercial sensor (NDVI of the commercial sensor 0.02, 0.05, 0.06 in turf grass, maize, and wheat); however, even with the reduced precision the cost of the sensor and robustness of N fertilizer algorithms compensate for this apparent weakness. The Pocket Sensor is a viable tool to determine NDVI in wheat and maize and make nitrogen recommendations based upon the data collected with this sensor.Department of Plant and Soil Science

Leveraging the genomics revolution with high-throughput phenotyping for crop improvement of abiotic stresses

Doctor of PhilosophyGenetics Interdepartmental Program - Plant PathologyJesse A. PolandA major challenge for 21st century plant geneticists is to predict plant performance based on genetic information. This is a daunting challenge, especially when there are thousands of genes that control complex traits as well as the extreme variation that results from the environment where plants are grown. Rapid advances in technology are assisting in overcoming the obstacle of connecting the genotype to phenotype. Next generation sequencing has provided a wealth of genomic information resulting in numerous completely sequenced genomes and the ability to quickly genotype thousands of individuals. The ability to pair the dense genotypic data with phenotypic data, the observed plant performance, will culminate in successfully predicting cultivar performance. While genomics has advanced rapidly, phenomics, the science and ability to measure plant phenotypes, has slowly progressed, resulting in an imbalance of genotypic to phenotypic data. The disproportion of high-throughput phenotyping (HTP) data is a bottleneck to many genetic and association mapping studies as well as genomic selection (GS). To alleviate the phenomics bottleneck, an affordable and portable phenotyping platform, Phenocart, was developed and evaluated. The Phenocart was capable of taking multiple types of georeferenced measurements including normalized difference vegetation index and canopy temperature, throughout the growing season. The Phenocart performed as well as existing manual measurements while increasing the amount of data exponentially. The deluge of phenotypic data offered opportunities to evaluate lines at specific time points, as well as combining data throughout the season to assess for genotypic differences. Finally in an effort to predict crop performance, the phenotypic data was used in GS models. The models combined molecular marker data from genotyping-by-sequencing with high-throughput phenotyping for plant phenotypic characterization. Utilizing HTP data, rather than just the often measured yield, increased the accuracy of GS models. Achieving the goal of connecting genotype to phenotype has direct impact on plant breeding by allowing selection of higher yielding crops as well as selecting crops that are adapted to local environments. This will allow for a faster rate of improvement in crops, which is imperative to meet the growing global population demand for plant products

Sequenced-Based Paternity Analysis to Improve Breeding and Identify Self-Incompatibility Loci in Intermediate Wheatgrass (Thinopyrum Intermedium)

Key Message Paternity assignment and genome-wide association analyses for fertility were applied to a Thinopyrum intermedium breeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes. Abstract In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p \u3c 0.001). Shannon’s diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns

Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium).

Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG

GTOSat: Radiation Belt Dynamics from the Inside

GTOSat, a 6U SmallSat integrated and tested at NASA Goddard Space Flight Center (GSFC), has a scheduled launch date of July 31st, 2022, on an Atlas V. From a low inclination geosynchronous transfer orbit (GTO), GTOSat has the primary science goal of advancing our quantitative understanding of acceleration and loss of relativistic electrons in the Earth’s outer radiation belt. It will measure energy spectra and pitch angles of both the seed and the energized electron populations simultaneously using a compact, high-heritage Relativistic Electron Magnetic Spectrometer (REMS) built by The Aerospace Corporation. A boom-mounted Fluxgate Magnetometer (FMAG), developed by NASA GSFC, will provide 3-axis knowledge of the ambient local magnetic field. The spacecraft bus uses a combination of commercial and in-house/custom designed components. Design, integration, and testing of the spacecraft bus was performed by a small, dedicated team at GSFC. Throughout development GTOSat has encountered numerous challenges, expected and unexpected, that we’re ready to share with the community

Morphological Classification of Microscopic Charcoal as an Indicator of Fuel Type: Developing a System and Applying it to Records from Two Lakes in Southern Pacific Costa Rica

Charcoal fragments in lake sediments are proxies for past fire activity. Charcoal presence indicates fire occurrence, while the morphology of charcoal particles can reveal the types of plants that burned, or fuel types, and hint at whether fires were natural or set by people. I developed a classification system for charred microscopic particles using a reference collection developed from laboratory charcoalification of modern plant samples and limited prior literature. The classification includes three primary morphologies: graminoid leafy, dicotyledon (dicot) leafy, and woody along with multiple subtypes. I applied this classification to pollen slides spanning the last two millennia prepared from sediment cores from two nearby lakes in southern Pacific Costa Rica, Laguna Zoncho and Laguna Santa Elena. Previous studies documented prehistoric agriculture, forest recovery, historic agriculture, and changes in climate at both lakes that show broadly similar trends but with differences in the scale and possibly timing of prehistoric agricultural decline and in historic patterns of biomass burning. I compared charcoal morphologies in multiple cores from Laguna Zoncho, and between Lagunas Zoncho and Santa Elena, to explore whether the new classification system could improve understanding of site differences. The Laguna Zoncho 1997 core showed a positive relationship between grass pollen and Graminoid charcoal percentages and between tree pollen and Compact charcoal percentages, and supported previous findings of agricultural decline and forest recovery in the century leading into the Spanish Conquest. The Santa Elena core demonstrated a more negative relationship between grass pollen and Graminoid charcoal and between tree pollen and Compact charcoal. Charcoal morphology showed little change around the Conquest, with trends suggesting morphology may be more sensitive to the expansion of agriculture than its cessation. Higher Graminoid charcoal percentages corresponded with high charcoal concentration and influx at both lakes, indicating that fires during intervals of high fire activity were characteristically fueled by grasses and sedges. Percentages for Graminoid, Compact, and Leafy charcoal morphology were similar across the Laguna Zoncho cores, suggesting that charcoal morphology may not be strongly affected by the position of a core within a lake, though more research is needed

