Genome-wide association studies of 14 agronomic traits in rice landraces

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ～ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ～ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.     

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.     

A genome-wide association study in Han Chinese identifies new susceptibility loci for ankylosing spondylitis

To identify susceptibility loci for ankylosing spondylitis, we performed a two-stage genome-wide association study in Han Chinese. In the discovery stage, we analyzed 1,356,350 autosomal SNPs in 1,837 individuals with ankylosing spondylitis and 4,231 controls; in the validation stage, we analyzed 30 suggestive SNPs in an additional 2,100 affected individuals and 3,496 controls. We identified two new susceptibility loci between EDIL3 and HAPLN1 at 5q14.3 (rs4552569; P = 8.77 × 10(-10)) and within ANO6 at 12q12 (rs17095830; P = 1.63 × 10(-8)). We also confirmed previously reported associations in Europeans within the major histocompatibility complex (MHC) region (top SNP, rs13202464; P < 5 × 10(-324)) and at 2p15 (rs10865331; P = 1.98 × 10(-8)). We show that rs13202464 within the MHC region mainly represents the risk effect of HLA-B*27 variants (including HLA-B*2704, HLA-B*2705 and HLA-B*2715) in Chinese. The two newly discovered loci implicate genes related to bone formation and cartilage development, suggesting their potential involvement in the etiology of ankylosing spondylitis.     

A genome-wide association study in Chinese men identifies three risk loci for non-obstructive azoospermia

Non-obstructive azoospermia (NOA) is one of the most severe forms of male infertility. Its pathophysiology is largely unknown, and few genetic influences have been defined. To identify common variants contributing to NOA in Han Chinese men, we performed a three-stage genome-wide association study of 2,927 individuals with NOA and 5,734 controls. The combined analyses identified significant (P < 5.0 × 10(-8)) associations between NOA risk and common variants near PRMT6 (rs12097821 at 1p13.3: odds ratio (OR) = 1.25, P = 5.7 × 10(-10)), PEX10 (rs2477686 at 1p36.32: OR = 1.39, P = 5.7 × 10(-12)) and SOX5 (rs10842262 at 12p12.1: OR = 1.23, P = 2.3 × 10(-9)). These findings implicate genetic variants at 1p13.3, 1p36.32 and 12p12.1 in the etiology of NOA in Han Chinese men.     

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder

Transitional cell carcinoma (TCC) is the most common type of bladder cancer. Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer.     

Behavior Model Construction for Client Side of Modern Web Applications

Most of the behavior models with respect to Web applications focus on sequencing of events,without regard for the changes of parameters or elements and the relationship between trigger conditions of events and Web pages.As a result,these models are not sufficient to effectively represent the dynamic behavior of the Web2.0 application.Therefore,in this paper,to appropriately describe the dynamic behavior of the client side of Web applications,we define a novel Client-side Behavior Model(CBM) for Web applications and present a user behavior trace-based modeling method to automatically generate and optimize CBMs.To verify the effectiveness of our method,we conduct a series of experiments on six Web applications according to three types of user behavior traces.The experimental results show that our modeling method can construct CBMs automatically and effectively,and the CBMs built are more precise to represent the dynamic behavior of Web applications.     

四川省人口文化素质空间分布特征分析

本文以第五次、六次人口普查数据为基础,将人均受教育年限作为切入点,在GIS软件支持下,采用标准差、变异系数、空间自相关分析法等,从地理学视角系统地分析了四川省人口文化素质的空间分布特征,得出3点结论,最后,有针对性地提出了相关建议。     

水栖性的棘胸蛙身体大小不随环境水热梯度及净初级生产力梯度而分化

之前的研究发现不同地理种群棘胸蛙(Quasipaa spinosa)的身体大小随着环境生产力以及年最低温的降低而增大,因为更大的身体利于在生产力水平较低的环境中耐受饥饿并利于在寒冷的环境条件下保存热量.然而在种间水平上进行的相关研究发现:由于大部分时间生活在水体这种相对稳定的环境中,水栖性无尾类的身体大小并不受宏观水热波动的影响.为了更好地探究这个问题,我们以棘胸蛙为研究对象,在之前的基础上选择更多的研究地点及更多的环境因子,研究其身体大小的地理分化格局并探究潜在机制.与之前的发现不同,作为一种水栖性无尾类,棘胸蛙的身体大小并不受环境水热梯度以及净初级生产力梯度的影响.导致这种现象的原因可能是水栖性的生境偏好缓和了棘胸蛙受到的来自宏观环境水热波动的影响,所以它们并不通过改变身体大小来适应宏观环境梯度.此外由于棘胸蛙的肉食性,环境初级生产力并不能有效地衡量其食物供给,其身体大小是否受到食物供给量的影响仍有待深入探究.     

地测地理信息系统的研究与应用

文章阐述了地测基础资料对煤矿的意义,介绍地测地理信息系统的研发思路,并总结了该系统的应用对煤矿地测管理的意义。     

助成胶作用和氧化镧掺杂对活性氧化铝热稳定性的影响

研究水溶液成胶制备氧化铝过程中,掺杂氧化镧及利用聚乙二醇助成胶对氧化铝热稳定性和比表面的影响。通过XRD表征手段和TG检测方法来检测氧化铝在不同温度焙烧后的晶相改变和热失重情况,并利用BET检测方法检测不同温度焙烧后的比表面。实验结果表明,氧化镧的掺杂可提高氧化铝的热稳定性,利用聚乙二醇助成胶可有效提高氧化铝的比表面。