Systems Mapping: How to Improve the Genetic Mapping of Complex Traits Through Design Principles of Biological Systems

Background: Every phenotypic trait can be viewed as a “system” in which a group of interconnected componentsfunction synergistically to yield a unified whole. Once a system’s components and their interactions have beendelineated according to biological principles, we can manipulate and engineer functionally relevant components toproduce a desirable system phenotype.Results: We describe a conceptual framework for mapping quantitative trait loci (QTLs) that control complex traitsby treating trait formation as a dynamic system. This framework, called systems mapping, incorporates a system ofdifferential equations that quantifies how alterations of different components lead to the global change of traitdevelopment and function through genes, and provides a quantitative and testable platform for assessing theinterplay between gene action and development. We applied systems mapping to analyze biomass growth data ina mapping population of soybeans and identified specific loci that are responsible for the dynamics of biomasspartitioning to leaves, stem, and roots.Conclusions: We show that systems mapping implemented by design principles of biological systems is quiteversatile for deciphering the genetic machineries for size-shape, structural-functional, sink-source and pleiotropicrelationships underlying plant physiology and development. Systems mapping should enable geneticists to shedlight on the genetic complexity of any biological system in plants and other organisms and predict itsphysiological and pathological states

Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems

<p>Abstract</p> <p>Background</p> <p>Every phenotypic trait can be viewed as a "system" in which a group of interconnected components function synergistically to yield a unified whole. Once a system's components and their interactions have been delineated according to biological principles, we can manipulate and engineer functionally relevant components to produce a desirable system phenotype.</p> <p>Results</p> <p>We describe a conceptual framework for mapping quantitative trait loci (QTLs) that control complex traits by treating trait formation as a dynamic system. This framework, called systems mapping, incorporates a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function through genes, and provides a quantitative and testable platform for assessing the interplay between gene action and development. We applied systems mapping to analyze biomass growth data in a mapping population of soybeans and identified specific loci that are responsible for the dynamics of biomass partitioning to leaves, stem, and roots.</p> <p>Conclusions</p> <p>We show that systems mapping implemented by design principles of biological systems is quite versatile for deciphering the genetic machineries for size-shape, structural-functional, sink-source and pleiotropic relationships underlying plant physiology and development. Systems mapping should enable geneticists to shed light on the genetic complexity of any biological system in plants and other organisms and predict its physiological and pathological states.</p

Apple Quality Evaluation Based on Entropy Weight Method, Grey Relational Degree Method and Low-field Nuclear Magnetic Resonance Detection

To study the quality characteristics of different apple varieties and establish a comprehensive evaluation model of apple quality, taking five varieties of apples (Tianshui Huaniu, Aksu Tangxin, Marshal Huang, Cream Fuji, and Luochuan Red Fuji) as the research object, the four texture characteristics, including hardness, adhesion, chewability, cohesion, and four physical and chemical indicators, including water content, titratable acid (TA), soluble sugar (SS), and soluble solid content (SSC) were tested. Combining the low-field nuclear magnetic resonance detection technology, the correlation between the water distribution and the physicochemical and texture characteristics of apple was explored, and the main indicators for evaluating apple quality were established by principal component analysis. Based on the entropy weight method, each core index was given weight, and a grey correlation degree evaluation model was established. The results showed that there were significant differences in various indexes of different varieties of apples (P<0.05), and there was a high correlation between their water distribution and texture characteristics and physical and chemical indexes. The spin-spin relaxation time T22 (immobilized water), T21 (bound water) and TA, SS, SSC were established as the core indexes. The weight calculated by entropy weight method showed that the sum of T22 and T21 was 35.31%, accounting for the largest proportion, indicating that the water distribution had the greatest impact on apple quality. The grey correlation analysis showed that the quality of Tianshui Huaniu and Aksu Tangxin was better. The method adopted in this study could quickly and accurately establish the quality evaluation model of apples, and provide a new method for the quality evaluation of fruits and vegetables including apples

