Biology subjects

Morris, G.

Publications and source records attributed to Morris, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Flywheel Genomics: Simultaneous trait discovery and genetic gain in plant breeding

Genomic mapping has yielded extensive catalogs of quantitative trait loci underlying agronomic traits, yet translating these discoveries into breeding gains remains inefficient. Here, we introduce Flywheel Genomics, a framework that integrates trait discovery directly within rapid cycling breeding populations. Using empirical data from a smallholder-oriented sorghum breeding program, we demonstrate that recurrent intermating and selection maintain genetic diversity, effective population size, and recombination while reducing confounding from plant height and maturity. Within this population, we resolve loci underlying simple adaptive and complex environmentally responsive traits and generate large segregating populations for mapping and near-isogenic lines for locus validation. We further demonstrate applicability in a public wheat breeding program, where known agronomic loci were readily detected. Simulations show that rapid cycling better preserves the population genetic properties required for Flywheel Genomics than conventional pure line development. By integrating discovery with improvement, Flywheel Genomics reframes breeding programs as engines of both crop improvement and genetic insight.

genetics↗

bioRxiv2026

A simple model of the co-emergence of grid and place fields

Grid cells in the medial entorhinal cortex and place cells in the hippocampus together support spatial navigation. The two regions are reciprocally connected, and there is a chicken-and-egg problem for how both arise and reinforce each other during development. Current computational accounts either derive one type from the other or use network dynamics to model the emergence of one type in isolation. We introduce a unified recurrent network model that instantiates Dales Law (every neuron is either excitatory or inhibitory), and is trained to predict the next sensory observation from masked previous sensory observations and egocentric motion. To our knowledge, this is the first single-objective model in which grid and place cells co-emerge without supervision of either type, or reliance on pre-existing spatial-cell representations. The two kinds of spatial codes coexist across 1,000 different training configurations, with their balance set by the amount of sensory noise and masking. Without retraining, the network qualitatively reproduces experimentally observed grid fragmentation in hairpin mazes, grid merging after wall removal, lattice alignment across connected rooms, locally ordered 3D fields observed in freely flying bats, as well as the developmental order in which place cells precede grid cells. We interpret these results in terms of two complementary encoding pressures within a single sensory-prediction objective: (1) correcting errors or reconstructing missing components of sensory observations, and (2) prediction of the next sensory state during navigation. Our results suggest a circuit-level account of the co-emergence of grid and place cells, and experimentally testable predictions for the two kinds of spatial codes. Codes for experiments are available at 1,2.

neuroscience↗

bioRxiv2026

Spatial remapping in the subicular complex and entorhinal cortex follows 1 low-dimensional geometric principles

Neurons in the hippocampal formation are part of the brains cognitive map, representing the spatial structure of the environment through coordinated activity across place cells, grid cells, border cells, head-direction cells and others1-5. Although remapping between environments has been extensively documented6-9, it remains unknown whether transitions between maps reflect unconstrained reorganization or obey a systematic transformation principle. To address this question, we recorded large neuronal populations from the subicular complex and entorhinal cortex in awake, behaving mice navigating environments spanning a wide range of geometries. We asked whether spatial representations across rooms could be related through a shared class of coordinate transformations. Despite pronounced heterogeneity and apparent randomness in single-cell remapping, population-level decoding across environments demonstrated a consistent low-dimensional affine transformation of coordinates, comprising rotation, scaling, shear, reflection, and translation. Thus, what appears as complex remapping at the level of individual neurons reduces to a compact geometric rule at the level of neural assemblies. These results indicate that the hippocampal formation maintains a structured internal coordinate template that is flexibly tailored to environmental geometry. This may serve as the organisms internal model of space.

neuroscience↗

bioRxiv2026

Epistatic fitness landscapes emerge from parallel adaptive walks in breeding network metapopulations

