110 Works

Genomic prediction enables rapid selection of high-performing genets in an intermediate wheatgrass (Thinopyrum intermedium) breeding program

Jared Crain, Lee DeHaan & Jesse Poland
In an era of constrained and depleted natural resources, perennial grains could provide sustainable food production in addition to beneficial ecosystem services like reduced erosion and increased atmospheric carbon capture. One such perennial, intermediate wheatgrass (IWG; Thinopyrum intermedium) has been undergoing continuous breeding for domestication and improvement to develop a perennial grain crop since the 1980’s. However, as a perennial species, IWG has required 2-5 years per selection generation. Therefore, starting in 2017 genomic selection...

Data for genetic characterization and curation of diploid a-genome wheat species

Laxman Adhikari, Jesse Poland, Jon Raupp, Shuangye Wu, Duane Wilson, Bernd Friebe, Dal-Hoe Koo & Narinder Singh
Diploid A-genome relatives of wheat comprises T. urartu, T. monococcum subsp. monococcum (domesticated einkorn) and T. monococcum subsp. aegilopoides (wild einkorn). About 930 accessions of A-genome diploid wheat species preserved in the gene bank of the Wheat Genetics Resource Center (WGRC) at Kansas State University were genotyped using genotyping-by-sequencing (GBS). We constructed four pooled GBS libraries (384- and 288-plex) using restriction enzymes (Pst1-Msp1) combinations and the libraries were sequenced on the Illumina platform. The sequence...

Accelerating wheat breeding for end-use quality through association mapping and multivariate genomic prediction

Shichen Zhang-Biehn, Allan Fritz, Guorong Zhang, Byron Evers, Rebecca Regan & Jesse Poland
In hard winter wheat breeding, the evaluation of end-use quality is expensive and time-consuming, being relegated to the final stages of the breeding program after selection for many traits including disease resistance, agronomic performance and grain yield. In this study, our objectives were to identify genetic variants underlying baking quality traits through genome-wide association mapping (GWAS) and develop improved genomic selection (GS) models for the quality traits in hard winter wheat. Advanced breeding lines (n=462)...

Data from: Changes in spatial variance during a grassland to shrubland state transition

Zak Ratajczak, Paolo D'Odorico, Jesse B. Nippert, Scott L. Collins, Nathaniel A. Brunsell & Sujith Ravi
State transitions are changes in ecosystem structure and self-reinforcing feedbacks that are initiated when an exogenous driver variable crosses a threshold. Reversing state transitions is difficult and costly. While some state transitions are relatively rapid, many take years to decades. Outside of theoretical models, very little is known about slower state transitions and how they unfold in time and space. We quantified changes in spatial variance as a mesic grassland ecosystem shifts to a shrub-dominated...

Data from: River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community

Tyler J. Pilger, Keith B. Gido, David L. Propst, James E. Whitney & Thomas F. Turner
Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species’ genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for...

Data from: Comparative transcriptomics support evolutionary convergence of diapause responses across Insecta

Gregory J. Ragland & Evan Keep
Diapause is a common phenotype that is broadly phylogenetically dispersed across Insecta and appears to have multiple evolutionary origins. Nevertheless, there are clear commonalities in diapause regulation across insect taxa. In the present study, we report a meta-analysis of diapause whole transcriptomic data sets from 11 different insect species that addresses three questions: (i) how similar are whole-transcriptome diapause responses across species within and across different diapause life-cycle stages; (ii) do the most closely-related species...

Data from: The conservation value of high elevation habitats to North American migrant birds

W. Alice Boyle & Kathy Martin
The basic patterns of faunal community composition and habitat associations of high elevation mountainous regions are poorly-known. This is true for the avifauna of western North America where our knowledge of high elevation use is primarily restricted to breeding assemblages. Here we report on systematic avian surveys of high elevation habitats over four years in British Columbia conducted during the post-breeding and fall migration periods (Aug–Oct). We detected a remarkable diversity of birds (95 species...

Data from: A before-and-after assessment of patch-burn grazing and riparian fencing along headwater streams

Danelle M. Larson, Walter K. Dodds, Matt R. Whiles, Jessica N. Fulgoni & Thomas R. Thompson
Fire and grazing are common in grasslands world-wide to maintain grass cover and cattle production. The effects of fire, cattle grazing and riparian fencing efficacy on prairie stream ecology are not well characterized at catchment scales. We examined alterations to stream water quality and biology from patch-burn grazing (PBG) in tallgrass prairie during a five-year, replicated, catchment scale experiment that used a Before-After/Control-Impact (BACI) design and was analysed by mixed-effects models. Treatments included two patch-burned...