Evaluation of a Reduced Cost Active NDVI Sensor for Crop Nutrient Management

There are methods to increase fertilizer nitrogen use efficiency through optical sensor-based nitrogen application; however, the sensors are expensive and cost prohibitive to farmers in the developing world. This study evaluated a novel, reduced cost, prototype, and optical sensor to determine if it could be used with the same level of accuracy as a commercial sensor. The stability of the prototype sensor (pocket sensor) to maintain an accurate calibration over time, the effect of operator on sensor readings, and sensor performance in maize and wheat were assessed. Evaluation of the sensor performance was conducted in existing wheat and maize trials, as well as turf grass canopies at the International Maize and Wheat Improvement Center, Ciudad Obregon, Mexico.The prototype sensors were highly correlated to the commercial GreenSeeker NDVI sensor in turf grass, wheat, and maize canopies (r2>0.97, r2>0.95, and r2>0.91, resp.). The Pocket Sensors lacked some precision in comparison to the commercial sensor; however, even with the reduced precision, the cost of the sensor and robustness of N fertilizer algorithms compensate for this apparent weakness. The pocket sensor is a new and viable tool to assess wheat and maize nitrogen status and make nitrogen recommendations based upon the data collected with this sensor

Evaluation of field‐based single plant phenotyping for wheat breeding

Abstract High‐throughput phenotyping (HTP) has the potential to revolutionize plant breeding by providing scientists with exponentially more data than was available through traditional observations. Even though data collection is rapidly increasing, the optimum use of this data and implementation in the breeding program has not been thoroughly explored. In an effort to apply HTP to the earliest stages of a plant breeding program, we extended field‐based HTP pipelines to evaluate and extract data from spaced single plants. Using a panel of 340 winter wheat (Triticum aestivum L.) lines planted in full plots and grid‐spaced single plants for two growing seasons, we evaluated relationships between single plants and full plot yields. Normalized difference vegetation index (NDVI) was collected multiple times through the growing season using an unoccupied aerial vehicle. NDVI measurements during grain filling stage from both single plants and full plots were typically positively associated with their respective grain yield with correlation ranging from ‐0.22 to 0.74. The relationship between single plant NDVI and full plot yield, however, was variable between seasons ranging from ‐0.40 to 0.06. A genome wide association analysis (GWAS) identified the same marker trait associations in both full plots and single plants, but also displayed variability between growing seasons. Strong genotype by environment interactions could impede selection on quantitative traits, yet these methods could provide an effective tool for plant breeding programs to quickly screen early‐generation germplasm. Efficient use of early‐generation, affordable HTP data could improve overall genetic gain in plant breeding

Development and Evolution of an Intermediate Wheatgrass Domestication Program

Ecological intensification of agriculture is a proposed strategy to enhance the production of food while expanding ecosystem services and reducing inputs. Perennial plants that are directly harvested for human food are a novel means of ecological intensification, by potentially providing unprecedented levels of ecological services, such as increased soil carbon and reduced nutrient leaching. However, existing herbaceous perennial plants produce low yields of harvestable seed. Therefore, we initiated a domestication program to improve the grain yield of the perennial intermediate wheatgrass (Thinopyrum intermedium [Host] Barkworth & D.R. Dewey). The breeding program has adapted to changing resources and to results from previous generations, with methods becoming more elaborate as the program has matured over six breeding cycles. Average predicted gains from selection accumulated over five cycles were 143, 181 and 60% respectively, for seed yield per head, percent naked seed and mass per seed. We did not detect negative correlations that would indicate simultaneously achieving increased grain yield and sustained perenniality would be particularly difficult. Heritability estimates based on genetic markers were the same or higher than those calculated from a pedigree, indicating that markers have potential to expedite breeding efforts

Facilitating United States Service Members\u27 Transition Out of the Military: A Self-Determination Theory Perspective

The purpose of the current qualitative research was to explore the role of veterans’ basic psychological needs during the military transition. Using purposive and snowball sampling, 16 veterans (n = 13 male, n = 3 female; Mage = 38.3, SDage = 5.8 years) of the United States military (n = 8 Army, n = 4 Marine Corps, n = 3 Navy) were recruited to participate in semi-structured interviews. Reflexive thematic analysis of the qualitative data revealed seven themes: (a) veterans experienced different levels of relatedness in the military community during their transition, (b) perceptions of choice and control had varying influences on veterans’ sense of autonomy during their transition, (c) veterans experienced a false sense of competence starting the transition, (d) figuring out how to transfer military experiences and skills to civilian jobs posed a meaningful challenge for veterans’ sense of competence throughout the application process, (e) multiple factors helped veterans regain their sense of competence during the job search, (f) veterans experienced difficulties adjusting to new civilian job environment, and (g) family played a major role in fostering veterans’ sense of autonomy during the transition. These findings offer multiple conceptual and practical implications, including the context-specificity of perceived competence and relatedness, challenge of skill transfer, and temporality of backup plans, that can be used to help service members’ transition more effectively