Life Sciences Commons^™

Joint Use Of Genome, Pedigree, And Their Interaction With Environment For Predicting The Performance Of Wheat Lines In New Environments, Réka Howard, Daniel Gianola, Osval Montesinos-Lopez, Philomin Juliana, Ravi Singh, Jesse Poland, Sandesh Shrestha, Paulino Pérez-Rodriguez, José Crossa, Diego Jarquin

Department of Agronomy and Horticulture: Faculty Publications

Genome-enabled prediction plays an essential role in wheat breeding because it has the potential to increase the rate of genetic gain relative to traditional phenotypic and pedigree-based selection. Since the performance of wheat lines is highly influenced by environmental stimuli, it is important to accurately model the environment and its interaction with genetic factors in prediction models. Arguably, multi-environmental best linear unbiased prediction (BLUP) may deliver better prediction performance than single-environment genomic BLUP. We evaluated pedigree and genome-based prediction using 35,403 wheat lines from the Global Wheat Breeding Program of the International Maize and Wheat Improvement Center (CIMMYT). We implemented …

A World Of Cobenefits: Solving The Global Nitrogen Challenge, Benjamin Z. Houlton, Maya Almaraz, Viney Aneja, Amy T. Austin, Edith Bai, Kenneth G. Cassman, Jana E. Compton, Eric A. Davidson, Jan Willem Erisman, James N. Galloway, Baojing Gu, Guolin Yao, Luiz A. Martinelli, Kate Scow, William H. Schlesinger, Thomas P. Tomich, Chao Wang, Xin Zhang

Department of Agronomy and Horticulture: Faculty Publications

Nitrogen is a critical component of the economy, food security, and planetary health. Many of the world's sustainability targets hinge on global nitrogen solutions, which, in turn, contribute lasting benefits for (i) world hunger; (ii) soil, air, and water quality; (iii) climate change mitigation; and (iv) biodiversity conservation. Balancing the projected rise in agricultural nitrogen demands while achieving these 21st century ideals will require policies to coordinate solutions among technologies, consumer choice, and socioeconomic transformation.

A Two-Amino Acid Difference In The Coat Protein Of Satellite Panicum Mosaic Virus Isolates Is Responsible For Differential Synergistic Interactions With Panicum Mosaic Virus, R. V. Chowda-Reddy, Nathan A. Palmer, Serge Edme, Gautam Sarath, Frank A. Kovacs, Gary Y. Yuen, Robert Mitchell, Satyanarayana Tatineni

Department of Agronomy and Horticulture: Faculty Publications

Panicum mosaic virus (PMV) (genus Panicovirus, family Tombusviridae) and its molecular parasite, Satellite panicum mosaic virus (SPMV), synergistically interact in coinfected proso and pearl millet (Panicum miliaceum L.) plants resulting in a severe symptom phenotype. In this study, we examined synergistic interactions between the isolates of PMV and SPMV by using PMV-NE, PMV85, SPMV-KS, and SPMV-Type as interacting partner viruses in different combinations. Coinfection of proso millet plants by PMV-NE and SPMV-KS elicited severe mosaic, chlorosis, stunting, and eventual plant death compared with moderate mosaic, chlorotic streaks, and stunting by PMV85 and SPMV-Type. In reciprocal combinations, coinfection …

Evaluation Of Spray Pattern Uniformity Using Three Unique Analyses As Impacted By Nozzle, Pressure, And Pulse-Widthmodulation Duty Cycle, Thomas R. Butts, Joe D. Luck, Bradley K. Fritz, W. Clint Hoffmann, Greg R. Kruger

Department of Agronomy and Horticulture: Faculty Publications

BACKGROUND: The increasing popularity of pulse-width modulation (PWM) sprayers requires that application interaction effects on spray pattern uniformity be completely understood to maintain a uniform overlap of spray, thereby reducing crop injury potential andmaximizing coverage on target pests. The objective of this researchwas to determine the impacts of nozzle type (venturi vs. non-venturi), boom pressure, and PWMduty cycle on spray pattern uniformity. Research was conducted using an indoor spray patternator located at the University of Nebraska-Lincoln in Lincoln, NE, USA. Coefficient of variation (CV), root mean square error (RMSE), and average percent error (APE) were used to characterize spray pattern …