Data from: The importance of core habitat for a threatened species in changing landscapes

Mark R. Herse, Kimberly A. With & W. Alice Boyle
1. Habitat loss, fragmentation and alteration of the landscape matrix are interdependent processes, collectively responsible for most recent species extinctions. Thus, determining the extent to which these landscape processes affect animals is critical for conservation. However, researchers have often assumed that interdependent effects are independently related to animals’ responses, underestimating the importance of one or several landscape processes in driving species declines. 2. We demonstrate how to disentangle the interdependent effects of habitat area, fragmentation,...

Data from: Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations

Takeshi Kawakami, Brian J. Darby & Mark C. Ungerer
Next generation sequencing (NGS) technologies provide a rapid means to generate genomic resources for species exhibiting interesting ecological and evolutionary variation but for which such resources are scant or nonexistent. In the current report, we utilize 454 pyrosequencing to obtain transcriptome information for multiple individuals and tissue types from geographically disparate and ecologically differentiated populations of the perennial sunflower species Helianthus maximiliani. A total of 850,275 raw reads were obtained averaging 355 bp in length....

Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure

Brian J. Darby, Tim C. Todd & Michael A. Herman
Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field...

Data from: Isolation-driven functional assembly of plant communities on islands

Luka Negoita, Jason D. Fridley, Mark V. Lomolino, Glen Mittelhauser, Joseph M. Craine & Evan Weiher
The physical and biotic environment is often considered the primary driver of functional variation in plant communities. Here, we examine the hypothesis that spatial isolation may also be an important driver of functional variation in plant communities where disturbance and dispersal limitation may prevent species from occupying all suitable habitats. To test this hypothesis, we surveyed the vascular plant composition of 30 islands in the Gulf of Maine, USA, and used available functional trait and...

Data from: Adaptive, but not condition-dependent, body shape differences contribute to assortative mating preferences during ecological speciation

Ryan Greenway, Shannon Drexler, Lenin Arias-Rodriguez & Michael Tobler
Assortative mating is critical for reproductive isolation during speciation, however, the mechanisms underlying mating preferences are often unknown. Assortative mating can be mediated through preferences for condition-dependent and adaptive (“magic”) traits, but rigorously testing these hypotheses has been impeded by trait covariation in living organisms. We used computer-generated models to examine the role of body shape in producing association preferences between fish populations undergoing ecological speciation in different habitat types. We demonstrate that body shape...

Enhancing crop domestication through genomic selection, a case study of intermediate wheatgrass

Jared Crain, Prabin Bajgain, James Anderson, Xiaofei Zhang, Lee DeHaan & Jesse Poland
Perennial grains could simultaneously provide food for humans and a host of ecosystem services, including reduced erosion, minimized nitrate leaching, and increased carbon capture. Yet most of the world’s food and feed is supplied by annual grains. Efforts to domesticate intermediate wheatgrass (Thinopyrumn intermedium, IWG) as a perennial grain crop have been ongoing since the 1980’s. Currently, there are several breeding programs within North America and Europe working toward developing IWG into a viable crop....

Improving wheat yield prediction using secondary traits and high-density phenotyping under heat stressed environments

Mohammad Rahman, Jared Crain, Jesse Poland, Ravi Singh & Atena Haghighattalab
A primary selection target for wheat (Triticum aestivum) improvement is grain yield. However, the selection for yield is limited by the extent of field trials, fluctuating environments, and the time needed to obtain multiyear assessments. Secondary traits such as spectral reflectance and canopy temperature (CT), which can be rapidly measured many times throughout the growing season, are frequently correlated with grain yield and could be used for indirect selection in large populations particularly in earlier...

Using machine learning to model nontraditional spatial dependence in occupancy data

Narmadha Mohankumar & Trevor Hefley
Spatial models for occupancy data are used to estimate and map the true presence of a species, which may depend on biotic and abiotic factors as well as spatial autocorrelation. Traditionally researchers have accounted for spatial autocorrelation in occupancy data by using a correlated normally distributed site-level random effect, which might be incapable of modeling nontraditional spatial dependence such as discontinuities and abrupt transitions. Machine learning approaches have the potential to model nontraditional spatial dependence,...