Global networks of crop breeding programs leverage diverse germplasm, but diversity increases the complexity of maintaining stability in their elite genepools. To characterize genetic heterogeneity in breeding metapopulations and develop insights on how to manage it, we simulated the evolution of breeding populations on fitness landscapes. We revealed the geometric decrease in the average effect size of alleles segregating as standing variation that become fixed along an adaptive walk. We also demonstrated how independent adaptive walks of subpopulations are influenced by genetic drift, leading to cryptic genetic heterogeneity among elite genepools. This variation is released when elite lines derived from independent subpopulations are crossed, leading to segregation for 2-4X more major QTL in admixed families as in unadmixed families, and 2-4X more epistatic interactions. The emergent property of fitness epistasis for traits under stabilizing selection is well-understood in evolutionary genetics, but under-appreciated in crop quantitative genetics. To highlight the importance of this phenomenon, we constructed an empirical genotype-to-fitness landscape from the sorghum NAM, a global admixed prebreeding resource, demonstrating the utility of fitness landscapes for inferring genetic compatibilities within metapopulations. Our findings suggest that in breeding networks, strategies for effective germplasm exchange must account for epistasis in the oligogenic component of the genetic architecture of locally-adapted traits. Article summaryModern public sector crop improvement happens in networks of breeding programs that routinely exchange genetic information. Traditional models for understanding quantitative traits have limited predictiveness in situations with such genetic heterogeneity. This study uses breeding simulations and empirical data to show the utility of the fitness landscape framework for characterizing the genetic architecture of complex traits in breeding metapopulations. By simulating the evolution of breeding programs and integration into networks, it demonstrates how epistatic interactions between large-effect alleles are a fundamental property that must be accounted for when exchanging germplasm. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/712732v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1b9d693org.highwire.dtl.DTLVardef@1b66666org.highwire.dtl.DTLVardef@1fcc2cdorg.highwire.dtl.DTLVardef@1596260_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2026

MicroRNA-sensing plasmid system for dynamic control of functional ion channel expression

Gene therapy offers the potential for long-term treatment or cures for a range of chronic diseases. However, permanent gene therapy expression may not be desirable. Efforts have been made to create systems which can be switched on/off by stimuli including light, designer drugs, or cellular contexts such as increased electrical activity. Here, we designed a novel plasmid system in which ion channel expression, and therefore function, is regulated by microRNA (miR) - an endogenous class of short noncoding RNAs which negatively regulate gene expression via binding the 3 untranslated region of target transcripts. We modified an existing voltage-gated potassium channel gene therapy with a binding cassette for miR-193a-3p, and transfected this miR-193-OFF system in neuro2A cells. Co-transfection with an inhibitor or mimic of miR-193a-3p respectively enhanced or repressed expression of our transgene, assessed using a GFP marker. Using whole-cell voltage clamp, we observed enhanced voltage-gated potassium currents in cells co-transfected with a miR-193a-3p inhibitor, compared with a non-targeting control oligonucleotide. Together, this demonstrates the concept of a novel miR-mediated molecular switch which can bias therapeutic ion channel expression based on a specific miR signal. As miRs are a ubiquitous molecular mechanism, our approach could be applied to a wide range of cellular and disease contexts, potentially expanding gene therapy to new patient populations.

neuroscience↗

bioRxiv2025

REMI: Reconstructing Episodic Memory During Intrinsic Path Planning

Grid cells in the medial entorhinal cortex (MEC) and place cells in the hippocampus (HC) both form spatial representations. Grid cells fire in triangular grid patterns, while place cells fire at specific locations and respond to contextual cues. How do these interacting systems support not only spatial encoding but also internally driven path planning, such as navigating to locations recalled from cues? Here, we propose a system-level theory of MEC-HC wiring that explains how grid and place cell patterns could be connected to enable cue-triggered goal retrieval, path planning, and reconstruction of sensory experience along planned routes. We suggest that place cells autoassociate sensory inputs with grid cell patterns, allowing sensory cues to trigger recall of goal-location grid patterns. We show analytically that grid-based planning permits shortcuts through unvisited locations and generalizes local transitions to long-range paths. During planning, intermediate grid states trigger place cell pattern completion, reconstructing sensory experiences along the route. Using a single-layer RNN modeling the HC-MEC loop with a planning subnetwork, we demonstrate these effects in both biologically grounded navigation simulations using RatatouGym and visually realistic navigation tasks using Habitat Sim. Codes for experiments, simulations, and vision encoder are available at 1,2,3.

neuroscience↗

bioRxiv2023

Field phenomics reveals genetic variation for transpiration response to vapor pressure deficit in sorghum