Static and dynamical properties of the spin-5/2 nearly ideal triangular lattice antiferromagnet Ba3MnSb2O9

We study the ground state and spin excitation in Ba3MnSb2O9, an easy-plane S = 5/2 triangular lattice antiferromagnet. By combining single-crystal neutron scattering, electric spin resonance (ESR), and spin wave calculations, we determine the frustrated quasi-two-dimensional spin Hamiltonian parameters describing the material. While the material has a slight monoclinic structural distortion, which could allow for isosceles triangular exchanges and biaxial anisotropy by symmetry, we observe no deviation from the behavior expected for spin waves in the in-plane 120o state. Even the easy-plane anisotropy is so small that it can only be detected by ESR in our study. In conjunction with the quasi-two-dimensionality, our study establishes that Ba3MnSb2O9 is a nearly ideal triangular lattice antiferromagnet with the quasi-classical spin S = 5/2, which suggests that it has the potential for an experimental study of Z- or Z2-vortex excitations

A biophoton method for identifying the quality states of fresh Chinese herbs

Introduction: The quality of Chinese herbs is the basis for ensuring their safety and efficacy. However, the quality evaluation system is imperfect. In particular, there is a lack of quality evaluation methods for fresh Chinese herbs during growth. The biophoton is a common phenomenon and provides complete information about the interior of the living system, which is consistent with the holistic concept of traditional Chinese medicine. Therefore, we aim to correlate the biophoton characteristics with the quality states to find the biophoton parameters that can characterize the quality states of fresh Chinese herbs.Methods: The biophoton characteristics of motherwort and safflower were measured and characterized by the counts per second (CPS) in the steady state and the initial intensity (I0) and coherent time (T) of delayed luminescence. The active ingredient content was measured by ultra-high-performance liquid chromatography (UPLC). The pigment content of motherwort leaves was measured by UV spectrophotometry. The t-test and correlation analysis were performed on the experimental results.Results: The CPS and I0 of motherwort and I0 of safflower showed a significant downward trend during the growth process, and their active ingredient content showed a trend that increased and then decreased. The CPS, I0, and the content of active ingredients and pigments in a healthy state were significantly higher than those in a poor state, while T showed the opposite results. The CPS and I0 were all significantly and positively correlated with the content of active ingredients and pigments, while the T of motherwort showed the opposite results.Conclusion: It is feasible to identify the quality states of fresh Chinese herbs by using their biophoton characteristics. Both CPS and I0 have better correlations with the quality states and can be considered characteristic parameters of the quality of fresh Chinese herbs

Temporal variability of visibility and its parameterizations in Ningbo, China

Simultaneous and continuous measurements of visibility, meteorological parameters and air pollutants were carried out at a suburban site in Ningbo from June 1, 2013 to May 31, 2015. The characteristics of visibility and their relationships with air pollutants and meteorological factors were investigated using multiple statistical methods. Daily visibility ranged from 0.6 to 34.1 km, with a mean value of 11.8 km. During the 2-year experiment, 43.4% of daily visibility was found to be less than 10.0 km and only 9.2% was greater than 20.0 km. Visibility was lower in winter with a frequency of 53.4% in the range of 0.0–5.0 km. Annual visibility had an obvious diurnal variation, with the lowest and highest visibility being 7.5 km at approximately 06:00 local time and 15.6 km at approximately 14:00 local time, respectively. Multiple correspondence analysis (MCA) indicated that the different ranges of visibility were significantly affected by different levels of pollutants and meteorological conditions. Based on the analyses, visibility was found to be an exponential function of PM2.5 concentrations within a certain range of relative humidity. Thus, non-linear models combining multiple linear regressions with exponential regression were subsequently developed using the data collected from June 2014 to May 2015, and the data from June 2013 to May 2014 was used to evaluate the performance of the model. It was demonstrated that the derived models can quantitatively describe the relationships between visibility, air quality and meteorological parameters in Ningbo