Other Plant Sciences Commons^™

Plant And Soil Responses To Sediment Deposition And Nutrient Enrichment In Healthy, Deteriorating, And Newly Created Coastal Marshes In Barataria Basin, Louisiana: Implications For Mississippi River Sediment Diversions, Gina N. Groseclose

LSU Master's Theses

To offset wetland loss in the Mississippi River Delta, sediment diversions that will re-introduce river water and sediment into wetlands are being planned for the lower Mississippi River. River diversions will also deliver high nutrient loads, which may reduce belowground plant productivity, reducing inputs of organic matter important for marsh accretion to keep pace with sea-level rise. However, belowground productivity responses to the combinatory effects of sediment and nutrients are unknown. To test the hypotheses that nutrient enrichment and sediment deposition interact to influence vegetation structure, belowground plant productivity and decomposition, and surface accretion, a field experiment was implemented in …

Perioperative And Oncological Outcomes Following Minimally Invasive Versus Open Pancreaticoduodenectomy For Pancreatic Duct Adenocarcinoma, Rui Sun, Jiawen Yu, Yifan Zhang

Department of Agronomy and Horticulture: Faculty Publications

Background The outcomes of minimally invasive pancreaticoduodenectomy have not been adequately compared with those of open pancreaticoduodenectomy in patients with pancreatic ductal adenocarcinoma. We performed a meta‐analysis to compare the perioperative and oncological outcomes of these two pancreaticoduodenectomy procedures specifically in patients with pancreatic ductal adenocarcinoma.

Methods Before this study was initiated, a specific protocol was designed and has been registered in PROSEPRO (ID: CRD42020149438). Using the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines, PubMed, EMBASE, Web of Science, Cochrane Central Register, and ClinicalTrials.gov databases were systematically searched for studies published between January 1994 and October 2019. …

Soil-Nitrogen, Potentially Mineralizable-Nitrogen, And Field Condition Information Marginally Improves Corn Nitrogen Management, Jason Clark, Fabián G. Fernández, Kristen S. Veum, James J. Camberato, Paul R. Carter, Richard Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A.M. Laboski, Emerson Nafziger, Carl J. Rosen, John E. Sawyer, John F. Shanahan

Department of Agronomy and Horticulture: Faculty Publications

Anaerobic potentially mineralizable nitrogen (PMN) combined with preplant nitrate test (PPNT) or pre-sidedress nitrate test (PSNT) may improve corn (Zea mays L.) N management. Forty-nine corn N response studies were conducted across the U.S. Midwest to evaluate the capacity of PPNT and PSNT to predict grain yield, N uptake, and economic optimal N rate (EONR) when adjusted by soil sampling depth, soil texture, temperature, PMN, and initial NH₄–N from PMN analysis. Pre-plant soil samples were obtained for PPNT (0- to 30-, 30- to 60-, 60- to 90-cm depths) and PMN (0- to 30-cm depth) before corn planting …

Leaf Traits Can Be Used To Predict Rates Of Litter Decomposition, Marc Rosenfield, Jennifer L. Funk, Jason K. Keller, Catrina Clausen, Kimberlee Cyphers

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Strong relationships exist between litter chemistry traits and rates of litter decomposition. However, leaf traits are more commonly found in online trait databases than litter traits and fewer studies have examined how well leaf traits predict litter decomposition rates. Furthermore, while bulk leaf nitrogen (N) content is known to regulate litter decomposition, few studies have explored the importance of N biochemistry fractions, such as protein and amino acid concentration. Here, we decomposed green leaves and naturally senesced leaf litter of nine species representing a wide range of leaf functional traits. We evaluated the ability of traits associated with leaf and …

Effects Of Pyric Herbivory On Prairie-Chicken (Tympanuchus Spp) Habitat, Heath D. Starns, Samuel D. Fuhlendorf, Robert D. Elmore, Dirac Twidwell, Eric T. Thacker, Torre J. Hovick, Barney Luttbeg

