Genomics and domestication of Field Pennycress (Thlaspi arvense)

University of Minnesota Ph.D. dissertation. May 2015. Major: Plant Biological Sciences. Advisors: M. David Marks, Donald Wyse. 1 computer file (PDF); xii, 267 pages.Thlaspi arvense (field pennycress) is a cold tolerant oilseed species that is being domesticated as a new rapid cycling, winter annual cover crop and feedstock for biodiesel production. Pennycress is related to Arabidopsis thaliana, a model species that has provided an in-depth understanding of many basic developmental and physiological plant processes, which will provide vital information for the rapid domestication of a wild species into a new crop. By targeting key pennycress traits for improvement, such as reducing seed dormancy, increasing rates of spring flowering and maturity, increasing yield, and modifying seed oil composition, we are poised to develop a new winter cash crop that can fit within the corn/soybean rotation. To enable a mutation breeding approach that utilizes the massive amount of Arabidopsis-based knowledge, genomic resources are needed to identify target genes believed to influence key traits. In this dissertation, the first comprehensive annotated transcriptome assembly and comparative analyses are presented, along with the first draft genome sequence for pennycress. In these analyses, target assembled transcripts and corresponding DNA sequences are identified and compared to Arabidopsis homologs and enable the forward and reverse genetic screening of large scale mutant populations. An analysis of winter and spring annual pennycress accessions is also presented, which identified several wild alleles of the pennycress FLOWERING LOCUS C homolog which was found to be responsible for differentiating between spring and winter annual phenotypes. The resources presented herein will provide an unprecedented set of tools to enable the rapid domestication of a new crop species

Can we constrain interior structure of rocky exoplanets from mass and radius measurements?

We present an inversion method based on Bayesian analysis to constrain the interior structure of terrestrial exoplanets, in the form of chemical composition of the mantle and core size. Specifically, we identify what parts of the interior structure of terrestrial exoplanets can be determined from observations of mass, radius, and stellar elemental abundances. We perform a full probabilistic inverse analysis to formally account for observational and model uncertainties and obtain confidence regions of interior structure models. This enables us to characterize how model variability depends on data and associated uncertainties. We test our method on terrestrial solar system planets and find that our model predictions are consistent with independent estimates. Furthermore, we apply our method to synthetic exoplanets up to 10 Earth masses and up to 1.7 Earth radii as well as to exoplanet Kepler-36b. Importantly, the inversion strategy proposed here provides a framework for understanding the level of precision required to characterize the interior of exoplanets. Our main conclusions are: (1) observations of mass and radius are sufficient to constrain core size; (2) stellar elemental abundances (Fe, Si, Mg) are key constraints to reduce degeneracy in interior structure models and to constrain mantle composition; (3) the inherent degeneracy in determining interior structure from mass and radius observations does not only depend on measurement accuracies but also on the actual size and density of the exoplanet. We argue that precise observations of stellar elemental abundances are central in order to place constraints on planetary bulk composition and to reduce model degeneracy. [...]Comment: 19 pages, 18 figures, accepted in Astronomy & Astrophysics (no changes to previous version

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

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

Patterns of genetic variation in a prairie wildflower, Silphium integrifolium, suggest a non-prairie origin and locally adaptive variation

PREMISE: Understanding the relationship between genetic structure and geography provides information about a species’ history and can be used for breeding and conservation goals. The North American prairie is interesting because of its recent origin and subsequent fragmentation. Silphium integrifolium, an iconic perennial American prairie wildflower, is targeted for domestication, having undergone a few generations of improvement. We present the first application of population genetic data in this species to address the following goals: (1) improve breeding by characterizing genetic structure and (2) identify the species geographic origin and potential targets and drivers of selection during range expansion. METHODS: We developed a reference transcriptome as a genotyping reference for samples from throughout the species range. Population genetic analyses were used to describe patterns of genetic variation, and demographic modeling was used to characterize potential processes that shaped variation. Outlier scans for selection and associations with environmental variables were used to identify loci linked to putative targets and drivers of selection. RESULTS: Genetic variation partitioned samples into three geographic clusters. Patterns of variation and demographic modeling suggest that the species origin is in the American Southeast. Breeding program accessions are from the region with lowest observed genetic variation. CONCLUSIONS: This prairie species did not originate within the prairie. Breeding may be improved by including accessions from outside of the germplasm founding region. The geographic structuring and the identified targets and drivers of adaptation can guide collecting efforts toward populations with beneficial agronomic traits

