17 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...

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....

Assessing corrosion resistance of 2D nanomaterial-based coatings on stainless steel substrates

Shakir Bin Mujib, Santanu Mukherjee, Zongkan Ren & Gurpreet Singh
Two dimensional (2D) materials have elicited considerable interest in the past decade due to a diverse array of novel properties ranging from high surface to mass ratios, a wide range of band gaps (insulating boron nitride to semiconducting transition metal dichalcogenides), high mechanical strength and chemical stability. Given the superior chemo-thermo-mechanical properties, 2D materials may provide transformative solution to a familiar yet persistent problem of significant socio-economic burden: the corrosion of stainless steel (SS). With...

Data from: Lineage and latitudinal variation in Phragmites australis tolerance to herbivory: implications for invasion success

Jordan Croy, Laura Meyerson, Warwick Allen, Ganesh Bhattarai & James T. Cronin
Herbivores play a critical role in plant invasions either by facilitating or inhibiting species establishment and spread. However, relatively few studies with invasive plant species have focused on the role of plant tolerance and how it varies geographically to influence invasion success. We conducted a common garden study using two lineages (native and invasive) of the grass Phragmites australis that are prevalent in North American wetlands. Using 31 populations collected across a broad geographic range,...

Influences of patch-burn grazing on headwater prairie streams and subsequent recovery

Jessica Fulgoni, Matt Whiles, Walter Dodds, Danelle Larson, Karen Jackson & Bartosz Grudzinski
1. Patch-burn grazing (PBG) can promote terrestrial heterogeneity and biodiversity, but can temporarily increase stream nutrients, ecosystem metabolism, and alter macroinvertebrate assemblages. The impacts of grazing on stream channel morphology and post-PBG recovery patterns are unclear. 2. We assessed the influence of grazing in PBG managed grassland streams in Missouri, USA, and subsequent recovery when grazing ceased for two years. We hypothesized that grazing would degrade water quality, stream biotic integrity, and channel morphology, but...

Development of whole-genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding

Jared Crain, Atena Haghighattalab, Lee DeHaan & Jesse Poland
The development of perennial grain crops is driven by the vision of simultaneous food production and enhanced ecosystem services. Typically, perennial crops like intermediate wheatgrass (IWG, Thinopyrum intermedium) have low seed yield and other detrimental agronomic traits. Next generation sequencing has made genomic selection (GS) a tractable and viable breeding method. To investigate how an IWG breeding program may utilize GS, we evaluated 3,658 plants over two years for 46 traits to build a training...

Functional consequences of phenotypic variation between locally adapted populations: swimming performance and ventilation in extremophile fish

Michael Tobler, Lenin Arias-Rodriguez & Henry Camarillo
Natural selection drives the evolution of traits to optimize organismal performance, but optimization of one aspect of performance can often influence other aspects of performance. Here, we asked how phenotypic variation between locally adapted fish populations affects locomotion and ventilation, testing for functional trade-offs and trait-performance correlations. Specifically, we investigated two populations of livebearing fish (Poecilia mexicana) that inhabit distinct habitat types (hydrogen-sulfide-rich springs and adjacent nonsulfidic streams). For each individual, we quantified different metrics...

The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

S. Evan Staton, Bradley H. Bakken, Benjamin K. Blackman, Mark A. Chapman, Nolan C. Kane, Shunxue Tang, Mark C. Ungerer, Steven J. Knapp, Loren H. Rieseberg & John M. Burke
Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence...

Data on universities offering undergraduate degrees that train students for soil science careers at universities in the USA and its territories

Eric C. Brevik, Holly Dolliver, Susan Edinger-Marshall, Danny Itkin, Jodi Johnson-Maynard, Garrett Liles, Monday Mbila, Colby Moorberg, Yaniria Sanchez-De Leon, Joshua J. Steffan, April Ulery & Karen Vaughan
Several soil science education studies over the last 15 years have focused on the number of students enrolled in soil science programs. However, no studies have quantitatively addressed the number of undergraduate soil science preparatory programs that exist in the United States, which means we do not have solid data concerning whether overall program numbers are declining, rising, or holding steady. This also means we do not have complete data on the same trends for...

