Morphologic and Transcriptomic Response to Weed Pressure in Multiple Maize (Zea mays L.) Selections and Teosinte (Zea mays L. ssp parviglumis) Lines

Sweet corn (Zea mays L. convar. saccharata var. rugosa) and modern dent variants (field maize, Zea mays L. indentata) have varying degrees of weed tolerance (ability to maintain yield under weed stress). Maize retains ~30% of its ancestral teosinte’s (Zea mays ssp parviglumis) genetic base. Transcriptomic response to weed pressure in maize and teosinte can lead to manipulation of the maize genome to minimize crop yield loss due to weed presence. In maize and teosinte under weed-free and weedstressed conditions, the objectives of this study were: 1) to evaluate transcriptomic responses of 2 teosinte lines; 2) to evaluate transcriptomic response in 5 maize selections in 4 different growing seasons; 3) to determine if mid-season growth parameters (chlorophyll, height, stem diameter, leaf area, or biomass) correlate with crop tolerance; and, 4) to compare and contrast transcriptomic responses among maize and teosinte selections. Four maize selections and 2 teosinte lines suffered grain yield (maize) or harvest biomass (teosinte) loss due to weed stress ranging from 13-44%. Each evaluated selection had a unique response to weeds, with 3 gene ontologies (jasmonic acid response/signaling, UDP-glucosyl and glucuronyltransferases, and quercetin glucosyltransferase) common to all selections evaluated. These common ontologies were not directly related to light depravation or quality, nutrient depravation, nor water stress, which were expected to be the primary mechanisms in weed response. This research suggests individual maize and teosinte selections have distinctive responses to weed stress

Maize, Switchgrass, and Ponderosa Pine Biochar Added to Soil Increased Herbicide Sorption and Decreased Herbicide Efficacy

Biochar, a by-product of pyrolysis made from a wide array of plant biomass when producing biofuels, is a proposed soil amendment to improve soil health. This study measured herbicide sorption and efficacy when soils were treated with low (1% w/w) or high (10% w/w) amounts of biochar manufactured from different feedstocks [maize (Zea mays) stover, switchgrass (Panicum vigatum), and ponderosa pine (Pinus ponderosa)], and treated with different post-processing techniques. Twenty-four hour batch equilibration measured sorption of 14C-labelled atrazine or 2,4-D to two soil types with and without biochar amendments. Herbicide efficacy was measured with and without biochar using speed of seed germination tests of sensitive species. Biochar amended soils sorbed more herbicide than untreated soils, with major differences due to biochar application rate but minor differences due to biochar type or post-process handling technique. Biochar presence increased the speed of seed germination compared with herbicide alone addition. These data indicate that biochar addition to soil can increase herbicide sorption and reduce efficacy. Evaluation for site-specific biochar applications may be warranted to obtain maximal benefits without compromising other agronomic practices

Varying Weed Densities Alter the Corn Transcriptome, Highlighting a Core Set of Weed-Induced Genes and Processes with Potential for Manipulating Weed Tolerance

The phenological responses of corn (Zea mays L.) to competition with increasing densities of winter canola (Brassica napus L.) as the weedy competitor were investigated. Changes in the corn transcriptome resulting from varying weed densities were used to identify genes and processes responsive to competition under controlled conditions where light, nutrients, and water were not limited. Increasing densities of weeds resulted in decreased corn growth and development and increased the number and expression intensity of competition-responsive genes. The physiological processes identified in corn that were consistently induced by competition with weeds included protein synthesis and various transport functions. Likewise, numerous genes involved in these processes, as well as several genes implicated in phytochrome signaling and defense responses, were noted as differentially expressed. The results obtained in this study, conducted under controlled (greenhouse) conditions, were compared with a previously published study where the response of corn to competition with other species was evaluated under field conditions. Approximately one-third of the genes were differentially expressed in response to competition under both field and controlled conditions. These competition-responsive genes represent a resource for investigating the signaling processes by which corn recognizes and responds to competition. These results also highlight specific physiological processes that might be targets for mitigating the response of crops to weeds or other competitive plants under field conditions