Department of Agronomy and Horticulture: Faculty Publications

The reduction and simplification of grasslands has led to the decline of numerous species of grassland fauna, particularly grassland-obligate birds. Prairie-chickens (Tympanuchus spp.) are an example of obligate grassland birds that have declined throughout most of their distribution and are species of conservation concern. Pyric herbivory has been suggested as a land management strategy for enhancing prairie-chicken habitat and stabilizing declining population trends. We assessed differences in vegetation structure created by pyric herbivory compared to fire-only treatments to determine whether pyric herbivory increased habitat heterogeneity for prairie-chickens, spatially or temporally. Our study was performed at four sites in the southern …

Production And Selection Of Quality Protein Popcorn Hybrids Using A Novel Ranking System And Combining Ability Estimates, Leandra Parsons, Ying Ren, Abou Yobi, Preston Hurst, Ruthie Angelovici, Oscar Rodriguez, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Popcorn varieties are agronomically sub-optimal and genetically limited compared to other maize subspecies. To increase genetic diversity and improve popcorn agronomics, dent germplasm has been introduced to popcorn with limited success and generally, major loss of popping. Between 2013 and 2018, 12 Quality Protein Popcorn (QPP) inbreds containing Quality Protein Maize (QPM) and popcorn germplasm were produced that maintained popping while carrying the opaque-2 allele conferring elevated kernel lysine. This is an opportune trait in the growing market for healthier snacks and a model for mining QPM traits into popcorn. We crossed QPP inbreds to explore the effects of heterosis …

Genomic Prediction Enhanced Sparse Testing For Multi-Environment Trials, Diego Jarquin, Reka Howard, José Crossa, Yoseph Beyene, Manje Gowda, Johannes W.R. Martini, Giovanny Covarrubias Pazaran, Juan Burgueño, Angela Pacheco, Martin Grondona, Valentin Wimmer, Boddupalli M. Prasanna

Department of Agronomy and Horticulture: Faculty Publications

“Sparse testing” refers to reduced multi-environment breeding trials in which not all genotypes of interest are grown in each environment. Using genomic-enabled prediction and a model embracing genotype · environment interaction (GE), the non-observed genotype-in-environment combinations can be predicted. Consequently, the overall costs can be reduced and the testing capacities can be increased. The accuracy of predicting the unobserved data depends on different factors including (1) how many genotypes overlap between environments, (2) in how many environments each genotype is grown, and (3) which prediction method is used. In this research, we studied the predictive ability obtained when using a …

Irrigation, Carbon Amelioration, Nitrogen, And Stover Removal Effects On Continuous Corn, Marty Schmer, Virginia L. Jin, Richard B. Ferguson, Brian J. Wienhold

Department of Agronomy and Horticulture: Faculty Publications

Corn (Zea mays L.) residue or stover is harvested as supplemental feed for livestock and is a potential feedstock for cellulosic biofuels. Limited information is available on corn stover removal effects on grain yield under different irrigation rates, nitrogen (N) fertilizer rates, and practices to maintain soil carbon (C) and minimize soil erosion. We evaluated potential interactions between irrigation rate (full or limited), C amelioration practices (cover crop, surface-applied manure, or no amelioration practice), fertilizer N management (125 or 200 kg N ha⁻¹), and stover removal (residue removal or no residue removal), on no-till continuous corn …

Characterizing Variation In Nitrogen Use Efficiency In Wheat Genotypes Using Proximal Canopy Sensing For Sustainable Wheat Production, Mohammed A. Naser, Raj Khosla, Louis Longchamps, Subash Dahal

Department of Agronomy and Horticulture: Faculty Publications

Global nitrogen use efficiency (NUE) for cereal production is marginal and is estimated to be about 33%. Remote sensing tools have tremendous potential for improving NUE in crops through efficient nitrogen management as well as the identification of high-NUE genotypes. The objectives of this study were (i) to identify and quantify the variation in NUE across 24 winter wheat genotypes (Triticum aestivum L.) and (ii) to determine if the normalized difference vegetation index (NDVI) could characterize the variability in NUE across wheat genotypes. This study was conducted in 2010 and 2011 in the semi-arid climate of Northeastern Colorado across dryland …