Benchmarking Irrigation Water Use In Producer Fields In The Us Central Great Plains, Katherine E. B. Gibson, Justin E. Gibson, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Efficient use of freshwater resources is necessary to balance food production and long-term sustainability of irrigated agricultural systems. Here we developed a framework to benchmark irrigation water use relative to crop yield for individual fields based on site-specific weather and soil. Subsequently, we used the framework to diagnose on-farm irrigation management, in relation to crop production, in maize and soybean producer fields in Nebraska (USA).We found actual irrigation to be similar to estimated irrigation water requirement in about half of the fields (i.e. small water surplus). Remarkably, these fields attained yields similar to fields where actual irrigation exceeded water requirements …

Comparing Infiltration Rates In Soils Managed With Conventional And Alternative Farming Methods: A Meta-Analysis, Andrea D. Basche, Marcia S. Delonge

Department of Agronomy and Horticulture: Faculty Publications

Identifying agricultural practices that enhance water cycling is critical, particularly with increased rainfall variability and greater risks of droughts and floods. Soil infiltration rates offer useful insights to water cycling in farming systems because they affect both yields (through soil water availability) and other ecosystem outcomes (such as pollution and flooding from runoff). For example, conventional agricultural practices that leave soils bare and vulnerable to degradation are believed to limit the capacity of soils to quickly absorb and retain water needed for crop growth. Further, it is widely assumed that farming methods such as no-till and cover crops can improve …

History Of Grass Breeding For Grazing Lands In The Northern Great Plains Of The Usa And Canada, Kenneth P. Vogel, John Hendrickson

Department of Agronomy and Horticulture: Faculty Publications

• In the early 1930s there were millions of acres of extensively degraded grazing lands and abandoned and eroded cropland in the Northern Plains of the United States and Canada.

• Grass breeding and plant materials programs were established by both the US and Canadian governments and cooperating universities to develop revegetation materials.

• Efforts of a small number of research locations and people resulted in grass cultivars or varieties that were used to revegetate and preserve the soil on millions of acres of land.

• This is a brief history of the people, agencies, and universities that developed these …

Do Cover Crops And Corn Residue Removal Affect Soil Thermal Properties?, Michael Sindelar, Humberto Blanco-Canqui, Virginia L. Jin, Richard B. Ferguson

Department of Agronomy and Horticulture: Faculty Publications

Soil thermal properties govern the transport and storage of heat in the soil. How management practices such as crop residue removal and cover crop (CC) use affect these soil properties is not well understood. For example, CCs could provide physical cover and improve soil properties after main crop residue removal and thus ameliorate the negative effects of residue removal on soil thermal properties. We measured changes in soil thermal properties including soil thermal conductivity, thermal diffusivity, volumetric heat capacity, and related properties under corn (Zea mays L.) residue removal with and without winter cereal rye (Secale cereale L.) …

Predicting Longitudinal Traits Derived From High-Throughput Phenomics In Contrasting Environments Using Genomic Legendre Polynomials And B-Splines, Mehdi Momen, Malachy T. Campbell, Harkamal Walia, Gota Morota

Department of Agronomy and Horticulture: Faculty Publications

Recent advancements in phenomics coupled with increased output from sequencing technologies can create the platform needed to rapidly increase abiotic stress tolerance of crops, which increasingly face productivity challenges due to climate change. In particular, high-throughput phenotyping (HTP) enables researchers to generate large-scale data with temporal resolution. Recently, a random regression model (RRM) was used to model a longitudinal rice projected shoot area (PSA) dataset in an optimal growth environment. However, the utility of RRM is still unknown for phenotypic trajectories obtained from stress environments. Here, we sought to apply RRM to forecast the rice PSA in control and water-limited …

Dedicated Bioenergy Crops And Water Erosion, Bharat Sharma Acharya, Humberto Blanco-Canqui, Robert B. Mitchell, Richard Cruse, David Laird

Department of Agronomy and Horticulture: Faculty Publications

Information on the water quality impact of perennial warmseason grasses (WSGs) when grown in marginal lands as dedicated energy crops is limited. We studied how WSGs affected runoff, sediment, and nutrient losses and related near-surface soil properties to those of no-till corn (Zea mays L.) on an eroded soil in southwestern Iowa and a center pivot corner in east-central Nebraska. The experiment at the eroded soil was established in 2012, and treatments included ‘Liberty’ switchgrass (Panicum virgatum L.) and no-till continuous corn. The experiment at the pivot corner was established in 2013 with ‘Liberty’ switchgrass, ‘Shawnee’ switchgrass, low-diversity grass …

Shifting Avian Spatial Regimes In A Changing Climate, Caleb P. Roberts, Craig R. Allen, David G. Angeler, Dirac Twidwell

