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

Influencing Factors and Group Differences of Urban Consumers’ Willingness to Pay for Low-Carbon Agricultural Products in China

Developing low-carbon agriculture has become a development goal for low-carbon economies in various countries, and consumers’ awareness and willingness to pay (WTP) for low-carbon agricultural products is an important link in achieving the sustainable development of low-carbon agriculture. The theory of planned behavior is a widely used framework to explain consumers’ food choices. Considering the intrinsic norms of consumers, their perceptions of low-carbon agricultural products, and shifts in consumer behavior, our study adds the influence of environmental awareness and consumer preferences to the theoretical framework of analysis. We choose the contingent valuing method (CVM) and use 532 consumer questionnaires in Shanghai to validate Chinese urban consumers’ WTP for low-carbon products and its influencing factors. The findings show that Chinese urban consumers have a high overall awareness of low-carbon agricultural products and, after strengthening the conceptual information of consumers, most consumers agree that low-carbon vegetables are more conducive to ecological environment protection, quality, and safety guarantees than conventional vegetables. The existing analysis showed that some variables such as bid price, behavioral attitudes, subjective norms, and consumption preferences significantly influenced consumers’ willingness to pay for low-carbon leafy greens, while the effect of the environmental awareness variable was not significant. Further research found that consumers’ WTP for low-carbon leafy greens showed significant group differences across income, gender, age, and education. Therefore, to promote the consumption of low-carbon agricultural products in China, we should attach importance to the publicity and guidance of low-carbon vegetables and strengthen the certification of low-carbon vegetable products. This study can provide policy reference for reasonably regulating and subdividing China’s low-carbon agricultural products market

The causal relationship between osteoarthritis and bladder cancer: A Mendelian randomization study

Abstract Objective The causal association between osteoarthritis (OA) and bladder cancer remains unclear. This Mendelian randomization (MR) study was carried out to assess the potential causal effects of any OA, knee OA and hip OA, and bladder cancer. Method Genome‐wide association study (GWAS) summary data for OA and bladder cancer were obtained in GWAS CATALOG, UK Biobank, and FinnGen Consortium. Inverse‐variance weighted (IVW) approach was primarily conducted to evaluate the causal relationships between OA and bladder cancer, and MR‐Egger intercept and Cochran's Q test were mainly used to estimate heterogeneity and pleiotropy. MR‐PRESSO was used to test the presence of horizontal outliers. Leave‐one‐out analysis was utilized to ensure the reliability of the results. Results A higher genetic predisposition to any OA has a causal association with bladder cancer risk, while neither knee OA nor hip OA is causally linked to bladder cancer. MR‐Egger intercept analysis exhibited that any OA and knee OA had no pleiotropic effect on the risk of bladder cancer, and Cochran's Q test showed that any OA, knee OA and hip OA had no heterogeneity on bladder cancer risk. Neither MR PRESSO analysis nor leave‐one‐out analysis revealed any outlier SNPs. Conclusions This MR study exhibited a positive cause‐and‐effect relationship between any type of OA and bladder cancer risk, but not between site‐specific OA, knee OA and hip OA, and bladder cancer. Attention should be paid to the screening and prevention of bladder cancer in OA patients at any site

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.This article is from Nature 432 (2004): 717, doi:10.1038/nature03156.</p

Functional Classifications from GO, Focused on Plant-Specific Categories Outlined by Gramene

<p>(A) compares predicted genes from <i>Arabidopsis</i> and Beijing <i>indica</i>. (B) compares predicted genes from Beijing <i>indica</i> with nr-KOME cDNAs. We ignore categories with less than 0.1% of the genes.</p