Root traits reveal safety and efficiency differences in grasses and shrubs exposed to different fire regimes

Kimberly O'Keefe, Seton Bachle, Rachel Keen, E. Greg Tooley & Jesse Nippert
Roots are key components of terrestrial ecosystems, yet little is known about how root structure and function vary across a broad range of species, functional groups, and ecological gradients in situ. We assessed how woody and grass root anatomical traits vary among soil depths and different fire frequencies to better understand the water-use strategies exhibited by these two functional groups in tallgrass prairie experiencing woody encroachment. Specifically, we asked: (1) Do root anatomical traits differ...

Raw mass-standardized ionomic data from seven fish species and raw transcriptome sequences for mosquitofish inhabiting the Tar Creek Superfund Site in OK, USA

John Coffin, Joanna Kelley, Punidan Jeyasingh & Michael Tobler
Our understanding of the mechanisms mediating the resilience of organisms to environmental change remains lacking. Heavy metals negatively affect processes at all biological scales, yet organisms inhabiting contaminated environments must maintain homeostasis to survive. Tar Creek in Oklahoma, USA, contains high concentrations of heavy metals and an abundance of Western mosquitofish (Gambusia affinis), though several fish species persist at lower frequency. To test hypotheses about the mechanisms mediating the persistence and abundance of mosquitofish in...

Kernel weight contribution to yield genetic gain of maize: A global dataset of maize yield, kernel number, and kernel weight over the last century

Javier Fernandez, Carlos Messina, Andrea Salinas, P.V. Vara Prasad, Jesse Nippert & Ignacio Ciampitti
Studies characterizing the effect of a century of plant breeding on physiological traits are highly needed to identify candidate traits for future improvement in maize (Zea mays L.). A global evaluation of kernel weight progress over time requires the assembly of large and reliable data documenting genetic improvements in this trait across commercial breeding programs in different regions. We compiled a global dataset of yield and yield components from 34 published and unpublished studies comparing...

Data from: Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat

Paula Silva, Byron Evers, Alexandria Kieffaber, Xu Wang, Allan Fritz, Jared Crain, Jesse Poland & Liangliang Gao
Barley yellow dwarf is one of the major viral diseases of cereals. Phenotyping barley yellow dwarf in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species. The objectives of this study were to (1) evaluate the use of high-throughput phenotyping...

Mammals adjust diel activity across gradients of urbanization

Travis Gallo, Mason Fidino, Brian Gerber, Adam Ahlers, Julia Angstmann, Max Amaya, Amy Concilio, David Drake, Danielle Gray, Elizabeth Lehrer, Maureen Murray, Travis Ryan, Colleen St. Clair, Carmen Salsbury, Heather Sander, Theodore Stankowich, Jaque Williamson, Amy Belaire, Kelly Simone & Seth Magle
Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator-prey dynamics. Yet, changes in animal behavior within the shorter 24-hour light-dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While...

Data from: Population genetics and origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus)

Katherine E. Waselkov & Kenneth M. Olsen
Premise of the study: The evolution of invasiveness has been extensively studied in natural ecosystems; however, far less is known about the evolution of agricultural invasiveness, despite the major economic impact of weeds on crop productivity. Examining the population structure of recently arisen weeds can provide insights into evolutionary avenues to invasion of agroecosystems. Weeds that originate from wild plants are the most common yet least frequently studied type of agricultural invasive. Here we address...

Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...

Data from: Combining high-throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding

Jared Crain, Suchismita Mondal, Jessica Rutkoski, Ravi P. Singh & Jesse Poland
Genomics and phenomics have promised to revolutionize the field of plant breeding. The integration of these two fields has just begun and is being driven through big data by advances in next-generation sequencing and developments of field-based high-throughput phenotyping (HTP) platforms. Each year the International Maize and Wheat Improvement Center (CIMMYT) evaluates tens-of-thousands of advanced lines for grain yield across multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data for genomic selection (GS),...

Data from: Genomic analysis and prediction within a US public collaborative winter wheat regional testing nursery

Trevor W. Rife, Robert A. Graybosch & Jesse A. Poland
The development of inexpensive, whole-genome profiling enables a transition to allele-based breeding using genomic prediction models. These models consider alleles shared between lines to predict phenotypes and select new lines based on estimated breeding values. This approach can leverage highly-unbalanced datasets common to breeding programs. The Southern Regional Performance Nursery (SRPN) is a public nursery established by the USDA-ARS in 1931 to characterize performance and quality of near-release wheat varieties from breeding programs in the...

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