Department of Agronomy and Horticulture: Faculty Publications

In the present era of rapid global change, development of early warnings of ecological regime shifts is a major focus in ecology. Identifying and tracking shifts in spatial regimes is a new approach with potential to enhance understanding of ecological responses to global change. Here, we show strong directional non-stationarity of spatial regimes identified by avian community body mass data. We do this by tracking 46 years of avian spatial regime movement in the North American Great Plains. The northernmost spatial regime boundary moved >590 km northward, and the southernmost boundary moved >260 km northward. Tracking spatial regimes affords decadal …

Rapid Metabolism Increases The Level Of 2,4-D Resistance At High Temperature In Common Waterhemp (Amaranthus Tuberculatus), Chandrima Shyam, Amit J. Jhala, Greg Kruger, Mithila Jugulam

Department of Agronomy and Horticulture: Faculty Publications

Common waterhemp emerges throughout the crop growing season in the Midwestern United States, and as a result, the seedlings are exposed to a wide range of temperature regimes. Typically, 2,4-D is used in the Midwest to control winter annual broad-leaf weeds before planting soybean and in an early post-emergence application in corn and sorghum; however, the evolution of 2,4-D-resistant common waterhemp in several Midwestern states may limit the use of 2.4-D for controlling this problem weed. Moreover, temperature is one of the crucial factors affecting weed control efficacy of 2,4-D. This research investigated the effect of temperature on efficacy of …

Intelligence, Complexity, And Individuality In Sheep, Lori Marino, Debra Merskin

Animal Sentience

Domestic sheep (Ovis aries) are among the earliest animals domesticated for human use. They are consumed worldwide as mutton, hogget, and lamb, kept as wool and milk producers, and used extensively in scientific research. The popular stereotype is that sheep are docile, passive, unintelligent, and timid, but a review of the research on their behavior, affect, cognition, and personality reveals that they are complex, individualistic, and social.

Sacrificial Lambs, Clive Phillips

Animal Sentience

Sheep evolved from the mouflon as mountain animals, able to escape predation by leaping between rock ledges. Their defense was their agility. Humans brought them to the plains, where the agility was less useful, but their lack of aggression, speed or weaponry against predators made them a prime target to become one of man’s meat providers. A perfect animal in many ways, with extraordinary perceptive powers and some remarkable cognitive skills, they are often treated with complete disregard for their welfare. Yet sheep themselves won’t tell us this, for a sheep that alerted others to its weakness really would be …

Pulling The Wool From Our Eyes, Jennifer Vonk

Animal Sentience

Marino & Merskin review evidence of the complexity of sheep cognition, concluding that researchers ought to feel sheepish about misrepresenting ovine cognitive capacities. However, the failure to situate the data in critical context risks pulling the wool over readers’ eyes.

Is Knowing Enough To Change Human Attitudes And Actions?, Liv Baker

Animal Sentience

Marino & Merskin present evidence on key aspects of cognition, such as theory of mind, learning, emotional valence, and sociality, to make a convincing argument that sheep are due consideration as individual sentient beings. With this information, what will it take to produce a real, meaningful shift in our attitudes and actions towards other animals, including a species as disadvantaged as sheep? What else do we need to know?

Reflections On Sheep Rearing, Joyce D'Silva

Animal Sentience

Sheep rearing has an incredibly long history. Sometimes this alone can give credibility and status to a human practice. In the twenty-first century, it may be time to reassess our treatment of sheep and their place in nature. “Just because we’ve always done it” no longer has validity by itself. There are many other human practices which used to be accepted widely in certain societies and which we now may find abhorrent. With sheep intelligence now rightly regarded as an acceptable area of research within the academic community, it is a good time to reflect on our treatment of these …

Casting A Sheep’S Eye On Science, David M. Peña-Guzmán

Animal Sentience

Marino & Merskin review evidence that sheep are not just passive and reactive creatures. They have personalities that vary from individual to individual and endure over time. It follows that we must rethink what it means to study them scientifically.

Far More To Sheep Than Meets The Casual Eye, Bernard Rollin

Animal Sentience

Marino & Merskin’s survey of the cognitive and social capacities of sheep is an eye-opener about the individuality and emotionality of this most maligned of all farm animals. My own eyes had already been opened by an adopted orphaned lamb, so much more like a dog as a companion animal than the mindless robot I had been conditioned to expect. I am morally certain that Marino & Merskin’s survey will have a similar effect on readers open to changing their minds.

Smart Sheep Need More Protection, Michael L. Woodruff

Animal Sentience

The target article unequivocally establishes that sheep are far more intelligent and cognitively sophisticated than is generally acknowledged. For this reason, the authors advocate for significantly more stringent regulation of agricultural and research practices when sheep are used. I briefly review the existing US regulations governing the use of sheep in research and discuss the extent to which they are applied to sheep. I then discuss weaknesses in the current regulations, concluding that they should be changed to mandate housing all research animals in environments that accommodate the psychosocial needs of each species.

