Topological data analysis expands the genotype to phenotype map for 3D maize root system architecture.

A central goal of biology is to understand how genetic variation produces phenotypic variation, which has been described as a genotype to phenotype (G to P) map. The plant form is continuously shaped by intrinsic developmental and extrinsic environmental inputs, and therefore plant phenomes are highly multivariate and require comprehensive approaches to fully quantify. Yet a common assumption in plant phenotyping efforts is that a few pre-selected measurements can adequately describe the relevant phenome space. Our poor understanding of the genetic basis of root system architecture is at least partially a result of this incongruence. Root systems are complex 3D structures that are most often studied as 2D representations measured with relatively simple univariate traits. In prior work, we showed that persistent homology, a topological data analysis method that does not pre-suppose the salient features of the data, could expand the phenotypic trait space and identify new G to P relations from a commonly used 2D root phenotyping platform. Here we extend the work to entire 3D root system architectures of maize seedlings from a mapping population that was designed to understand the genetic basis of maize-nitrogen relations. Using a panel of 84 univariate traits, persistent homology methods developed for 3D branching, and multivariate vectors of the collective trait space, we found that each method captures distinct information about root system variation as evidenced by the majority of non-overlapping QTL, and hence that root phenotypic trait space is not easily exhausted. The work offers a data-driven method for assessing 3D root structure and highlights the importance of non-canonical phenotypes for more accurate representations of the G to P map.

Research on Vibration Reduction Performance of Electromagnetic Active Seat Suspension Based on Sliding Mode Control.

Vehicle seats have a significant impact on the comfort of passengers. The development of seats is a field in which scholars are widely concerned. In this study, we add an electromagnetic levitation structure and design a new active seat suspension based on the passive seat suspension. Then, simulation research is carried out based on a C-level road surface combined with integral sliding mode control and state feedback control. The results show that both state feedback control and integral sliding mode control positively affect vehicle seat vibration reduction, and integral sliding mode control has a better anti-interference effect than state feedback control. At the same time, it is proved that the seat suspension has good working characteristics and economy.

Rapid and reliable screening of HLA-B*15:02 in four Chinese populations using single-tube multiplex real-time PCR assay.

AIM:  HLA-B*15:02 screening should be performed to prevent antiepileptic drug induced severe cutaneous adverse reactions in populations of Asian origin. This study aimed to develop fast and reliable HLA-B*15:02 genotyping method and to investigate the distribution of HLA-B*15:02 in different Chinese ethnicities. MATERIALS & METHODS: A single-tube multiplex real-time PCR assay for HLA-B*15:02 genotyping was established by combining allele-specific primers with TaqMan probes. RESULTS: The HLA-B*15:02 genotyping results in Bouyei (n = 100) by the established assay were completely consistent with the corresponding PCR sequence-based typing findings. The percentage of HLA-B*15:02 carrier in Bouyei (19%; n = 100) was significantly higher than those of Han (1%; n = 100), Tibetan (0%; n = 100) and Uyghur (0%; n = 50) populations (p < 0.001). CONCLUSION: The novel method provides rapid, reliable and cost-effective detection of HLA-B*15:02 allele in clinical applications.

Rapid and Reliable Genotyping of HLA-B*57:01 in Four Chinese Populations Using a Single-Tube Duplex Real-Time Polymerase Chain Reaction Assay.

HLA-B*57:01 is strongly associated with severe adverse drug reaction induced by the anti-HIV drug abacavir (ABC) and antibiotic flucloxacillin. This study was dedicated to establishing a new method for HLA-B*57:01 genotyping and investigating the HLA-B*57:01 distribution pattern in four Chinese populations. A single-tube duplex real-time polymerase chain reaction (PCR) system was established by combining the amplification refractory mutation system and TaqMan probe. The reliability of this assay was validated by comparing the genotyping results with those by sequence-based typing. With this assay, the distribution of HLA-B*57:01 in 354 blood samples from four ethnic groups, namely, Han, Tibetan, Uighur, and Buyei, was determined. A 100% concordance was observed between the results of real-time PCR and sequence-based typing in 50 Uighur samples. As low as 0.016 ng DNA that carried HLA-B*57:01 could be detected with this assay. HLA-B*57:01 carriers identified in 100 Northern Han Chinese, 104 Buyeis, 100 Tibetans, and 50 Uighurs were 0, 1 (0.96%), 3 (3%), and 6 (12%), respectively. The carrier rate of HLA-B*57:01 in Uighur was significantly higher than those in Northern Han (p = .001) and Buyei (p = .005). The newly established real-time PCR assay provides a rapid and reliable tool for HLA-B*57:01 allele screening before the prescription of ABC and flucloxacillin in clinical practice.

Expanding Maize Genetic Resources with Predomestication Alleles: Maize-Teosinte Introgression Populations.