Assembly of Aegilops comosa chromosomes

Mahmoud Said, Kateřina Holušová, András Farkas, László Ivanizs, Eszter Gaál, Petr Cápal, Michael Abrouk, Mihaela Martis-Thiele, Balázs Kalapos, Jan Bartoš, Bernd Friebe, Jaroslav Doležel & István Molnár
We sequenced and assembled seven chromosomes of Aegilops comosa. The assembly with Meraculous resulted in ~ 50k - 186k scaffolds per chromosome with N50 size 6.4kb - 20.2kb. The scaffold sequences were used for development of molecular markers specific for cDNAs sequences mapped on Ae. comosa chromosomes Pairwise alignment of wheat cDNA-sequences and the chromosomal scaffolds of Ae. comosa identified candidate sequences. In order to analyze the structure and homeology of Aegilops chromosomes, forty-three mapped...

Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem

Nicole Soltis, Celine Caseys, Wei Zhang, Jason Corwin, Susanna Atwell & Daniel Kliebenstein
In plant-pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host-pathogen functional gene interactions are well described while little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Botrytis cinerea - Arabidopsis thaliana pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide...

Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

Jared Crain, Steve Larson, Kevin Dorn, Traci Hagedorn, Lee DeHaan & Jesse Poland
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...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Bridging the flux gap: sap flow measurements reveal species-specific patterns of water-use in a tallgrass prairie

Kimberly O'Keefe, David Bell, Katherine McCulloh & Jesse Nippert
Predicting the hydrological consequences following changes in grassland vegetation type (i.e., woody encroachment) requires an understanding of water flux dynamics at high spatiotemporal resolution for predominant species within grassland communities. However, grassland fluxes are typically measured at the leaf or landscape scale, which inhibits our ability to predict how individual species contribute to changing ecosystem fluxes. We used external heat balance sap flow sensors and a hierarchical Bayesian state-space modeling approach to bridge this “flux-gap”...

A genomics resource for genetics, physiology, and breeding of West African sorghum

Jacques Faye, Fanna Maina, Eyanawa Akata, Bassirou Sine, Cyril Diatta, Aissata Mamadou, Sandeep Marla, Sophie Bouchet, Niaba Teme, Jean-Francois Rami, Daniel Fonceka, Ndiaga Cisse & Geoffrey Morris
Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to...

Frequent burning causes large losses of carbon from deep soil layers in a temperate savanna

Adam Francis Pellegrini, Kendra K. McLauchlan, Sarah E. Hobbie, Michelle C. Mack, Abbey L. Marcotte, David M. Nelson, Steven Perakis, Peter B. Reich & Kyle Whittinghill
1. Fire activity is changing dramatically across the globe, with uncertain effects on ecosystem processes, especially belowground. Fire‐driven losses of soil carbon (C) are often assumed to occur primarily in the upper soil layers because the repeated combustion of aboveground biomass limits organic matter inputs into surface soil. However, C losses from deeper soil may occur if frequent burning reduces root biomass inputs of C into deep soil layers or stimulates losses of C via...

Data from: Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains’ climate gradient: Implications for climate change and restoration

Loretta C. Johnson, Matthew Galliart, Sofia Sabates, Hannah Tetreault, Angel DeLaCruz, Johnny Bryant, Jacob Alsdurf, Mary Knapp, Nora Bello, Sara Baer, Brian Maricle, David Gibson, Jesse Poland, Paul St. Amand, Natalie Unruh, Olivia Parrish & Loretta Johnson
Plant response to climate depends on a species’ adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, wet ecotypes originating from western KS to Illinois that span 500 to 1,200 mm rainfall year-1. We aimed to answer: (1)...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Kansas State University
  • The Land Institute
  • University of Minnesota
  • University of Florida
  • University of California, Irvine
  • Donald Danforth Plant Science Center
  • University of Kansas
  • Stanford University
  • New Mexico State University
  • Institut National de la Recherche Agronomique du Niger