Sentient Animals Do Not Just Live In The Present, John Webster

Animal Sentience

Sheep are particularly well-equipped with the cognitive and emotional skills appropriate to their phenotype and natural environment. These include spatial memory, the benefits of safety in numbers, and the ability to recognise special individuals in large flocks by sight and by sound. Marino & Merskin’s target article reviews convincing evidence on whether sheep are more or less clever than other mammalian species. Sheep are very good at being sheep. But sentient animals do not just live in the present. Their emotional state is not simply dictated by events of the moment. If they learn, they can cope; if not, they …

Positive Sentience Is Underrated, Teya Brooks Pribac

Animal Sentience

My commentary focuses on two aspects of ovine (well-)being considered in the review: the developmental context and (un)fulfilled potentialities.

Sheeple? The Need For More Research On Sheep Cognition, Michael Colombo, Damian Scarf

Animal Sentience

Marino & Merskin (2019) provide a comprehensive review of the cognitive abilities of sheep. If research with other animals is any guide, there may be justification for the view that the abilities of sheep have been underestimated, and their review will likely stimulate more research into sheep cognition.

Sheep In Aesop’S And Phaedrus’S Fables, Matteo Colombo, Chiara Raucea

Animal Sentience

Sheep feature in various animal fables. Marino & Merskin suggest that “we” view sheep as “docile, passive, unintelligent, and timid,” but animal fables do not support this view. In Aesop’s and Phaedrus’s fables, sheep are a primary target of injustice; but they are not passive targets. Sheep endure injustice actively and honestly. They are intelligent, aware and outspoken about their own condition.

Using Sheep Psychology To Guide Sheep Policy, Ralph Adolphs

Animal Sentience

Marino & Merskin’s valuable review of the literature on sheep cognition shows how entrenched common views of these animals’ mental lives are disputed by the research literature. Yet the evidence they muster faces three challenges that their target article does not discuss: (1) the behavioral tasks are strongly anthropocentric; (2) neuroscientific data are absent; and (3) applications are not discussed. I touch on all three of these here.

Why Are Sheep Sheepish? How Perception Affects Animal Stereotyping, Robert G. Franklin Jr.

Animal Sentience

Marino & Merskin present compelling evidence that many stereotypes of sheep are incorrect. One factor that may play an important role in animal stereotyping is the physical appearance of animals, which can directly lead to stereotyping through automatic mental processes. Sheep have a round and babyish appearance that directly evokes judgments of warmth and docility. Depictions of sheep in art, and especially cartoons, reinforce this stereotype.

The Mental Lives Of Sheep And The Quest For A Psychological Taxonomy, Carrie Figdor

Animal Sentience

Research into nonhuman cognition has broadened and deepened in recent years. It supports and motivates a shift toward an ecological rather than an anthropocentric approach to cognition.

Debunking Human Prejudice And Blindness, Peter J. Li

Animal Sentience

Human prejudice and blindness to animal suffering are shocking. Despite their differences in culture, politics, and religious beliefs, humans have one thing in common. They see nonhuman animals as inferior and have since time immemorial assumed a dominant position in an asymmetrical human-animal relationship. When it comes to human-animal relations, there is no “clash of civilizations.” Human prejudice and blindness are predicated on “common sense assumptions” about the natural world and nonhuman animals in particular. Marino & Merskin’s review is part of the growing effort to debunk the assumptions that have shaped human actions so as to end the injustice …

Applied Cognition Research To Improve Sheep Welfare, Kristina Horback

Animal Sentience

If a change is going to occur in the care and management of domestic sheep, there needs to be a collaborative effort across many disciplines. This review by Marino & Merskin of the literature on cognitive processing in domestic sheep is limited by the inherent bias of the authors, including the impracticable goal of eliminating sheep production. Animal welfare concerns about the management of commercial sheep are valid; however, in order to make a difference, we need to develop an application for this knowledge about cognitive abilities in sheep.

Guilty As Charged, Sergio M. Pellis

Animal Sentience

Sheep have had a bad rap with regard to their behavioral capabilities, and to a large extent, that negative view of sheep has arisen from our failure as human observers to view the world from the perspective of the sheep themselves. Studies sensitive to what sheep identify as of value in the world have revealed a different picture: sheep have cognitive, emotional and social complexity beyond our crude stereotype. Clearly, what we need to do is to evaluate non-human animals on their own terms and not as a reflection of ourselves.