Lithologic Controls on Silicate Weathering Regimes of Temperate Planets

Weathering of silicate rocks at a planetary surface can draw down CO2 from the atmosphere for eventual burial and long-term storage in the planetary interior. This process is thought to provide essential negative feedback to the carbonate-silicate cycle (carbon cycle) to maintain clement climates on Earth and potentially similar temperate exoplanets. We implement thermodynamics to determine weathering rates as a function of surface lithology (rock type). These rates provide upper limits that allow the maximum rate of weathering in regulating climate to be estimated. This modeling shows that the weathering of mineral assemblages in a given rock, rather than individual minerals, is crucial to determine weathering rates at planetary surfaces. By implementing a fluid-transport-controlled approach, we further mimic chemical kinetics and thermodynamics to determine weathering rates for three types of rocks inspired by the lithologies of Earthʼs continental and oceanic crust, and its upper mantle. We find that thermodynamic weathering rates of a continental crust-like lithology are about one to two orders of magnitude lower than those of a lithology characteristic of the oceanic crust. We show that when the CO2 partial pressure decreases or surface temperature increases, thermodynamics rather than kinetics exerts a strong control on weathering. The kinetically and thermodynamically limited regimes of weathering depend on lithology, whereas the supply-limited weathering is independent of lithology. Our results imply that the temperature sensitivity of thermodynamically limited silicate weathering may instigate a positive feedback to the carbon cycle, in which the weathering rate decreases as the surface temperature increases

Molecular tools enabling pennycress (\u3ci\u3eThlaspi arvense\u3c/i\u3e) as a model plant and oilseed cash cover crop

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, which makes translational research straightforward. We developed an Agrobacterium-mediated floral dip transformation method (0.5% transformation efficiency) and introduced CRISPR-Cas9 constructs to produce indel mutations in the putative FATTY ACID ELONGATION1 (FAE1) gene, thereby abolishing erucic acid production and creating an edible seed oil comparable to that of canola. We also stably transformed pennycress with the Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene, producing low-viscosity acetyltriacylglycerol- containing seed oil suitable as a diesel-engine drop-in fuel. Adoption of pennycress as a model system will accelerate oilseed-crop translational research and facilitate pennycress’ rapid domestication to meet the growing sustainable food and fuel demands

High-speed spatial control of the intensity, phase and polarisation of vector beams using a digital micro-mirror device

The dynamic spatial control of light fields is essential to a range of applications, from microscopy to optical micro-manipulation and communications. Here we describe the use of a single digital micro-mirror device (DMD) to generate and rapidly switch vector beams with spatially controllable intensity, phase and polarisation. We demonstrate local spatial control over linear, elliptical and circular polarisation, allowing the generation of radially and azimuthally polarised beams and Poincaré beams. All of these can be switched at rates of up to 4kHz (limited only by our DMD model), a rate ∼2 orders of magnitude faster than the switching speeds of typical phase-only spatial light modulators. The polarisation state of the generated beams is characterised with spatially resolved Stokes measurements. We also describe detail of technical considerations when using a DMD, and quantify the mode capacity and efficiency of the beam generation. The high-speed switching capabilities of this method will be particularly useful for the control of light propagation through complex media such as multimode fibers, where rapid spatial modulation of intensity, phase and polarisation is required

