A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Systematical Detection of Significant Genes in Microarray Data by Incorporating Gene Interaction Relationship in Biological Systems

Many methods, including parametric, nonparametric, and Bayesian methods, have been used for detecting differentially expressed genes based on the assumption that biological systems are linear, which ignores the nonlinear characteristics of most biological systems. More importantly, those methods do not simultaneously consider means, variances, and high moments, resulting in relatively high false positive rate. To overcome the limitations, the SWang test is proposed to determine differentially expressed genes according to the equality of distributions between case and control. Our method not only latently incorporates functional relationships among genes to consider nonlinear biological system but also considers the mean, variance, skewness, and kurtosis of expression profiles simultaneously. To illustrate biological significance of high moments, we construct a nonlinear gene interaction model, demonstrating that skewness and kurtosis could contain useful information of function association among genes in microarrays. Simulations and real microarray results show that false positive rate of SWang is lower than currently popular methods (T-test, F-test, SAM, and Fold-change) with much higher statistical power. Additionally, SWang can uniquely detect significant genes in real microarray data with imperceptible differential expression but higher variety in kurtosis and skewness. Those identified genes were confirmed with previous published literature or RT-PCR experiments performed in our lab

Farmland Transfer, Scale Management and Economies of Scale Assessment: Evidence from the Main Grain-Producing Shandong Province in China

Promoting farmland transfer through the farmland rental market is an essential instrument to achieve the centralized scale operation of farmland in China. However, few studies have explored or verified the economies of scale after land concentration. This study uses face-to-face interviews to randomly select 395 farmers engaged in land scale management in 68 villages of 11 cities in Shandong Province. Based on these data, a production cost function model is used to measure the cost elasticity of farmland scale management and further empirically test whether farmland scale management can achieve economies of scale in actual agricultural production. The empirical results show that the development of farmland scale operation can reduce production costs and realize the economy of scale. In other words, the scale of farmland management still has the possibility of further expansion. More importantly, we find the operation cost of farmland is significantly influenced by the price of farmland transfer, fixed capital input and labor input, especially the scale operator with rich planting experience and good cultural quality is an important human capital stock, which can make significant contribution to reducing production cost and developing the positive effect of scale operation. To promote farmland scale management in China, we should pay attention to reducing the transferring cost and transaction cost of farmland by building the land transfer market trading platform, increasing the subsidies for farmland transfer and developing agricultural mechanization, which is helpful to improve agricultural productivity and realize the scale economy. This research can provide a reference for rational land scale management and land use policymaking

The effect of customer satisfaction on floral product purchase behavior, evidence from Shanghai, China

Abstract China's flower industry is developing rapidly, and the size of the retail market is increasing year by year. Studying the factors influencing residents' flower purchasing behavior and understanding their flower needs can help promote the sustainable development of the flower industry. Based on customer satisfaction theory, this paper uses 838 consumer research questionnaires from 15 districts in Shanghai to analyze the influence of customer satisfaction on residents' flower purchasing behavior by conducting a binary logit model and to investigate the moderating effect of flower purchasing purpose on the influence of satisfaction. The results show that price satisfaction and satisfaction with promotional methods have a significant negative effect on flower purchasing behavior, service satisfaction has a significant positive effect on purchasing behavior, and different customer purchase purposes lead to different intensities of the effect of satisfaction on purchasing behavior. According to the conclusion of the study, three countermeasures are proposed: to popularize the knowledge of flower culture, guide the concept of flower consumption, and promote the transformation of flower consumption to daily consumption; to conduct regular research on consumers by flower merchants to clarify consumers' needs and improve their satisfaction; to clarify consumers' purchase intention, increase the investment in the research and development and cultivation of flower products, and improve the supply level of flowers

Measurement of Green Total Factor Productivity and Its Spatial Convergence Test on the Pig-Breeding Industry in China

The pig-breeding industry is one of the pillar industries of China’s agriculture. Improving the green total factor productivity of pig breeding is the basis for ensuring the stable supply of pork, and is also the key to the green transformation of the pig industry. The existing studies about the green total factor productivity of pig breeding lack an analysis of regional coordination and the spillover of spatial technology efficiency at the macro level, and most studies focus on the impact of agricultural production’s environment pollution and other undesirable outputs. Based on the input–output index system of the pig-breeding industry’s green production, the DDF directional distance function model and the Malmquist–Luenberger (ML) productivity index were combined to measure the green total factor productivity of the pig-breeding industry. Moran’s I-Theil index model was used to measure and reveal the technical efficiency differences among the dominant regions of the pig-breeding industry in China and the σ-convergence test was adopted to reveal the convergence trend of green total factor productivity. The results showed that: (1) The growth level of green total factor productivity of pig breeding in China was generally low from 2006 to 2018, and there were obvious regional and scale differences. (2) The green total factor productivity of pig breeding in each province had spatial autocorrelation; that is, there was technology spillover. From 2006 to 2018, with the advance of time, a pattern of gradual evolution from low-level equilibrium to high-level imbalance was formed. (3) Through the convergence test, the convergence trend of large and medium-scale development between different regions fluctuated, while the convergence trend of small-scale development between different regions was not obvious. Therefore, it is necessary to increase investment in technological innovation, promote the large-scale and standardized development of the pig-breeding industry, and strengthen the promotion of technology in producing areas with advantages in pig breeding