Drought adaptation for water-limited environments relies on traits that optimize plant water budgets. Limited transpiration (LT) reduces water demand under high vapor pressure deficit (VPD) (i.e., dry air condition), conserving water for efficient use during the reproductive stage. Although studies in controlled environments report genetic variation for LT, confirming its replicability in field conditions is critical for developing water-resilient crops. Here we test the existence of genetic variation for LT in sorghum in field trials and whether canopy temperature (TC) is a surrogate method to discriminate this trait. We phenotyped transpiration response to VPD (TR-VPD) via stomatal conductance (gs), canopy temperature (TC) from fixed IRT sensors (TCirt), and unoccupied aerial system thermal imagery (TCimg) in 11 genotypes. Replicability among phenomic approaches for three genotypes revealed genetic variability for TR-VPD. Genotypes BTx2752 and SC979 carry the LT trait, while genotype DKS54-00 has the non-LT trait. TC can determine differences in TR-VPD. However, the broad sense heritability (H2) and correlations suggest that canopy architecture and stand count hampers TCirt and TCimg measurement. Unexpectedly, observations of gs and VPD showed non-linear patterns for genotypes with LT and non-LT traits. Our findings provide further insights into the genetics of plant water dynamics.

genetics↗

bioRxiv2023

Brain cell-specific origin of circulating microRNA biomarkers in experimental temporal lobe epilepsy

The diagnosis of epilepsy is complex and challenging and would benefit from the availability of molecular biomarkers, ideally measurable in a biofluid such as blood. Experimental and human epilepsy are associated with altered brain and blood levels of various microRNAs (miRNAs). Evidence is lacking, however, as to whether any of the circulating pool of miRNAs originates from the brain. To explore the link between circulating miRNAs and the pathophysiology of epilepsy, we first sequenced argonaute 2 (Ago2)-bound miRNAs in plasma samples collected from mice subject to status epilepticus induced by intraamygdala microinjection of kainic acid. This identified time-dependent changes in plasma levels of miRNAs with known neuronal and microglial-cell origins. To explore whether the circulating miRNAs had originated from the brain, we generated mice expressing FLAG-Ago2 in neurons or microglia using tamoxifen-inducible Thy1 or Cx3cr1 promoters, respectively. FLAG immunoprecipitates from the plasma of these mice after seizures contained miRNAs, including let-7i-5p and miR-19b-3p. Taken together, these studies confirm that a portion of the circulating pool of miRNAs in experimental epilepsy originates from the brain, increasing support for miRNAs as mechanistic biomarkers of epilepsy.

neuroscience↗

bioRxiv2022

Time or distance: predictive coding of Hippocampal cells

The discovery of place cells within the hippocampus has pointed to the importance of the hippocampus for navigation. The more recent discovery of hippocampal time cells has broadened the perspective of encoding in the hippocampus. An alternative hypothesis to the existence of time cells is based on the notion that hippocampal cells deduce location by integrating travelled distance ("path integration"). According to this alternate hypothesis, time cells, which fire at particular times when animals are running on a treadmill without changing location, actually encode accumulated distance on the treadmill. To examine this hypothesis, Kraus et al.1 performed treadmill experiments in which animals either ran for a fixed time or a fixed distance with varying velocities. Two distinct coding modes of hippocampal principal cells were found. Some cells encoded travelled distance and others elapsed time, thus refuting the notion that all hippocampal cells were performing path integration. Using the data from these experiments, we asked whether the two populations depended on the type of task the rats were engaged in. We show that the type of experiment determined the cells encoding, such that in fixed-distance experiments distance-encoding cells dominated, while on fixed-time experiments time-encoding cells dominated. These results suggest that the cells encoding contains a predictive element, dependent on the important variables of the experiment.

neuroscience↗

bioRxiv2022

MicroRNA-335-5p suppresses voltage-gated sodium channel expression and may be a target for seizure control