A Pipeline Strategy for Grain Crop Domestication

In the interest of diversifying the global food system, improving human nutrition, and making agriculture more sustainable, there have been many proposals to domesticate wild plants or complete the domestication of semidomesticated orphan crops. However, very few new crops have recently been fully domesticated. Many wild plants have traits limiting their production or consumption that could be costly and slow to change. Others may have fortuitous preadaptations that make them easier to develop or feasible as high-value, albeit low-yielding, crops. To increase success in contemporary domestication of new crops, we propose a pipeline approach, with attrition expected as species advance through the pipeline. We list criteria for ranking domestication candidates to help enrich the starting pool with more preadapted, promising species. We also discuss strategies for prioritizing initial research efforts once the candidates have been selected: developing higher value products and services from the crop, increasing yield potential, and focusing on overcoming undesirable traits. Finally, we present new-crop case studies that demonstrate that wild species’ limitations and potential (in agronomic culture, shattering, seed size, harvest, cleaning, hybridization, etc.) are often only revealed during the early phases of domestication. When nearly insurmountable barriers were reached in some species, they have been (at least temporarily) eliminated from the pipeline. Conversely, a few species have moved quickly through the pipeline as hurdles, such as low seed weight or low seed number per head, were rapidly overcome, leading to increased confidence, farmer collaboration, and program expansion.Fil: DeHaan, Lee R.. The Land Institute; Estados UnidosFil: Van Tassel, David L.. The Land Institute; Estados UnidosFil: Anderson, James A.. University of Minnesota; Estados UnidosFil: Asselin, Sean R.. University of Manitoba; CanadáFil: Barnes, Richard. University of Minnesota; Estados UnidosFil: Baute, Gregory J.. University of British Columbia; CanadáFil: Cattani, Douglas J.. University of Manitoba; CanadáFil: Culman, Steve W.. Ohio State University; Estados UnidosFil: Dorn, Kevin M.. University of Minnesota; Estados UnidosFil: Hulke, Brent S.. United States Department of Agriculture. Agriculture Research Service; Estados UnidosFil: Kantar, Michael. University of British Columbia; CanadáFil: Larson, Steve. Forage and Range Research Laboratory; Estados UnidosFil: David Marks, M.. University of Minnesota; Estados UnidosFil: Miller, Allison J.. Saint Louis University; Estados UnidosFil: Poland, Jesse. Kansas State University; Estados UnidosFil: Ravetta, Damián Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Museo Paleontológico Egidio Feruglio; ArgentinaFil: Rude, Emily. University of Wisconsin; Estados UnidosFil: Ryan, Matthew R.. Cornell University; Estados UnidosFil: Wyse, Don. University of Minnesota; Estados UnidosFil: Zhang, Xiaofei. University of Minnesota; Estados Unido

The Association between Mental Health and Violence among a Nationally Representative Sample of College Students from the United States

Objectives Recent violent attacks on college campuses in the United States have sparked discussions regarding the prevalence of psychiatric disorders and the perpetration of violence among college students. While previous studies have examined the potential association between mental health problems and violent behavior, the overall pattern of findings flowing from this literature remain mixed and no previous studies have examined such associations among college students. Methods The current study makes use of a nationally representative sample of 3,929 college students from the National Epidemiologic Study on Alcohol and Related Conditions (NESARC) to examine the prevalence of seven violent behaviors and 19 psychiatric disorder diagnoses tapping mood, anxiety, personality, and substance use disorders. Associations between individual and composite psychiatric disorder diagnoses and violent behaviors were also examined. Additional analyses were adjusted for the comorbidity of multiple psychiatric diagnoses. Results The results revealed that college students were less likely to have engaged in violent behavior relative to the non-student sample, but a substantial portion of college students had engaged in violent behavior. Age- and sex-standardized prevalence rates indicated that more than 21% of college students reported at least one violent act. In addition, more than 36% of college students had at least one diagnosable psychiatric disorder. Finally, the prevalence of one or more psychiatric disorders significantly increased the odds of violent behavior within the college student sample. Conclusions These findings indicate that violence and psychiatric disorders are prevalent on college campuses in the United States, though perhaps less so than in the general population. In addition, college students who have diagnosable psychiatric disorders are significantly more likely to engage in various forms of violent behavior