Teosinte ( subsp. H. H. Iltis & Doebley) has greater genetic diversity than maize inbreds and landraces ( subsp. ). There are, however, limited genetic resources to efficiently evaluate and tap this diversity. To broaden resources for genetic diversity studies in maize, we developed and evaluated 928 near-isogenic introgression lines (NILs) from 10 teosinte accessions in the B73 background. Joint linkage analysis of the 10 introgression populations identified several large-effect quantitative trait loci (QTL) for days to anthesis (DTA), kernel row number (KRN), and 50-kernel weight (Wt50k). Our results confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects enabling future research into the genetic basis of these traits. Additionally, we used a targeted set of NILs to validate the effects of a KRN QTL located on chromosome 2. These introgression populations offer novel tools for QTL discovery and validation as well as a platform for initiating fine mapping.

Genetic Analysis of Kernel Traits in Maize-Teosinte Introgression Populations.

Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays) kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis). In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL) for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits.

How can we harness quantitative genetic variation in crop root systems for agricultural improvement?

Root systems are a black box obscuring a comprehensive understanding of plant function, from the ecosystem scale down to the individual. In particular, a lack of knowledge about the genetic mechanisms and environmental effects that condition root system growth hinders our ability to develop the next generation of crop plants for improved agricultural productivity and sustainability. We discuss how the methods and metrics we use to quantify root systems can affect our ability to understand them, how we can bridge knowledge gaps and accelerate the derivation of structure-function relationships for roots, and why a detailed mechanistic understanding of root growth and function will be important for future agricultural gains.

Rapid and reliable genotyping of HLA-B*58:01 in four Chinese populations using a single-tube duplex real-time PCR assay.

AIM: HLA-B*58:01 is strongly associated with allopurinol-induced severe cutaneous adverse reactions. This study aimed to develop a new and convenient method for HLA-B*58:01 genotyping and to investigate HLA-B*58:01 distribution in different Chinese populations. MATERIALS & METHODS: Combining of sequence-specific primers and TaqMan probe, a single-tube duplex real-time PCR assay for HLA-B*58:01 typing was established. RESULTS: The HLA-B*58:01 genotyping result in Buyei (n = 100) by real-time PCR showed 100% concordance with those by sequence-based typing. The prevalence of HLA-B*58:01 carrier in Buyei (17%, n = 100) was significantly higher than those in Northern Han (4%, n = 100), Tibetan (5.1%, n = 99) and Uighur (2%, n = 50) populations (p < 0.05). CONCLUSION: The newly developed reliable assay was appropriate for HLA-B*58:01 detection prior to allopurinol administration in clinical settings.

Control of grain size, shape and quality by OsSPL16 in rice.

Grain size and shape are important components of grain yield and quality and have been under selection since cereals were first domesticated. Here, we show that a quantitative trait locus GW8 is synonymous with OsSPL16, which encodes a protein that is a positive regulator of cell proliferation. Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice. Conversely, a loss-of-function mutation in Basmati rice is associated with the formation of a more slender grain and better quality of appearance. The correlation between grain size and allelic variation at the GW8 locus suggests that mutations within the promoter region were likely selected in rice breeding programs. We also show that a marker-assisted strategy targeted at elite alleles of GS3 and OsSPL16 underlying grain size and shape can be effectively used to simultaneously improve grain quality and yield.

Natural variation at the DEP1 locus enhances grain yield in rice.

Grain yield is controlled by quantitative trait loci (QTLs) derived from natural variations in many crop plants. Here we report the molecular characterization of a major rice grain yield QTL that acts through the determination of panicle architecture. The dominant allele at the DEP1 locus is a gain-of-function mutation causing truncation of a phosphatidylethanolamine-binding protein-like domain protein. The effect of this allele is to enhance meristematic activity, resulting in a reduced length of the inflorescence internode, an increased number of grains per panicle and a consequent increase in grain yield. This allele is common to many Chinese high-yielding rice varieties and likely represents a relatively recent introduction into the cultivated rice gene pool. We also show that a functionally equivalent allele is present in the temperate cereals and seems to have arisen before the divergence of the wheat and barley lineages.

[The effect of local vibration on blood-lipids and whole blood viscosity].

OBJECTIVE: To study the effects of local vibration on blood-lipids and whole blood viscosity. METHODS: The total cholesterol (TC), triglyceride (TG), high density lipoprotein (HDL), low density lipoprotein (LDL), whole blood viscosity, apolipoprotein (Apo-), red blood cell (RBC), platelet (PLT), mean corpuscular volume (MCV), serum-protein, postprandial blood sugar (PBS), and serum-protein of experimental and control workers were detected. The difference of the means and abnormal rates of two groups were compared. RESULTS: The means of TG, TC, HDL in exposed group [(1.01 +/- 0.85), (3.25 +/- 0.61), (1.14 +/- 0.20) mmol/L respectively] were significantly lower than that of control group [(1.89 +/- 1.47), (3.87 +/- 0.82), (1.22 +/- 0.26) mmol/L, respectively, P < 0.01 or P < 0.05]. Apo-A was also decreased [(1.13 +/- 0.29) g/L vs (1.23 +/- 0.16) g/L, P < 0.01]. The mean of whole blood viscosity were significantly increased in exposed group [(2.76 +/- 0.42) mPa.s vs (2.54 +/- 0.33) mPa.s, P < 0.01]. The abnormal rate of Apo-A was significantly higher in exposed group (23.30%) than that in control (4.50%, P < 0.01). CONCLUSION: Local vibration may induce decrease in blood lipids, increase in blood viscosity and changes in some other blood parameters.