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

OsTBP2.1, a TATA-Binding Protein, Alters the Ratio of <i>OsNRT2.3b</i> to <i>OsNRT2.3a</i> and Improves Rice Grain Yield

The OsNRT2.3a and OsNRT2.3b isoforms play important roles in the uptake and transport of nitrate during rice growth. However, it is unclear which cis-acting element controls the transcription of OsNRT2.3 into these specific isoforms. In this study, we used a yeast one-hybrid assay to obtain the TATA-box binding protein OsTBP2.1, which binds to the TATA-box of OsNRT2.3, and verified its important role through transient expression and RNA-seq. We found that the TATA-box of OsNRT2.3 mutants and binding protein OsTBP2.1 together increased the transcription ratio of OsNRT2.3b to OsNRT2.3a. The overexpression of OsTBP2.1 promoted nitrogen uptake and increased rice yield compared with the wild-type; however, the OsTBP2.1 T-DNA mutant lines exhibited the opposite trend. Detailed analyses demonstrated that the TATA-box was the key cis-regulatory element for OsNRT2.3 to be transcribed into OsNRT2.3a and OsNRT2.3b. Additionally, this key cis-regulatory element, together with the binding protein OsTBP2.1, promoted the development of rice and increased grain yield

A general and rapid synthesis of metal sulphides hollow spheres that have properties enhanced by salt-assisted aerosol decomposition: a case of ZnS and other multicomponent solid solutions

Synthesis of hollow structures of metal sulphides generally involves various templates and complex chemical processing. In the present study, a general and rapid method of salt-assisted aerosol decomposition (SAD) is presented for the synthesis of hollow spheres of various metal sulfides, including ZnS, ternary sulfides, and solid solutions. The NaCl salt plays a critical role in the formation of hollow spheres of metal sulfides. The hollow spherical microstructure was formed from solid by using a small amount of water soluble NaCl salt. The formation of metal sulphide hollow spheres differs from previous mechanisms and is referred to as molten salt heterogeneous nucleation (MSHN). The present method offers the most promising advantage for controlling the multicomponent composition of hollow spheres. Furthermore, hollow spheres of sulphides have much enhanced properties such as photoluminescence of ZnS:Mn2+and photocatalytic dye degradation of ZnIn2S4due to the role of molten salt in the promotion of crystallization, The present method could be explored further by applying the process to other compounds such as sulfides, oxides, and nitrides

Improved glomerular filtration rate estimation by an artificial neural network.

BACKGROUND: Accurate evaluation of glomerular filtration rates (GFRs) is of critical importance in clinical practice. A previous study showed that models based on artificial neural networks (ANNs) could achieve a better performance than traditional equations. However, large-sample cross-sectional surveys have not resolved questions about ANN performance. METHODS: A total of 1,180 patients that had chronic kidney disease (CKD) were enrolled in the development data set, the internal validation data set and the external validation data set. Additional 222 patients that were admitted to two independent institutions were externally validated. Several ANNs were constructed and finally a Back Propagation network optimized by a genetic algorithm (GABP network) was chosen as a superior model, which included six input variables; i.e., serum creatinine, serum urea nitrogen, age, height, weight and gender, and estimated GFR as the one output variable. Performance was then compared with the Cockcroft-Gault equation, the MDRD equations and the CKD-EPI equation. RESULTS: In the external validation data set, Bland-Altman analysis demonstrated that the precision of the six-variable GABP network was the highest among all of the estimation models; i.e., 46.7 ml/min/1.73 m(2) vs. a range from 71.3 to 101.7 ml/min/1.73 m(2), allowing improvement in accuracy (15% accuracy, 49.0%; 30% accuracy, 75.1%; 50% accuracy, 90.5% [P<0.001 for all]) and CKD stage classification (misclassification rate of CKD stage, 32.4% vs. a range from 47.3% to 53.3% [P<0.001 for all]). Furthermore, in the additional external validation data set, precision and accuracy were improved by the six-variable GABP network. CONCLUSIONS: A new ANN model (the six-variable GABP network) for CKD patients was developed that could provide a simple, more accurate and reliable means for the estimation of GFR and stage of CKD than traditional equations. Further validations are needed to assess the ability of the ANN model in diverse populations