Genome Wide Association Study Reveals Plant Loci Controlling Heritability Of The Rhizosphere Microbiome, Siwen Deng, Daniel F. Caddell, Gen Xu, Lindsay Dahlen, Lorenzo Washington, Jinliang Yang, Devin Coleman-Derr

Department of Agronomy and Horticulture: Faculty Publications

Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to the host genotype and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we …

Assessing Approaches For Stratifying Producer Fields Based On Biophysical Attributes For Regional Yield-Gap Analysis, Spyridon Mourtzinis, Patricio Grassini, Juan I. Rattalino Edreira, José F. Andrade, Peter M. Kyveryga, Shawn P. Conley

Department of Agronomy and Horticulture: Faculty Publications

Large databases containing producer field-level yield and management records can be used to identify causes of yield gaps. A relevant question is how to account for the diverse biophysical background (i.e., climate and soil) across fields and years, which can confound the effect of a given management practice on yield. Here we evaluated two approaches to group producer fields based on biophysical attributes: (i) a technology extrapolation domain spatial framework (‘TEDs’) that delineates regions with similar (long-term average) annual weather and soil water storage capacity and (ii) clusters based on field-specific soil properties and weather during each crop …

Resilience To Large, “Catastrophic” Wildfires In North America's Grassland Biome, Victoria M. Donovan, Dirac Twidwell, Daniel R. Uden, Tsegaye Tadesse, Brian D. Wardlow, Christine H. Bielski, Matthew O. Jones, Brady W. Allred, David E. Naugle, Craig R. Allen

Department of Agronomy and Horticulture: Faculty Publications

Wildfires are ecosystem‐level drivers of structure and function in many vegetated biomes. While numerous studies have emphasized the benefits of fire to ecosystems, large wildfires have also been associated with the loss of ecosystem services and shifts in vegetation abundance. The size and number of wildfires are increasing across a number of regions, and yet the outcomes of large wildfire on vegetation at large‐scales are still largely unknown. We introduce an exhaustive analysis of wildfire‐scale vegetation response to large wildfires across North America's grassland biome. We use 18 years of a newly released vegetation data set combined with 1,390 geospatial …

Variance Heterogeneity Genome-Wide Mapping For Cadmium In Bread Wheat Reveals Novel Genomic Loci And Epistatic Interactions, Waseem Hussain, Malachy T. Campbell, Diego Jarquin, Harkamal Walia, Gota Morota

Department of Agronomy and Horticulture: Faculty Publications

Genome-wide association mapping identifies quantitative trait loci (QTL) that influence the mean differences between the marker genotypes for a given trait. While most loci influence the mean value of a trait, certain loci, known as variance heterogeneity QTL (vQTL) determine the variability of the trait instead of the mean trait value (mQTL). In the present study, we performed a variance heterogeneity genome-wide association study (vGWAS) for grain cadmium (Cd) concentration in bread wheat. We used double generalized linear model and hierarchical generalized linear model to identify vQTL associated with grain Cd. We identified novel vQTL regions on chromosomes 2A and …

A Global Perspective On Sustainable Intensification Research, Kenneth Cassman, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Despite general agreement that meeting food demand without further loss of natural ecosystems requires sustainable intensification, there is little dialogue about the research agenda needed to achieve it. To that end, we evaluate current trajectories towards sustainable intensification, review published research on the topic, identify missing links, and propose a prioritization framework to fill gaps. Although progress towards sustainable intensification is behind schedule, we are optimistic that current trends can get back on course assuming a well-prioritized and adequately funded research portfolio and appropriate policies and institutions to support it.