Measurement of Green Total Factor Productivity and Its Spatial Convergence Test on the Pig-Breeding Industry in China

The pig-breeding industry is one of the pillar industries of China’s agriculture. Improving the green total factor productivity of pig breeding is the basis for ensuring the stable supply of pork, and is also the key to the green transformation of the pig industry. The existing studies about the green total factor productivity of pig breeding lack an analysis of regional coordination and the spillover of spatial technology efficiency at the macro level, and most studies focus on the impact of agricultural production’s environment pollution and other undesirable outputs. Based on the input–output index system of the pig-breeding industry’s green production, the DDF directional distance function model and the Malmquist–Luenberger (ML) productivity index were combined to measure the green total factor productivity of the pig-breeding industry. Moran’s I-Theil index model was used to measure and reveal the technical efficiency differences among the dominant regions of the pig-breeding industry in China and the σ-convergence test was adopted to reveal the convergence trend of green total factor productivity. The results showed that: (1) The growth level of green total factor productivity of pig breeding in China was generally low from 2006 to 2018, and there were obvious regional and scale differences. (2) The green total factor productivity of pig breeding in each province had spatial autocorrelation; that is, there was technology spillover. From 2006 to 2018, with the advance of time, a pattern of gradual evolution from low-level equilibrium to high-level imbalance was formed. (3) Through the convergence test, the convergence trend of large and medium-scale development between different regions fluctuated, while the convergence trend of small-scale development between different regions was not obvious. Therefore, it is necessary to increase investment in technological innovation, promote the large-scale and standardized development of the pig-breeding industry, and strengthen the promotion of technology in producing areas with advantages in pig breeding

Study on Optimization of Port Railway Transportation Mode

With the continuous development of port economy and the continuous promotion of industrial transformation and upgrading in China, the mode of gathering and distributing transportation in port area has gradually become the core factor to enhance the competitiveness of the whole logistics chain of port. It always play an important role in the port collection and distribution system. Especially for inland economic hinterland ports, it is of great significance to develop railway transportation and optimize port railway collection and distribution system. Based on the development and application of the theory of port railway transportation at home and abroad, this paper briefly analyzes the present situation and trend of port railway transportation mode. Combined with the demand characteristics of the current port railway transportation system and the problems that need to be further improved after the reform of freight organization, the form and task of optimizing the port railway transportation mode are clarified

NADH oxidase of Mycoplasma synoviae is a potential diagnostic antigen, plasminogen/fibronectin binding protein and a putative adhesin

Abstract Background Mycoplasma synoviae (MS) is an important pathogen causing respiratory diseases and arthritis in chickens and turkeys, thus, resulting in serious economic losses to the poultry industry. Membrane-associated proteins are thought to play important roles in cytoadherence and pathogenesis. NADH oxidase (NOX) is an oxidoreductase involved in glycolysis, which is thought to be a multifunctional protein and potential virulence factor in some pathogens. However, little is known regarding the NOX of MS (MSNOX). We previously demonstrated that MSNOX was a metabolic enzyme distributed in not only the cytoplasm but also the MS membrane. This study was aimed at exploring NOX’s potential as a diagnostic antigen and its role in MS cytoadherence. Results Western blots and ELISAs indicated that recombinant MSNOX (rMSNOX) protein reacted with sera positive for various MS isolates, but not MG isolates or other avian pathogens, thus, suggesting that rMSNOX is a potential diagnostic antigen. In addition, rabbit anti-rMSNOX serum showed substantial complement-dependent mycoplasmacidal activity toward various MS isolates and MG Rlow. MSNOX protein was found not only in the cytoplasm but also on the membrane of MS through suspension immunofluorescence and immunogold electron microscopy assays. Indirect immunofluorescence assays indicated that rMSNOX adhered to DF-1 cells, and this adherence was inhibited by rabbit anti-rMSNOX, but not anti-MG serum. Furthermore, indirect immunofluorescence and colony counting assays confirmed that the rabbit anti-rMSNOX serum inhibited the adherence of various MS isolates but not MG Rlow to DF-1 cells. Moreover, plasminogen (Plg)- and fibronectin (Fn)-binding assays demonstrated that rMSNOX bound Plg and Fn in a dose-dependent manner, thereby further confirming that MSNOX may be a putative adhesin. Conclusion MSNOX was identified to be a surface immunogenic protein that has good immunoreactivity and specificity in Western blot and ELISA, and therefore, may be used as a potential diagnostic antigen in the future. In addition, rMSNOX adhered to DF-1 cells, an effect inhibited by rabbit anti-rMSNOX, but not anti-MG serum, and anti-rMSNOX serum inhibited the adherence of various MS isolates, but not MG Rlow, to DF-1 cells, thus indicating that the inhibition of adherence by anti-MSNOX serum was MS specific. Moreover, rMSNOX adhered to extracellular matrix proteins including Plg and Fn, thus suggesting that NOX may play important roles in MS cytoadherence and pathogenesis. Besides, rabbit anti-rMSNOX serum presented complement-dependent mycoplasmacidal activity toward both MS and MG, indicating the MSNOX may be further studied as a potential protective vaccine candidate