There remains an urgent need for new therapies for drug-resistant epilepsy (DRE). Sodium channel blockers are effective for seizure control in common forms of epilepsy, but loss of sodium channel function underlies some genetic forms of epilepsy. Approaches that provide bi-directional control of sodium channel expression are needed. MicroRNAs (miRNA) are small non-coding RNAs which negatively regulate gene expression. Here, we show that genome-wide miRNA screening of hippocampal tissue from a rat epilepsy model, mice treated with the novel anti-seizure medicine cannabidiol (CBD) and plasma from patients with DRE, converge on a single target, miR-335-5p. Pathway analysis on predicted and validated miR-335-5p targets identified multiple voltage-gated sodium channels (VGSCs). Intracerebroventricular injection of antisense oligonucleotides against miR-335-5p resulted in upregulation of Scn1a, Scn2a and Scn3a in the mouse brain and an increased action potential rising phase and greater excitability of hippocampal pyramidal neurons in brain slice recordings, consistent with VGSCs as functional targets of miR-335-5p. Blocking of miR-335-5p also increased voltage-gated sodium currents in human iPSC-derived neurons. Inhibition of miR-335-5p increased susceptibility to tonic-clonic seizures in the pentylenetetrazole seizure model, whereas AAV9-mediated overexpression of miR-335-5p reduced seizure severity and improved survival. These studies suggest modulation of miR-335-5p may be a means to regulate VGSCs and affect brain excitability and seizures. Changes to miR-335-5p may reflect compensatory mechanisms to control excitability and could provide new biomarker or therapeutic strategies for different types of drug-resistant epilepsy. Significance StatementDespite the clinical availability of over 30 anti-seizure medications (ASMs), around 30% of people with epilepsy do not achieve seizure freedom. MicroRNAs are small non-coding RNAs which negatively regulate protein expression by binding to target mRNAs. Here, we identified the brain-enriched miR-335-5p to be commonly altered in three heterogenous miRNA profiling datasets. Bi-directional modulation of miR-335-5p identified a potential homeostatic role of miR-335-5p in brain excitability involving voltage-gated sodium channels. Electrophysiological and in vivo approaches revealed pro-epileptic activity of miR-335-5p inhibition whereas overexpression of miR-335-5p resulted in anti-epileptic activity. Overall, targeting miR-335-5p could provide a new approach in the modulation of brain excitability, with possible therapeutic applications in drug-resistant epilepsies and other neurological diseases.

neuroscience↗

bioRxiv2022

Experience, not time, determines representational drift in the hippocampus

Memories of past events can be recalled long after the event, indicating stability. But new experiences are also integrated into existing memories, indicating plasticity. In the hippocampus, spatial representations are known to remain stable, but have also been shown to drift over long periods of time. We hypothesized that experience, more than the passage of time, is the driving force behind memory plasticity. We compared the stability of place cells in the hippocampus of mice traversing two similar, familiar tracks for different durations. We found that the more time spent in an environment, the greater the representational drift, regardless of the total elapsed time. Our results suggest that spatial representation is a dynamic process, related to the ongoing experiences within a specific context, and is related to the accumulation of new memories rather than to passive forgetting. HighlightsO_LIRepresentational drift is related to experience within an environment. C_LIO_LIRepresentational drift is a dynamic context-wide process. C_LIO_LIPlace cell number decreases with experience, spatial information content increases. C_LI

neuroscience↗

bioRxiv2022

Goal-directed action is transiently impaired in an hAPP-J20 mouse model of Alzheimer's disease, and in aging male mice regardless of genotype

Cognitive-behavioural testing in preclinical models of Alzheimers disease has typically been limited to visuo-spatial memory tests and has failed to capture the broad scope of deficits patients also display in goal-directed action control. The current study addresses this gap by providing the first comprehensive investigation of how goal-directed actions are affected in a transgenic mouse model of Alzheimers disease. Specifically, we tested outcome devaluation performance - a popular test of goal-directed action - in male and female human amyloid precursor protein (hAPP)-J20 mice. Mice were first trained to press a left and right lever for unique pellet and sucrose outcomes respectively (counterbalanced) over four days. On test, mice were fed one of the two outcomes to reduce its value via sensory specific satiety and subsequently given a choice between levers. Goal-directed action was intact for 36-week-old wildtype mice of both sexes, because they responded more on the lever associated with the still-valued outcome than that associated with the devalued outcome (i.e. Valued > Devalued). Goal-directed action was impaired (Valued = Devalued) for J20 mice of both sexes, and for 52-week-old male mice regardless of genotype. Following an additional 4 days of lever press training (i.e., 8 days lever pressing in total), outcome devaluation was intact for all mice regardless of age or genotype. Immunohistochemical analysis revealed that increased microglial expression in the dorsal CA1 region of the hippocampus was associated with poorer outcome devaluation performance on initial tests, but not with tests performed after 8 days of lever pressing. Together, these data demonstrate that goal-directed action is transiently impaired in J20 mice of both sexes and in aging male mice regardless of genotype, and that this impairment is related to neuroinflammation in the dorsal CA1 region of the hippocampus.