De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology …

Optimum Rates Of Surface-Applied Coal Char Decreased Soil Ammonia Volatilization Loss, Dinesh Panday, Maysoon M. Mikha, Harold P. Collins, Virginia L. Jin, Michael Kaiser, Jennifer Cooper, Arindam Malakar, Bijesh Maharjan

Department of Agronomy and Horticulture: Faculty Publications

Fertilizer N losses from agricultural systems have economic and environmental implications. Soil amendment with high C materials, such as coal char, may mitigate N losses. Char, a coal combustion residue, obtained from a sugar factory in Scottsbluff, NE, contained 29% C by weight. A 30-d laboratory study was conducted to evaluate the effects of char addition on N losses via nitrous oxide (N₂O) emission, ammonia (NH₃) volatilization, and nitrate (NO₃–N) leaching from fertilized loam and sandy loam soils. Char was applied at five different rates (0, 6.7, 10.1, 13.4, and 26.8 Mg C ha …

Using Ndvi To Differentiate Wheat Genotypes Productivity Under Dryland And Irrigated Conditions, Mohammed A. Naser, Raj Khosla, Louis Longchamps, Subash Dahal

Department of Agronomy and Horticulture: Faculty Publications

Crop breeders are looking for tools to facilitate the screening of genotypes in field trials. Remote sensing-based indices such as normalized difference vegetative index (NDVI) are sensitive to biomass and nitrogen (N) variability in crop canopies. The objectives of this study were (i) to determine if proximal sensor-based NDVI readings can differentiate the yield of winter wheat (Triticum aestivum L.) genotypes and (ii) to determine if NDVI readings can be used to classify wheat genotypes into grain yield productivity classes. This study was conducted in northeastern Colorado in 2010 and 2011. The NDVI readings were acquired weekly from March to …

The State Of Sustainable Agriculture And Agroecology Research And Impacts: A Survey Of U.S. Scientists, Marcia Delonge, Tali Robbins, Andrea Basche, Lindsey Haynes-Maslow

Department of Agronomy and Horticulture: Faculty Publications

A growing body of research suggests that although sustainable agriculture, particularly agroecology, can address challenges such as those related to climate change, ecosystem services, food insecurity, and farmer livelihoods, the transition to such systems remains limited. To gain insight into the state of U.S. sustainable agriculture and agroecology, we developed a 28-question mixed-method survey that was administered to scientists in these fields. Respondents (N=168) represented diverse locations, institutions, and career stages. They offered varied definitions of sustainable agriculture, with 40% considering economic and social well-being to be core components. Respondents identified the amount and duration of public research funding as …

Ecological Strategies Begin At Germination: Traits, Plasticity, And Survival In The First Four Days Of Plant Life, Julie E. Larson, Brian L. Anacker, Sara Wanous, Jennifer L. Funk

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

1. We commonly use trait variation to characterize plant function within and among species and understand how vegetation responds to the environment. Seedling emergence is an especially vulnerable window affecting population and community dynamics, yet trait‐based frameworks often bypass this earliest stage of plant life. Here we assess whether traits vary in ecologically‐meaningful ways when seedlings are just days old. How do shared evolutionary history and environmental conditions shape trait expression, and can traits explain which seedlings endure drought?.
2. We measured seedling traits in the first four days of life for 16 annual plant species under two water treatments, exploring trait …

Restoring The Fire–Grazing Interaction Promotes Tree–Grass Coexistence By Controlling Woody Encroachment, Jane F. Capozzelli, James R. Miller, Diane M. Debinski, Walter H. Schacht

Department of Agronomy and Horticulture: Faculty Publications

Woody encroachment can convert grasslands and savannas to shrublands and woodlands, so understanding the processes which regulate woody encroachment is necessary to conserve or restore these ecosystems.We hypothesized that recreating the fire–grazing interaction would limit woody encroachment because focal grazing increases fuel accumulation on unburned areas and increases browsing on emergent woody plants in burned areas. This study was conducted in the Grand River Grasslands of Iowa and Missouri (USA) on 11 sites (15.4–35.0 ha). Each site was assigned to one treatment: patch-burn-graze (n = 4), with spatially discrete prescribed fires and free access by cattle (the fire–grazing interaction); graze-andburn …

Combination Of Biological And Chemical Soil Tests Best Predict Maize Nitrogen Response, M. D. Mcdaniel, Daniel T. Walters, L. G. Bundy, Xiaofei Li, Rhae A. Drijber, John E. Sawyer, Michael J. Castellano, C. A.M. Laboski, Peter C. Scharf

