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"Miller, Allison"
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Crop genetic erosion
Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.
Journal Article
From forest to field: Perennial fruit crop domestication
Premise of the study: Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits. Key results: We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops. Conclusions: Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction.Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.
Journal Article
S100A9 Induced Inflammatory Responses Are Mediated by Distinct Damage Associated Molecular Patterns (DAMP) Receptors In Vitro and In Vivo
Release of endogenous damage associated molecular patterns (DAMPs), including members of the S100 family, are associated with infection, cellular stress, tissue damage and cancer. The extracellular functions of this family of calcium binding proteins, particularly S100A8, S100A9 and S100A12, are being delineated. They appear to mediate their functions via receptor for advanced glycation endproducts (RAGE) or TLR4, but there remains considerable uncertainty over the relative physiological roles of these DAMPs and their pattern recognition receptors. In this study, we surveyed the capacity of S100 proteins to induce proinflammatory cytokines and cell migration, and the contribution RAGE and TLR4 to mediate these responses in vitro. Using adenoviral delivery of murine S100A9, we also examined the potential for S100A9 homodimers to trigger lung inflammation in vivo. S100A8, S100A9 and S100A12, but not the S100A8/A9 heterodimer, induced modest levels of TLR4-mediated cytokine production from human PBMC. In contrast, for most S100s including S100A9, RAGE blockade inhibited S100-mediated cell migration of THP1 cells and major leukocyte populations, whereas TLR4-blockade had no effect. Intranasal administration of murine S100A9 adenovirus induced a specific, time-dependent predominately macrophage infiltration that coincided with elevated S100A9 levels and proinflammatory cytokines in the BAL fluid. Inflammatory cytokines were markedly ablated in the TLR4-defective mice, but unexpectedly the loss of TLR4 signaling or RAGE-deficiency did not appreciably impact the S100A9-mediated lung pathology or the inflammatory cell infiltrate in the alveolar space. These data demonstrate that physiological levels of S100A9 homodimers can trigger an inflammatory response in vivo, and despite the capacity of RAGE and TLR4 blockade to inhibit responses in vitro, the response is predominately independent of both these receptors.
Journal Article
Grapevine scion gene expression is driven by rootstock and environment interaction
Background
Grafting is a horticultural practice used widely across woody perennial crop species to fuse together the root and shoot system of two distinct genotypes, the rootstock and the scion, combining beneficial traits from both. In grapevine, grafting is used in nearly 80% of all commercial vines to optimize fruit quality, regulate vine vigor, and enhance biotic and abiotic stress-tolerance. Rootstocks have been shown to modulate elemental composition, metabolomic profiles, and the shape of leaves in the scion, among other traits. However, it is currently unclear how rootstock genotypes influence shoot system gene expression as previous work has reported complex and often contradictory findings.
Results
In the present study, we examine the influence of grafting on scion gene expression in leaves and reproductive tissues of grapevines growing under field conditions for three years. We show that the influence from the rootstock genotype is highly tissue and time dependent, manifesting only in leaves, primarily during a single year of our three-year study. Further, the degree of rootstock influence on scion gene expression is driven by interactions with the local environment.
Conclusions
Our results demonstrate that the role of rootstock genotype in modulating scion gene expression is not a consistent, unchanging effect, but rather an effect that varies over time in relation to local environmental conditions.
Journal Article
Non-invasive real-time genomic monitoring of the critically endangered kākāpō
We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō ( Strigops habroptilus ). We first established an environmental DNA metabarcoding protocol to identify the distribution of kākāpō and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality kākāpō reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kākāpō population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on kākāpō distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.
Journal Article
A machine learning approach to identifying important features for achieving step thresholds in individuals with chronic stroke
While many factors are associated with stepping activity after stroke, there is significant variability across studies. One potential reason to explain this variability is that there are certain characteristics that are necessary to achieve greater stepping activity that differ from others that may need to be targeted to improve stepping activity.
Using two step thresholds (2500 steps/day, corresponding to home vs. community ambulation and 5500 steps/day, corresponding to achieving physical activity guidelines through walking), we applied 3 different algorithms to determine which predictors are most important to achieve these thresholds.
We analyzed data from 268 participants with stroke that included 25 demographic, performance-based and self-report variables. Step 1 of our analysis involved dimensionality reduction using lasso regularization. Step 2 applied drop column feature importance to compute the mean importance of each variable. We then assessed which predictors were important to all 3 mathematically unique algorithms.
The number of relevant predictors was reduced from 25 to 7 for home vs. community and from 25 to 16 for aerobic thresholds. Drop column feature importance revealed that 6 Minute Walk Test and speed modulation were the only variables found to be important to all 3 algorithms (primary characteristics) for each respective threshold. Other variables related to readiness to change activity behavior and physical health, among others, were found to be important to one or two algorithms (ancillary characteristics).
