An independent validation study of loci associated with nematode resistance in sheep

Gastrointestinal nematode infection is a constraint on sheep production worldwide. Selective breeding programmes to enhance resistance to nematode infection are currently being implemented in a number of countries. Identification of loci associated with resistance to infection or causative mutations for resistance would enable more effective selection. Loci associated with indicator traits for nematode resistance has been identified in previous studies. In this study, Scottish Blackface, Texel and Suffolk lambs were used to validate the effects at eight genomic regions previously associated with nematode resistance (OAR3, 4, 5, 7, 12, 13, 14, 21). No SNP was significantly associated with nematode resistance at the region‐wide level but seven SNPs in three of the regions (OAR4, 12, 14) were nominally associated with trichostrongyle egg count in this study and six of these were also significant when fitted as single SNP effects. Nematodirus egg count was nominally associated with SNPs on OAR3, 4, 7 and 12.     

大青沟残遗森林植物群落特点及种间联结性研究

大青沟残遗森林植物群落分布于科尔沁沙地,是一个非常特殊的森林群落类型。在野外调查的基础上,分析了其群落学特点,并分析了对群落整体功能有重要影响的３１个乔、灌木种类的种间联结性。结果表明,大青沟落叶阔叶林主要由具复叶、小叶和中叶的落叶大高位芽植物和中高位芽植物所组成。植物种类丰富,计有维管植物１０６科,３５９属,７０９种,约占整个内蒙古植物种数的三分之一。主要木本植物之间发生联结的情况较多,既有正联结,也有负联结。     

Instrumental outcome devaluation with representation-mediated conditioning

In three experiments, rats were trained to perform two instrumental behaviours (R1 and R2) in the presence of discriminative stimuli (Sd1 and Sd2, respectively) to obtain a common food outcome (O1). Acquisition of the two discriminations was followed by switching the outcome accompanying R2 performance from O1 to a new one (O2). Experiment 1 showed paired presentations of O2 with a lithium chloride (LiCl) injection resulted in a reduction in the R2 performance. In the subsequent two experiments, each Sd was paired with LiCl injection and its effects on outcome consumption and instrumental performance were investigated. A reduction in the O2 consumption subsequent to the Sd devaluation was found in Experiments 2 and 3. Experiment 3 revealed a reduced R2 performance in an extinction test, following the animals’ consummatory access to the outcomes in training context. These results demonstrate representation-mediated outcome devaluation in the course of the Sd devaluation.     

鼎湖山地带性植被种间联结变化研究

研究鼎湖山地带性植被厚壳桂属（Cryptocarya）群落种间联结15年的变化,以期揭示该群落随时间演替过程中种间关系的变化情况。结果表明,群落的优势种种类组成基本没变化,但与15年前比较,优势种群的种对正负联结比例基本一致,但种间关系趋向平缓,高的正或负联结系数值少见;阳生性的先锋种与中生性建群种的联结系数值增大;群落中的2个亚群丛分化更为明显。表明南亚热带地带性顶极群落稳定是相对的,而波动变化是明显的,尤其是当群落循环演替的进程加剧时。     

随机SNP在全基因组关联研究人群分层分析中的应用

在复杂疾病的全基因组关联研究中,人群分层现象会增加结果的假阳性率,因此考虑人群遗传结构、控制人群分层是很有必要的。而在人群分层研究中,使用随机选择的SNP的效果还有待进一步探讨。文章利用HapMap Phase2人群中无关个体的Affymetrix SNP 6.0芯片分型数据,在全基因组上随机均匀选择不同数量的SNP,同时利用f值和Fisher精确检验方法筛选祖先信息标记（Ancestry Informative Markers,AIMs）。然后利用HapMap Phase3中的无关个体的数据,以F-statistics和STRUCTURE分析两种方法评估所选出的不同SNP组合对人群的区分效果。研究发现,随机均匀分布于全基因组的SNP可用于识别人群内部存在的遗传结构。文章进一步提示,在全基因组关联研究中,当没有针对特定人群的AIMs时,可在全基因组上随机选择3000以上均匀分布的SNP来控制人群分层。     