animal behavior and cognition↗

bioRxiv2022

MicroRNA inhibition using antimiRs in acute human brain tissue sections

IntroductionAn emerging pre-clinical approach for the treatment of pharmacoresistant epilepsy is targeting the microRNA (miRNA) system. MiRNAs are short noncoding RNAs that suppress gene expression at the post-transcriptional level. Targeting miRNAs, which is possible using antisense oligonucleotide antimiRs can produce broad effects on gene expression suited to the complex pathophysiology in temporal lobe epilepsy. Potent anti-seizure and disease- modifying effects have been reported for antimiRs targeting microRNA-134 (antimiR-134). To date, however, pre-clinical testing has been performed using in vitro cell cultures and rodent models. It is uncertain how well this approach will translate to the clinic. Here, we develop an antimiR testing platform in human brain tissue sections. MethodologyHuman brain specimens were obtained with consent from patients undergoing resective surgery to treat focal drug-resistant epilepsy. Neocortical specimens were submerged in modified artificial cerebrospinal fluid (ACSF), dissected for clinical neuropathological examination, and unused material transferred for sectioning. Individual tissue sections were incubated in oxygenated ACSF, containing either antimiR-134 or a non-targeting control antimiR, for 24 hours at room temperature. RNA integrity was assessed using BioAnalyzer processing, and individual miRNA levels measured using RT-qPCR. ResultsACSF transport had no obvious impact on any clinical neurosurgical or neuropathological procedure and specimens were confirmed to be viable following this process. RNA was well- preserved by transportation of specimens in ACSF, with RNA integrity scores significantly higher than tissue transported without ACSF. AntimiR-134 mediated a specific and dose- dependent knockdown of miR-134 in human neocortical sections, with approximately 75% reduction of miR-134 at 1 {micro}M and 90% reduction at 3 {micro}M. These doses did not have off- target effects on expression of a selection of three other miRNAs (miR-10, miR-129 or miR- 132). SignificanceThis is the first demonstration of antimiR-134 effects in live human brain tissues. The findings lend further support to the preclinical development of miR-134 and offer a flexible platform for the pre-clinical testing of antimiRs, and other antisense oligonucleotide therapeutics, in human brain. Key pointsO_LIASO antimiRs are promising treatments for pharmacoresistant epilepsy C_LIO_LIWe developed a pipeline to preserve live human neocortical brain specimens from people undergoing resective surgery C_LIO_LIRNA integrity was sufficient to measure miRNA levels in human brain tissues transported in modified ACSF C_LIO_LIIncubation of acute human neocortical specimens in antimiR-134 resulted in potent and specific reduction in miR-134 levels C_LIO_LIAcute human brain slices are a promising model for testing ASOs C_LI

neuroscience↗

bioRxiv2021

The eukaryotic translation initiation factor eIF4E reprogrammes the splicing machinery anddrives alternative splicing

Aberrant RNA splicing contributes to the pathogenesis of many malignancies including Acute Myeloid Leukemia (AML). While mutation is the best described mechanism underpinning aberrant splicing, recent studies show that predictions based on mutations alone likely underestimate the extent of this dysregulation. Here, we show that elevation of the eukaryotic translation initiation factor eIF4E reprogrammes splicing of nearly a thousand RNAs in model cell lines. Further, in AML patient specimens which did not harbour known splice factor mutations, [~]4000 transcripts were differentially spliced based on eIF4E levels and this was associated with poor prognosis. Inhibition of eIF4E in cell lines reverted the eIF4E-dependent splice events examined. Splicing targets of eIF4E act in biological processes consistent with its role in malignancy. This altered splicing program likely arose from eIF4E-dependent increases in the production of spliceosome components including SF3B1 and U2AF1 which are frequently mutated in AML. Notably, eIF4E did not drive mutation of these factors, only their production. eIF4E also physically associated with many splice factors including SF3B1, U2AF1, and UsnRNAs. Interestingly, eIF4E interacted with both pre-mRNA splicing substrates as well as the resulting product RNAs suggesting that eIF4E could chaperone RNAs throughout splicing as well as other aspects of post-splicing transcript regulation. Importantly, many eIF4E-dependent splice events differed from those arising from splice factor mutation and were more extensive highlighting that these splicing profiles arise from distinct, but potentially overlapping, mechanisms. In all, our studies provide a paradigm for how dysregulation of a single factor, eIF4E, can reprogramme splicing.

cancer biology↗

bioRxiv2021

Germline variants that influence the tumor immune microenvironment also drive response to immunotherapy

