Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice

Manual phenotyping of rice tillers is time consuming and labor intensive and lags behind the rapid development of rice functional genomics. Thus, automated, non-destructive phenotyping of rice tiller traits at a high spatial resolution and high-throughput for large-scale assessment of rice accessions is urgently needed. In this study, we developed a high-throughput micro-CT-RGB (HCR) imaging system to non-destructively extract 730 traits from 234 rice accessions at 9 time points. We could explain 30% of the grain yield variance from 2 tiller traits assessed in the early growth stages. A total of 402 significantly associated loci were identified by GWAS, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at nine time points, which contained a major gene TAC1. Significant variants associated with tiller angle were enriched in the 3'-UTR of TAC1. Three haplotypes for the gene were found and rice accessions containing haplotype H3 displayed much smaller tiller angles. Further, we found two loci contained associations with both vigor-related HCR traits and yield. The superior alleles would be beneficial for breeding of high yield and dense planting

Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza

Tanshinones are the bioactive nor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones in Salvia genus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae

Do intraday data contain more information for volatility forecasting? Evidence from the Chinese commodity futures market

We compare volatility forecasts using daily data and intraday data at different frequencies from the Chinese commodity futures market. Focusing on aluminium, copper and fuel oil futures contracts with 3 months to maturity, our empirical results suggest that in the out-of-sample forecasting tests, there is little informational advantage in generating volatility forecasts using intraday data

Measuring the subprime crisis contagion: Evidence of change point analysis of copula functions

In this paper, we first determine the existence of structural changes in the dependence between time series of equity index returns of two markets using the change point testing method. The method is based on Archimedean copula functions, which are able to comprehensively describe dependence characteristics of random variables. The degree of financial contagion between markets is subsequently estimated using the tail dependence coefficient of copula functions before and after the change point. We empirically test our method by investigating financial contagion during the subprime crisis between the US S&P 500 index and five Asian markets, namely China, Japan, Korea, Hong Kong and Taiwan. Our results show that a statistically significant change point exists in the dependence between the US market and all Asian stock markets except Taiwan. The upper tail dependence is larger after the time of change, implying the existence of contagion during the banking crisis between the US and the Asian economies. The degree of financial contagion is also estimated and found to be consistent with market events and media reports during that period

implementing service-correlation aware service selection

International Business Machines China Company Limited (IBM); Zhejiang University (ZJU); Institute of Software, Chinese Academy of Sciences (ISCAS)In service-oriented system, by using service selection methods, service entities can be dynamically bound to abstract services. Major of current system have assumed that candidate services are independent of each other. However, recent research has discovered that services do have correlations which will impact Quality-of-Service (QoS) of the composition service [9]. This paper outlines the service-correlation-aware service selection approach, gives a detailed system design, and implements it as an Eclipse plug-in and integrates it into a composite service development environment. To demonstrate the practical utilization of this approach, we employ it to development of a travel agency system. The exploitation further validate that this solution can be applied to a large extent

Comparative physiological and metabolomic responses of four Brachypodium distachyon varieties contrasting in drought stress resistance

Brachypodium distachyon (Brachypodium) is not only a monocot grass species, but also a promising model organism of crop research. In this study, the drought resistance of four Brachypodium varieties was identified including drought stress-tolerant Bd1-1 and Bd21, drought stress-susceptible Bd3-1 and Bd18-1. Physiological assay showed that drought-tolerant varieties (Bd1-1 and Bd21) were more effective in maintenance of leaf water content, activation of catalase and peroxidase activities and accumulation of reduced glutathione, resulting in alleviated cell damage and lower reactive oxygen species level than drought-susceptible varieties (Bd3-1 and Bd18-1) in response to drought stress. In addition, 54 primary metabolites were differentially regulated among Brachypodium varieties and after drought stress treatment, indicating the complexity of Brachypodium response to drought stress. We also identified several commonly regulated metabolites especially some compatible solutes including proline and soluble sugars, which exhibited higher concentrations in the drought-tolerant varieties. Taken together, this study suggested that natural variation of Brachypodium varieties in response to drought stress might be connected with higher leaf water, enhanced accumulation of osmolyte and more effective antioxidant system, as well as the modulation of metabolic profiles under drought stress conditions

A Retroreflection Reduction Technique Based on the Wavefront Coded Imaging System

A novel anti-cat-eye effect imaging technique based on wavefront coding is proposed as a solution to the problem of previous anti-cat-eye effect imaging techniques where imaging quality was sacrificed to reduce the retroreflection from the photoelectric imaging equipment. With the application of the Fresnel–Kirchhoff diffraction theory, and the definition of generalized pupil function combining both phase modulation and defocus factors, the cat-eye echo formation of the wavefront coded imaging system is theoretically modeled. Based on the physical model, the diffracted spot profile distribution and the light intensity distribution on the observation plane are further simulated with the changes in the defocus parameter and the phase modulation coefficient. A verification test on the cat-eye laser echo power of the wavefront coded imaging system and that of the conventional imaging system at a 20 m distance are conducted, respectively. Simulations and experiment results show that compared with conventional imaging systems, the wavefront coding imaging system can reduce the retroreflection echo by two orders of magnitude while maintaining better imaging quality through defocusing

Analysis and Classification of Stride Patterns Associated with Children Development Using Gait Signal Dynamics Parameters and Ensemble Learning Algorithms

Measuring stride variability and dynamics in children is useful for the quantitative study of gait maturation and neuromotor development in childhood and adolescence. In this paper, we computed the sample entropy (SampEn) and average stride interval (ASI) parameters to quantify the stride series of 50 gender-matched children participants in three age groups. We also normalized the SampEn and ASI values by leg length and body mass for each participant, respectively. Results show that the original and normalized SampEn values consistently decrease over the significance level of the Mann-Whitney U test (p<0.01) in children of 3–14 years old, which indicates the stride irregularity has been significantly ameliorated with the body growth. The original and normalized ASI values are also significantly changing when comparing between any two groups of young (aged 3–5 years), middle (aged 6–8 years), and elder (aged 10–14 years) children. Such results suggest that healthy children may better modulate their gait cadence rhythm with the development of their musculoskeletal and neurological systems. In addition, the AdaBoost.M2 and Bagging algorithms were used to effectively distinguish the children’s gait patterns. These ensemble learning algorithms both provided excellent gait classification results in terms of overall accuracy (≥90%), recall (≥0.8), and precision (≥0.8077)