Crop Residue Management Challenges: A Special Issue Overview

The amount of crop residues that can be sustainability removed is highly variable and is a function of many factors including the soil, climatic, and plant characteristics. For example, leaving an insufficient amount of crop residue on the soil surface can be detrimental for soil quality, result in loss of soil organic matter (SOM), and increase soil erosion, whereas leaving excessive amounts can impair soil-seed contact, immobilize N, and/or keep soils cool and wet. This special issue evolved as an outcome of, “Crop Residues for Advanced Biofuels: Effects on Soil Carbon” workshop held in Sacramento, CA, in 2017. The goal of the special issue is to provide a forum for identifying knowledge gaps associated with crop residue management and to expand the discussion from a regional Midwestern U.S. to a global perspective. Several crop residue experiments as well as simulation modeling studies are included to examine effects of tillage, crop rotation, livestock grazing, and cover crops on greenhouse gas (GHG) emissions, crop yield, and soil or plant health. The special issue is divided into 4 sections that include (i) Estimating Crop Residue Removal and Modeling; (ii) Cultural Practice Impact on Soil Health; (iii) Residue Removal Impact on Soil and Plant Health; and (iv) Cultural Practice Impact on Carbon Storage and Greenhouse Gas Emissions

Winter Cereal Rye Cover Crop Decreased Nitrous Oxide Emissions During Early Spring

Despite differences between the cover crop growth and decomposition phases, few greenhouse gas (GHG) studies have separated these phases from each other. This study’s hypothesis was that a living cover crop reduces soil inorganic N concentrations and soil water, thereby reducing N2O emissions. We quantified the effects of a fall-planted living cereal rye (Secale cereale L.) cover crop (2017, 2018, 2019) on the following spring’s soil temperature, soil water, water-filled porosity (WFP), inorganic N, and GHG (N2O-N and CO2–C) emissions and compared these measurements to bare soil. The experimental design was a randomized complete block, where years were treated as blocks. Rye was fall planted in 2017, 2018, and 2019, but mostly emerged the following spring. The GHG emissions were near-continuously measured from early spring through June. Rye biomass was 1,049, 428, and 2,647 kg ha–1 in 2018, 2019, and 2020, respectively. Compared to the bare soil, rye reduced WFP in the surface 5 cm by 29, 15, and 26% in 2018, 2019, and 2020 and reduced soil NO3–N in surface 30 cm by 53% in 2019 (p = .04) and 65% in 2020 (p = .07), respectively. Rye changed the N2O and CO2 frequency emission signatures. It also reduced N2O emissions by 66% but did not influence CO2–C emissions during the period prior to corn (Zea mays L.) emergence (VE). After VE, rye and bare soils N2O emissions were similar. These results suggest that nitrous oxide (N2O-N) sampling protocols must account for early season impacts of the living cover

Chemical Amendments of Dryland Saline–Sodic Soils Did Not Enhance Productivity and Soil Health in Fields without Effective Drainage

A common restoration treatment for saline–sodic soils involves improving soil drainage, applying soil amendments (e.g., CaSO4, CaCl2, or elemental S), and leaching with water that has a relatively low electrical conductivity. However, due to high subsoil bulk densities and low drainable porosities, these treatments many not be effective in glaciated dryland systems. A 3-yr field study conducted in three model systems determined the impact of chemical amendments (none, CaCl2, CaSO4, and elemental S) on plant growth, microbial composition, temporal changes in electrical conductivity (ECe ), and the relative sodium content (%Na). Chemical amendments (i) either reduced or did not increase maize (Zea mays), soybean (Glycine max), and sorghum (Sorghum bicolor) yields; (ii) did not increase water infiltration or microbial biomass as determined using the phospholipid-derived fatty acid (PLFA) technique; and (iii) did not reduce ECe or %Na. These results were attributed to high bulk densities and low drainable porosities that reducing the drainage effectiveness in the model backslope and footslope soils, the presence of subsurface marine sediments that provided a source for sodium and other salts that could be transported through capillary action to the surface soil, high sulfate and gypsum contents in the surface soil, and relatively low microbial biomass values. The results suggests that an alternative multistep saline sodic soil restoration approach that involves increasing exchangeable Ca+2 through enhanced microbial and root respiration and increasing transpiration and soil drainage by seeding full season deep rooted perennial vegetation should be tested

A Genetic Deconstruction of Neurocognitive Traits in Schizophrenia and Bipolar Disorder