With the continued promise of immunotherapy as an avenue for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Approaches that intersect SNP modifiers of molecular phenotype, such as gene expression, with disease phenotypes have shown promise for implicating causal genetic factors. Here we evaluated 194 literature-curated TIME associations and 890 associations detected with 157 immune phenotype (IP) components found using genotypes from over 8,000 individuals in The Cancer Genome Atlas. Of these 1084, 233 associations comprising 219 unique TIME-SNPs were also cancer relevant, associating with cancer risk, survival, and/or immunotherapy treatment response. Many cancer relevant TIME-SNPS overlapped regions of active transcription, and were associated with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. TIME-SNPs associated with cancer risk and response to immunotherapy implicated genes involved in antigen presentation, especially by antigen presenting cells. The strongest associations with survival were with PD-L1 and CTLA-4, suggesting that SNPs modifying the potential for immune evasion could contribute to disease progression. To assess whether our approach could reveal novel cancer immunotherapy targets, we inhibited CTSS, a gene implicated by cancer risk and immunotherapy response-associated TIME-SNPs; CTSS inhibition resulted in slowed tumor growth and extended survival in vivo. These results validate the potential of cancer relevant TIME-SNPs to implicate target genes for countering immune suppressive characteristics of the TIME and set the stage for future host genetics analysis integrating germline variation and TIME characteristics. SignificanceA systematic screen for common germline variants associated with the tumor immune microenvironment across > 8000 tumors reveals novel cancer risk factors and targets for immunotherapy.

cancer biology↗

bioRxiv2019

A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy

MicroRNAs (miRNAs) are short noncoding RNAs that shape the gene expression landscape, including during the pathogenesis of temporal lobe epilepsy (TLE). In order to provide a full catalog of the miRNA changes that happen during experimental TLE, we sequenced Argonaute 2-loaded miRNAs in the hippocampus of three different animal models at regular intervals between the time of the initial precipitating insult to the establishment of spontaneous recurrent seizures. The commonly upregulated miRNAs were selected for a functional in vivo screen using oligonucleotide inhibitors. This revealed anti-seizure phenotypes upon inhibition of miR-10a-5p, miR-21a-5p and miR-142a-5p as well as neuroprotection-only effects for inhibition of miR-27a-3p and miR-431-5p. Proteomic data and pathway analysis on predicted and validated targets of these miRNAs indicated a role for TGF{beta} signaling in a shared seizure-modifying mechanism. Together, these results identify functional miRNAs in the hippocampus and a pipeline of new targets for seizure control in epilepsy.

neuroscience↗

bioRxiv2019

Genomics of sorghum local adaptation to a parasitic plant

Host-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential tradeoffs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and belowground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with tradeoffs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9 edited sorghum further indicate the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities. SIGNIFICANCE STATEMENTUnderstanding co-evolution in crop-parasite systems is critical to management of myriad pests and pathogens confronting modern agriculture. In contrast to wild plant communities, parasites in agricultural ecosystems are usually expected to gain the upper hand in co-evolutionary arms races due to limited genetic diversity of host crops in cultivation. Here, we develop a framework to characterize associations between genome variants in global landraces (traditional varieties) of the staple crop sorghum with the distribution of the devastating parasitic weed Striga hermonthica. We find long-term maintenance of diversity in genes related to parasite resistance, highlighting an important role of host adaptation for co-evolutionary dynamics in smallholder agroecosystems.

evolutionary biology↗

bioRxiv2019

Estimating Attentional Set-Shifting Dynamics in Varying Contextual Bandits

In this paper, we aim at estimating, on a trial-by-trial basis, the underlying decision-making process of an animal in a complex and changing environment. We propose a method for identifying the set of stochastic policies employed by the agent and estimating the transition dynamics between policies based on its behavior in a multidimensional discrimination task for measuring the properties of attentional set-shifting of the subject (both intra- and extra-dimensional). We propose using the Non-Homogeneous Hidden Markov Models (NHMMs) framework, to consider environmental state and rewards for modeling decision-making processes in a varying version of \"Contextual Bandits\". We employ the Expectation-Maximization (EM) procedure for estimating the models parameters similar to the Baum-Welch algorithm used to train standard HMMs. To measure the model capacity to estimate underlying dynamics, Monte Carlo analysis is employed on synthetically generated data and compared to the performance of classical HMM.

neuroscience↗