Comparison of F-18-labeled CXCR4 antagonist peptides for PET imaging of CXCR4 expression

Intramural Research Program of the National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH); National Research Council Research Associateship Award at NIH/NIBIBCXCR4 is overexpressed on tumor cells from many types of human cancers. A high level of CXCR4 expression often correlates with poor prognosis, chemotherapy resistance, and metastasis. The development of CXCR4-specific radiotracers for positron emission tomography (PET) imaging will allow in vivo evaluation of receptor expression level for diagnosis or therapeutic evaluation. Two new F-18-labeled radiotracers based on an Ac-TC14012 peptide, [F-18]FP-Ac-TC14012 and [F-18]FB-Ac-TC14012, were synthesized and characterized. The affinities of the 2-fluoropropionate (FP)-conjugated or 4-fluorobenzoate (FB)-conjugated peptides to CXCR4-transfected Chinese hamster ovarian (CHO) cells were evaluated in a competitive binding assay with [I-125]CXCL12 radioligand. The cell uptake and retention of [F-18]FP-labeled and [F-18]FB-labeled peptides were measured. The tumor targetability and pharmacokinetics of these two tracers were also evaluated by microPET imaging and biodistribution studies. The labeled peptides retained high binding affinity to CXCR4 and showed much higher uptake in CXCR4-positive CHO cells than in CXCR4-negative cells in vitro. The smaller and more hydrophilic [F-18]FP prosthetic group resulted in higher affinity and lower nonspecific cell uptake compared to the [F-18]FB-labeled peptide. Both radiotracers showed much higher accumulation in CXCR4-positive than CXCR4-negative tumor xenografts in mice and allowed clear visualization of CXCR4 expression by PET. Among the two, [F-18]FP-Ac-TC14012 showed higher tumor uptake and better tumor-to-background contrast. Unlike their N-terminal 4-F-benzoate analogs, these two tracers had minimal blood retention, likely due to reduced red blood cell binding. Metabolic organs, such as the liver and kidney, also showed high uptake. When blocked with low-dose cold peptide (10 mu g), the tumor uptake was significantly increased, most likely due to the increased concentration in blood circulation, as evidenced by decreased liver uptake. These results demonstrate that the [F-18]FP-labeled Ac-TC14012 peptide with high tumor uptake, low nonspecific binding, and good tumor-to-background contrast promises [F-18]FP-Ac-TC14012 as a PET tracer for in vivo PET imaging of CXCR4 expression

Manufacturing N,O-carboxymethyl chitosan-reduced graphene oxide under freeze-dying for performance improvement of Li-S battery

Lithium-sulfur (Li-S) batteries can provide far higher energy density than currently commercialized lithium ion batteries, but challenges remain before it they are used in practice. One of the challenges is the shuttle effect that originates from soluble intermediates, like lithium polysulfides. To address this issue, we report a novel laminar composite, N,O-carboxymethyl chitosan-reduced graphene oxide (CC-rGO), which is manufactured via the self-assembly of CC onto GO and subsequent reduction of GO under an extreme condition of 1 Pa and −50 °C. The synthesized laminar CC-rGO composite is mixed with acetylene black (AB) and coated on a commercial polypropylene (PP) membrane, resulting in a separator (CC-rGO/AB/PP) that can not only completely suppress the polysulfides penetration, but also can accelerate the lithium ion transportation, providing a Li-S battery with excellent cyclic stability and rate capability. As confirmed by theoretic simulations, this unique feature of CC-rGO is attributed to its strong repulsive interaction to polysulfide anions and its benefit for fast lithium ion transportation through the paths paved by the heteroatoms in CC