Department of Agronomy and Horticulture: Faculty Publications

Soil tests can help optimize nitrogen (N) fertilizer rates, thereby improving farmer profitability and environmental performance. In US Midwest maize (Zea mays) production, however, most soil N tests have limited accuracy to predict N fertilizer requirements. Here we tested the individual and combined ability of 30 soil tests (12 rapid N extractions, seven biological carbon or N tests, six long-term incubation kinetic parameters, and five other routine soil tests), as well as environmental and management data, to predict maize response to N fertilizer across 56 site-years in the US Midwest. Out of 30 soil tests, and across all …

Soybean Response To Water: Trait Identification And Prediction, Shawn Jenkins

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The rising demand for soybean [Glycine Max (L.) Merrill] taken in consideration with current climatic trends accentuates the importance of improving soybean seed yield response per unit water (WP). To further our understanding of the quantitative WP trait, a multi-omic approach was implemented for improved trait identification and predictive modeling opportunities. Through the evaluation of two recombinant inbred line populations jointly totaling 439 lines subjected to contrasting irrigation treatments, informative agronomic, phenomic, and genomic associations were identified. Across both populations, relationships were identified between lodging at maturity (r = -0.58, H = 0.86), canopy to air temperature differential …

Enhancing Hybrid Prediction In Pearl Millet Using Genomic And/Or Multi- Environment Phenotypic Information Of Inbreds, Diego Jarquin, Reka Howard, Zhikai Liang, Shashi K. Gupta, James C. Schnable, Jose Crossa

Department of Agronomy and Horticulture: Faculty Publications

Genomic selection (GS) is an emerging methodology that helps select superior lines among experimental cultivars in plant breeding programs. It offers the opportunity to increase the productivity of cultivars by delivering increased genetic gains and reducing the breeding cycles. This methodology requires inexpensive and sufficiently dense marker information to be successful, and with whole genome sequencing, it has become an important tool in many crops. The recent assembly of the pearl millet genome has made it possible to employ GS models to improve the selection procedure in pearl millet breeding programs. Here, three GS models were implemented and compared using …

Long-Term Ecological Research In Southern Brazil Grasslands: Effects Of Grazing Exclusion And Deferred Grazing On Plant And Arthropod Communities, Pedro M.A. Ferreira, Bianca O. Andrade, Luciana R. Podgaiski, Amanda C. Dias, Valerio D. Pillar, Gerhard E. Overbeck, Milton De S. Mendonca Jr., Ilsi I. Boldrini

Department of Agronomy and Horticulture: Faculty Publications

Grazing exclusion may lead to biodiversity loss and homogenization of naturally heterogeneous and species-rich grassland ecosystems, and these effects may cascade to higher trophic levels and ecosystem properties. Although grazing exclusion has been studied elsewhere, the consequences of alleviating the disturbance regime in grassland ecosystems remain unclear. In this paper, we present results of the first five years of an experiment in native grasslands of southern Brazil. Using a randomized block experimental design, we examined the effects of three grazing treatments on plant and arthropod communities: (i) deferred grazing (i.e., intermittent grazing), (ii) grazing exclusion and (iii) a control under …

Editorial: New Insights Into Mechanisms Of Epigenetic Modifiers In Plant Growth And Development, Ming Luo, Gabino Ríos, Tomasz Jacek Sarnowski, Shoudong Zhang, Nitin Mantri, Jean-Benoit Charron, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

In eukaryotic cells, chromatin, a highly dynamic nucleoprotein complex, plays a critical role in controlling gene expression notably by regulating the interaction between transcription factors and regulatory elements. The structure of the chromatin is determined by epigenetic mechanisms, including DNA methylation, histone modifications, and chromatin remodeling. A growing body of evidence indicates that epigenetic regulations are involved in plant adaptation to environmental stresses, and in plant development, including flowering control, fruit and root development, as well as seed maturation and germination. Furthermore, epigenetic mechanisms have the potential to stabilize cell identity and maintain tissue organization. Hence, epigenetic diversity is now …