Addressing physical capacity is necessary but not sufficient to achieve important step thresholds, as ancillary characteristics, such as readiness to change activity behavior and physical health may also need to be targeted. This delineation may explain heterogeneity across studies examining predictors of stepping activity in stroke.
Journal Article
Latent developmental and evolutionary shapes embedded within the grapevine leaf
Across plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences. Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a single leaf. Here, we measured the shapes of > 3200 leaves representing > 270 vines from wild relatives of domesticated grape (Vitis spp.) to determine whether leaf shapes attributable to genetics and development are separable from each other. We isolated latent shapes (multivariate signatures that vary independently from each other) embedded within the overall shape of leaves. These latent shapes can predict developmental stages independent from species identity and vice versa. Shapes predictive of development were then used to stage leaves from 1200 varieties of domesticated grape (Vitis vinifera), revealing that changes in timing underlie leaf shape diversity. Our results indicate that distinct latent shapes combine to produce a composite morphology in leaves, and that developmental and evolutionary contributions to shape vary independently from each other.
Journal Article
Leveraging Very-High Spatial Resolution Hyperspectral and Thermal UAV Imageries for Characterizing Diurnal Indicators of Grapevine Physiology
Efficient and accurate methods to monitor crop physiological responses help growers better understand crop physiology and improve crop productivity. In recent years, developments in unmanned aerial vehicles (UAV) and sensor technology have enabled image acquisition at very-high spectral, spatial, and temporal resolutions. However, potential applications and limitations of very-high-resolution (VHR) hyperspectral and thermal UAV imaging for characterization of plant diurnal physiology remain largely unknown, due to issues related to shadow and canopy heterogeneity. In this study, we propose a canopy zone-weighting (CZW) method to leverage the potential of VHR (≤9 cm) hyperspectral and thermal UAV imageries in estimating physiological indicators, such as stomatal conductance (Gs) and steady-state fluorescence (Fs). Diurnal flights and concurrent in-situ measurements were conducted during grapevine growing seasons in 2017 and 2018 in a vineyard in Missouri, USA. We used neural net classifier and the Canny edge detection method to extract pure vine canopy from the hyperspectral and thermal images, respectively. Then, the vine canopy was segmented into three canopy zones (sunlit, nadir, and shaded) using K-means clustering based on the canopy shadow fraction and canopy temperature. Common reflectance-based spectral indices, sun-induced chlorophyll fluorescence (SIF), and simplified canopy water stress index (siCWSI) were computed as image retrievals. Using the coefficient of determination (R2) established between the image retrievals from three canopy zones and the in-situ measurements as a weight factor, weighted image retrievals were calculated and their correlation with in-situ measurements was explored. The results showed that the most frequent and the highest correlations were found for Gs and Fs, with CZW-based Photochemical reflectance index (PRI), SIF, and siCWSI (PRICZW, SIFCZW, and siCWSICZW), respectively. When all flights combined for the given field campaign date, PRICZW, SIFCZW, and siCWSICZW significantly improved the relationship with Gs and Fs. The proposed approach takes full advantage of VHR hyperspectral and thermal UAV imageries, and suggests that the CZW method is simple yet effective in estimating Gs and Fs.
Journal Article
Distribution, hosts and long-term decline in abundance of the Patagonian lamprey inferred from diet assessment of albatrosses
Knowledge of lampreys during their marine phase is limited, and for the southern hemisphere species was gleaned from their predators (albatrosses) in the 1970s. Taking advantage of new methodologies and long-term data on predator diet and distributions, we infer diverse aspects of lamprey distribution and ecology. DNA analyses indicated that albatrosses at South Georgia prey on Patagonian lamprey Geotria macrostoma, originating from Argentina. Their core pelagic distribution when free swimming appears to be the Antarctic Polar Frontal zone (APFZ), and not South Georgia waters as assumed previously. If so, the APFZ would be the first known hotspot in abundance of an anadromous lamprey in oceanic waters. We could not identify a teleost fish that would be a likely host. Instead, we infer that the lamprey may prey on baleen whales, based on comparison of stable isotope ratios in lamprey with candidate host species, timing of appearance in albatross diets coincident with whale migrations, and circumstantial evidence (unexplained scarring recorded during the whaling era). We suggest that the lamprey do not tolerate cold Antarctic waters, and detach from southerly-migrating whales at the thermal boundary of the APFZ, where they become accessible to albatrosses in surface waters. Given strong evidence that relative importance of prey in seabird diets reflects availability in foraging areas, the steep decrease in the annual consumption of lamprey by albatrosses at South Georgia from > 550 tonnes in 1975–1976 and 1986, to very low levels in most years since 2012, is likely to indicate a major population decrease. Despite our unconventional means of assessing the population trend, there is a compelling case for listing of Patagonian lamprey at least as Near threatened by the International Union for the Conservation of Nature, and an urgent need to better understand anthropogenic threats in Argentina.
Journal Article