云南肺癌易感性与HLA-A，HLA-B，DRB1，DQB1等位基因频率的相关性研究

目的:测定云南肺癌患者人类白细胞抗原(human leukocyte antigen,HLA)-A、B、DRB1、DQB1等位基因出现频率,探讨HLA各等位基因位点与云南省肺癌发病易感性的相关性。方法:采用病例-对照相关分析方法,选取云南籍肺癌患者和健康个体各30例,应用序列特异性引物聚合酶链反应(polymerase chain reaction-sequence specific primer,PCR-SSP)对HLA-A、HLA-B、HLA-DRB1及HLA-DQB1等位基因频率进行测定,与正常组对比测算相对危险因子(relative risk,RR)。结果:肺癌组的HLA-A~*02频率为90.0%(A~*0201为主),B~*46频率为40.0%,DRB1~*15频率为40.0%,较对照组的43.30%、0%、10.0%明显升高(Pc0.05,RR1)。肺癌组的HLA-A~*31频率为3.30%,A~*33频率为6.70%,B~*27频率为3.30%,B~*52频率为6.70%,DRB1~*03频率为0%,DRB3~*01频率为60.0%,DQB1~*02频率为0%,DQB1~*06频率为0%,较对照组的23.30%、26.70%、26.70%、26.70%、23.30%、86.70%、23.30%、26.70%降低明显,(RR1,Pc0.05)。结论:云南肺癌易感性可能与HLA-A~*02的频率(90%)具有相关性;而HLA-A~*31、HLA-A~*33、HLA-B~*52、HLA-B~*27、HLA-DRB1-~*03、HLA-DRB3~*01、HLA-DQB1~*02及HLA-DQB1~*06在肺癌患者中的频率较低,在云南肺癌发病中可能具有遗传拮抗作用。     

Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.     

MicroPhenoDB Associates Metagenomic Datawith Pathogenic Microbes,Microbial Core Genes,and Human Disease Phenotypes

Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.     

Association of IREB2 and CHRNA3 polymorphisms with airflow obstruction in severe alpha-1 antitrypsin deficiency

Background

The development of COPD in subjects with alpha-1 antitrypsin (AAT) deficiency is likely to be influenced by modifier genes. Genome-wide association studies and integrative genomics approaches in COPD have demonstrated significant associations with SNPs in the chromosome 15q region that includes CHRNA3 (cholinergic nicotine receptor alpha3) and IREB2 (iron regulatory binding protein 2).We investigated whether SNPs in the chromosome 15q region would be modifiers for lung function and COPD in AAT deficiency.

Methods

The current analysis included 378 PIZZ subjects in the AAT Genetic Modifiers Study and a replication cohort of 458 subjects from the UK AAT Deficiency National Registry. Nine SNPs in LOC123688, CHRNA3 and IREB2 were selected for genotyping. FEV₁ percent of predicted and FEV₁/FVC ratio were analyzed as quantitative phenotypes. Family-based association analysis was performed in the AAT Genetic Modifiers Study. In the replication set, general linear models were used for quantitative phenotypes and logistic regression models were used for the presence/absence of emphysema or COPD.

Results

Three SNPs (rs2568494 in IREB2, rs8034191 in LOC123688, and rs1051730 in CHRNA3) were associated with pre-bronchodilator FEV₁ percent of predicted in the AAT Genetic Modifiers Study. Two SNPs (rs2568494 and rs1051730) were associated with the post-bronchodilator FEV₁ percent of predicted and pre-bronchodilator FEV₁/FVC ratio; SNP-by-gender interactions were observed. In the UK National Registry dataset, rs2568494 was significantly associated with emphysema in the male subgroup; significant SNP-by-smoking interactions were observed.

Conclusions

IREB2 and CHRNA3 are potential genetic modifiers of COPD phenotypes in individuals with severe AAT deficiency and may be sex-specific in their impact.     

鸡视网膜母细胞瘤基因1(RB1)多态性与体重性状的相关性

为探讨鸡视网膜母细胞瘤基因1(Retinoblastoma1,RB1)多态性对体重性状的影响,文章以东北农业大学高、低脂双向选择品系肉鸡为实验材料,采用MALDI-TOF-MS、PCR-RFLP方法进行基因多态性检测和个体基因型分析,共获得27个SNP位点的基因型数据。采用滑动窗口法构建单倍型,进而利用单位点和单倍型分别与鸡体重性状进行关联分析。结合单位点和单倍型分析结果,确定了RB1基因上4个显著影响1周龄体重的SNP位点,2个显著影响1、3周龄体重的SNP位点。研究结果表明RB1基因是影响鸡早期体重性状的重要候选基因。