Yield And Quality In Purple-Grained Wheat Isogenic Lines, Alexey Morgounov, Yasar Karaduman, Beyhan Akin, Sinan Aydogan, Peter Stephen Baenziger, Madhav Bhatta, Vladimir Chudinov, Susanne Dreisigacker, Velu Govindan, Safure Güler, Carlos Guzman, Ajit Nehe, Rachana Poudel, Devin J. Rose, Elena Gordeeva, Vladimir Shamanin, Kemal Subasi, Yuriy Zelenskiy, Elena Khlestkina

Department of Agronomy and Horticulture: Faculty Publications

Breeding programs for purple wheat are underway in many countries but there is a lack of information on the effects of Pp (purple pericarp) genes on agronomic and quality traits in variable environments and along the product chain (grain-flour-bread). This study was based on unique material: two pairs of isogenic lines in a spring wheat cv. Saratovskaya-29 (S29) background differing only in Pp genes and grain color. In 2017, seven experiments were conducted in Kazakhstan, Russia, and Turkey with a focus on genotype and environment interaction and, in 2018, one experiment in Turkey with a focus on grain, flour, and …

The Land Variational Ensemble Data Assimilation Framework: Lavendar V1.0.0, Ewan Pinnington, Tristan Quaife, Amos Lawless, Karina Williams, Tim Arkebauer, David Scoby

Department of Agronomy and Horticulture: Faculty Publications

The Land Variational Ensemble Data Assimilation Framework (LAVENDAR) implements the method of fourdimensional ensemble variational (4D-En-Var) data assimilation (DA) for land surface models. Four-dimensional ensemble variational data assimilation negates the often costly calculation of a model adjoint required by traditional variational techniques (such as 4D-Var) for optimizing parameters or state variables over a time window of observations. In this paper we present the first application of LAVENDAR, implementing the framework with the Joint UK Land Environment Simulator (JULES) land surface model. We show that the system can recover seven parameters controlling crop behaviour in a set of twin experiments. We …

Adaptive Capacity In Ecosystems, David G. Angeler, Hannah Fried-Petersen, Craig R. Allen, Ahjond Garmestani, Dirac L. Twidwell Jr, H.E. Birgé, W. Chuang, V. M. Donovan, T. Eason, C.P. Roberts, S.M. Sundstrom, C.L. Wonkka

Department of Agronomy and Horticulture: Faculty Publications

Understanding the adaptive capacity of ecosystems to cope with change is crucial to management. However, unclear and often confusing definitions of adaptive capacity make application of this concept difficult. In this paper, we revisit definitions of adaptive capacity and operationalize the concept. We define adaptive capacity as the latent potential of an ecosystem to alter resilience in response to change. We present testable hypotheses to evaluate complementary attributes of adaptive capacity that may help further clarify the components and relevance of the concept. Adaptive sampling, inference and modeling can reduce key uncertainties incrementally over time and increase learning about adaptive …

Soybean Nodule-Associated Non-Rhizobial Bacteria Inhibit Plant Pathogens And Induce Growth Promotion In Tomato, Serkan Tokgöz, Dilip K. Lakshman, Mahmoud H. Ghozlan, Hasan Pinar, Daniel P. Roberts, Amitava Mitra

Department of Plant Pathology: Faculty Publications

The root nodules are a unique environment formed on legume roots through a highly specific symbiotic relationship between leguminous plants and nodule-inducing bacteria. Previously, Rhizobia were presumed to be the only group of bacteria residing within nodules. However, recent studies discovered diverse groups of bacteria within the legume nodules. In this report soybean nodule-associated bacteria were studied in an effort to identify beneficial bacteria for plant disease control and growth promotion. Analysis of surface-sterilized single nodules showed bacterial diversity of the nodule microbiome. Five hundred non-rhizobial colonies from 10 nodules, 50 colonies per nodule, were tested individually against the tomato …

Characterization Of The Transcriptional Divergence Between The Subspecies Of Cultivated Rice (Oryza Sativa), Malachy T. Campbell, Qian Du, Kan Li, Sandeep Sharma, Chi Zhang, Harkamal Walia

Agronomy & Horticulture -- Faculty Publications

Background: Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1).

Results: The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and …