Background: Impairments in cognitive functions are common in patients suffering from psychiatric disorders, such as schizophrenia and bipolar disorder. Cognitive traits have been proposed as useful for understanding the biological and genetic mechanisms implicated in cognitive function in healthy individuals and in the dysfunction observed in psychiatric disorders. Methods: Sets of genes associated with a range of cognitive functions often impaired in schizophrenia and bipolar disorder were generated from a genome-wide association study (GWAS) on a sample comprising 670 healthy Norwegian adults who were phenotyped for a broad battery of cognitive tests. These gene sets were then tested for enrichment of association in GWASs of schizophrenia and bipolar disorder. The GWAS data was derived from three independent single-centre schizophrenia samples, three independent single-centre bipolar disorder samples, and the multi-centre schizophrenia and bipolar disorder samples from the Psychiatric Genomics Consortium. Results: The strongest enrichments were observed for visuospatial attention and verbal abilities sets in bipolar disorder. Delayed verbal memory was also enriched in one sample of bipolar disorder. For schizophrenia, the strongest evidence of enrichment was observed for the sets of genes associated with performance in a colour-word interference test and for sets associated with memory learning slope. Conclusions: Our results are consistent with the increasing evidence that cognitive functions share genetic factors with schizophrenia and bipolar disorder. Our data provides evidence that genetic studies using polygenic and pleiotropic models can be used to link specific cognitive functions with psychiatric disorders

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

Copy number variants (CNVs) have been strongly implicated in the genetic etiology of schizophrenia (SCZ). However, genome-wide investigation of the contribution of CNV to risk has been hampered by limited sample sizes. We sought to address this obstacle by applying a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. A global enrichment of CNV burden was observed in cases (OR=1.11, P=5.7×10−15), which persisted after excluding loci implicated in previous studies (OR=1.07, P=1.7 ×10−6). CNV burden was enriched for genes associated with synaptic function (OR = 1.68, P = 2.8 ×10−11) and neurobehavioral phenotypes in mouse (OR = 1.18, P= 7.3 ×10−5). Genome-wide significant evidence was obtained for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. Suggestive support was found for eight additional candidate susceptibility and protective loci, which consisted predominantly of CNVs mediated by non-allelic homologous recombination

No Reliable Association between Runs of Homozygosity and Schizophrenia in a Well-Powered Replication Study

It is well known that inbreeding increases the risk of recessive monogenic diseases, but it is less certain whether it contributes to the etiology of complex diseases such as schizophrenia. One way to estimate the effects of inbreeding is to examine the association between disease diagnosis and genome-wide autozygosity estimated using runs of homozygosity (ROH) in genome-wide single nucleotide polymorphism arrays. Using data for schizophrenia from the Psychiatric Genomics Consortium (n = 21,868), Keller et al. (2012) estimated that the odds of developing schizophrenia increased by approximately 17% for every additional percent of the genome that is autozygous (β = 16.1, CI(β) = [6.93, 25.7], Z = 3.44, p = 0.0006). Here we describe replication results from 22 independent schizophrenia case-control datasets from the Psychiatric Genomics Consortium (n = 39,830). Using the same ROH calling thresholds and procedures as Keller et al. (2012), we were unable to replicate the significant association between ROH burden and schizophrenia in the independent PGC phase II data, although the effect was in the predicted direction, and the combined (original + replication) dataset yielded an attenuated but significant relationship between Froh and schizophrenia (β = 4.86,CI(β) = [0.90,8.83],Z = 2.40,p = 0.02). Since Keller et al. (2012), several studies reported inconsistent association of ROH burden with complex traits, particularly in case-control data. These conflicting results might suggest that the effects of autozygosity are confounded by various factors, such as socioeconomic status, education, urbanicity, and religiosity, which may be associated with both real inbreeding and the outcome measures of interest

Age at first birth in women is genetically associated with increased risk of schizophrenia

Prof. Paunio on PGC:n jäsenPrevious studies have shown an increased risk for mental health problems in children born to both younger and older parents compared to children of average-aged parents. We previously used a novel design to reveal a latent mechanism of genetic association between schizophrenia and age at first birth in women (AFB). Here, we use independent data from the UK Biobank (N = 38,892) to replicate the finding of an association between predicted genetic risk of schizophrenia and AFB in women, and to estimate the genetic correlation between schizophrenia and AFB in women stratified into younger and older groups. We find evidence for an association between predicted genetic risk of schizophrenia and AFB in women (P-value = 1.12E-05), and we show genetic heterogeneity between younger and older AFB groups (P-value = 3.45E-03). The genetic correlation between schizophrenia and AFB in the younger AFB group is -0.16 (SE = 0.04) while that between schizophrenia and AFB in the older AFB group is 0.14 (SE = 0.08). Our results suggest that early, and perhaps also late, age at first birth in women is associated with increased genetic risk for schizophrenia in the UK Biobank sample. These findings contribute new insights into factors contributing to the complex bio-social risk architecture underpinning the association between parental age and offspring mental health.Peer reviewe