Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example

© The Author(s) 2017 This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/ genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.Peer reviewedFinal Published versio

MDA5 against enteric viruses through induction of interferon-like response partially via the JAK-STAT cascade

Enteric viruses including hepatitis E virus (HEV), human norovirus (HuNV), and rotavirus are causing global health issues. The host interferon (IFN) response constitutes the first-line defense against viral infections. Melanoma Differentiation-Associated protein 5 (MDA5) is an important cytoplasmic receptor sensing viral infection to trigger IFN production, and on the other hand it is also an IFN-stimulated gene (ISG). In this study, we investigated the effects and mode-of-action of MDA5 on the infection of enteric viruses. We found that MDA5 potently inhibited HEV, HuNV and rotavirus replication in multiple cell models. Overexpression of MDA5 induced transcription of important antiviral ISGs through IFN-like response, without triggering of functional IFN production. Interestingly, MDA5 activates the expression and phosphorylation of STAT1, which is a central component of the JAK-STAT cascade and a hallmark of antiviral IFN response. However, genetic silencing of STAT1 or pharmacological inhibition of the JAK-STAT cascade only partially attenuated the induction of ISG transcription and the antiviral function of MDA5. Thus, we have demonstrated that MDA5 effectively inhibits HEV, HuNV and rotavirus replication through provoking a non-canonical IFN-like response, which is partially dependent on JAK-STAT cascade

The interplay between host innate immunity and hepatitis E virus

Hepatitis E virus (HEV) infection represents an emerging global health issue, whereas the clinical outcomes vary dramatically among different populations. The host innate immune system provides a first-line defense against the infection, but dysregulation may partially contribute to severe pathogenesis. A growing body of evidence has indicated the active response of the host innate immunity to HEV infection both in experimental models and in patients. In turn, HEV has developed sophisticated strategies to counteract the host immune system. In this review, we aim to comprehensively decipher the processes of pathogen recognition, interferon, and inflammatory responses, and the involvement of innate immune cells in HEV infection. We further discuss their implications in understanding the pathogenic mechanisms and developing antiviral therapies

“Living” luminogens: light driven ACQ-to-AIE transformation accompanied with solid-state actuation

In situ ACQ-to-AIE transformation was achieved by light-induced [2+2] cycloaddition via through-space conjugation.</p

Robust Supramolecular Nano-Tunnels Built from Molecular Bricks

Chemists are always seeking new methods to construct porous lattice frameworks using simple motifs as the impetus. Different from the extensively reported frameworks which were stabilized by extended bonding, porous crystals of discrete organic molecules is an emerging area of porous materials with dynamic and flexible conformation, consisting exclusively of non-covalent interactions. Herein we report geometrically simple linear molecule that assemble into a supramolecular nano-tunnel through synergy of anionic trident and multiple intermolecular pi-pi stacking interactions. The nano-tunnel crystal exhibit exceptional chemical stability in concentrated HCl and NaOH aqueous solutions, which is rarely been seen in supramolecular organic frameworks and often related to designed extensive hydrogen bonding interactions. Upon thermal treatment, the formed nano-tunnel crystals go through multistage single-crystal-to-single-crystal phase transformations accompanied by thermosalient effect. Aggregation-induced emission joins with the adaptive pores render the crystals with responsive fluorescent change from blue to yellow and visible self-healing porosity transformation upon being stimulated. Furthermore, the desolvated pores exhibit highly selective CO2 adsorption at ambient temperature. &lt;br&gt;</jats:p

Positive/Negative Phototropism: Controllable Molecular Actuators with Different Bending Behavior

Herein, a series of molecular actuators based on the crystals of (E)‐2‐(4‐fluorostyryl)benzo[d]oxazole (BOAF4),(E)‐2‐(2,4‐difluorostyryl)benzo[d]oxazole (BOAF24), (E)‐2‐(4‐fluorostyryl)benzo[d]thiazole (BTAF4) and (E)‐2‐(2,4‐difluorostyryl)benzo[d]thiazole (BTAF24) showed unprecedented different bending behavior under UVirradiation. BOAF4 and BTAF4 bent towards light, whereas BOAF24 and BTAF24 bent away from light.Although the chemical structures of these compounds are similar, we found out the F‒H‒C interaction wasthe main driving force for the different molecular packing in the crystals, which led to the positive/negativephototropism of the actuators. Moreover, the theoretical calculation was carried out to reveal the mechanicalproperties of the crystals. Taking advantage of the photo responsive property, we achieved the potentialapplication in pushing objects, as well as enriching and removing pollutants. This system not only achieved aclass of molecular actuators with different bending behavior through introducing different number of F atom,but also realized pushing and catching behavior within one molecule, which opens a novel gate for crystalengineering</div

Robust Supramolecular Nano-Tunnels Built from Molecular Bricks

Chemists are always seeking new methods to construct porous lattice frameworks using simple motifs as the impetus. Different from the extensively reported frameworks which were stabilized by extended bonding, porous crystals of discrete organic molecules is an emerging area of porous materials with dynamic and flexible conformation, consisting exclusively of non-covalent interactions. Herein we report geometrically simple linear molecule that assemble into a supramolecular nano-tunnel through synergy of anionic trident and multiple intermolecular pi-pi stacking interactions. The nano-tunnel crystal exhibit exceptional chemical stability in concentrated HCl and NaOH aqueous solutions, which is rarely been seen in supramolecular organic frameworks and often related to designed extensive hydrogen bonding interactions. Upon thermal treatment, the formed nano-tunnel crystals go through multistage single-crystal-to-single-crystal phase transformations accompanied by thermosalient effect. Aggregation-induced emission joins with the adaptive pores render the crystals with responsive fluorescent change from blue to yellow and visible self-healing porosity transformation upon being stimulated. Furthermore, the desolvated pores exhibit highly selective CO2 adsorption at ambient temperature. <br /

Anti-Kasha System by Design: A New Gateway for Cell Differentiation Through Machine Learning

&lt;div&gt;Kasha’s rule, which claimed that all emissions of excitons are from the lowest excited state and independent of excitation energy, makes the utility of high energy excitons difficult and severely hinder the widespread application of organic photoluminescent materials in real-world. For decades, scientists try to break it to unleash the power of high energy excitons but get minimal progress, no rational guiding principles, and few applications. So far, anti-Kasha’s rule is still a purely academic concept. In this contribution, we proposed a designing principle for pure organic anti-Kasha’s rule system and synthesized a series of compounds by following this designing rule which are all display evident S 2 emission in dilute solutions as proposed. Besides, we introduced a convolutional neural network as an assistant to apply the anti-Kasha’s rule luminogens to cell differentiations with high accuracy (~98.3%), which provide a new direction of applications of anti-Kasha system.&lt;/div&gt;</jats:p