Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations

Background

Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F₂ intercross population and a Chinese Sutai half-sib population.

Results

We identified 14 and 39 loci that displayed significant associations with growth and fatness traits at the genome-wide level and chromosome-wide level, respectively. The strongest association was between a 750 kb region on SSC7 (SSC for Sus scrofa) and backfat thickness at the first rib. This region had pleiotropic effects on both fatness and growth traits in F₂ animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1). Unexpectedly, population genetic analysis revealed that the allele at this locus that reduces fatness and increases growth is derived from Chinese indigenous pigs and segregates in multiple Chinese breeds. The second strongest association was between the region around 82.85 Mb on SSC4 and average backfat thickness. PLAG1 (pleiomorphic adenoma gene 1), a gene under strong selection in European domestic pigs, is proximal to the top SNP and stands out as a strong candidate gene. On SSC2, a locus that significantly affects fatness traits mapped to the region around the IGF2 (insulin-like growth factor 2) gene but its non-imprinting inheritance excluded IGF2 as a candidate gene. A significant locus was also detected within a recombination cold spot that spans more than 30 Mb on SSCX, which hampered the identification of plausible candidate genes. Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits.

Conclusions

We confirm several previously reported QTL and provide a list of novel loci for porcine growth and fatness traits in two experimental populations with Chinese Taihu and Western pigs as common founders. We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0089-5) contains supplementary material, which is available to authorized users.     

Spatial Structures of the Environment and of Dispersal Impact Species Distribution in Competitive Metacommunities

The correspondence between species distribution and the environment depends on species’ ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics.     

Elevated ozone concentration decreases whole‐plant hydraulic conductance and disturbs water use regulation in soybean plants

Elevated tropospheric ozone (O₃) concentration has been shown to affect many aspects of plant performance including detrimental effects on leaf photosynthesis and plant growth. However, it is not known whether such changes are accompanied by concomitant responses in plant hydraulic architecture and water relations, which would have great implications for plant growth and survival in face of unfavorable water conditions. A soybean (Glycine max (L.) Merr.) cultivar commonly used in Northeast China was exposed to non‐filtered air (NF, averaged 24.0 nl l^?1) and elevated O₃ concentrations (eO₃, 40 nl l^?1 supplied with NF air) in six open‐top chambers for 50 days. The eO₃ treatment resulted in a significant decrease in whole‐plant hydraulic conductance that is mainly attributable to the reduced hydraulic conductance of the root system and the leaflets, while stem and leaf petiole hydraulic conductance showed no significant response to eO₃. Stomatal conductance of plants grown under eO₃ was lower during mid‐morning but significantly higher at midday, which resulted in substantially more negative daily minimum water potentials. Moreover, excised leaves from the eO₃ treated plants showed significantly higher rates of water loss, suggesting a lower ability to withhold water when water supply is impeded. Our results indicate that, besides the direct detrimental effects of eO₃ on photosynthetic carbon assimilation, its influences on hydraulic architecture and water relations may also negatively affect O₃‐sensitive crops by deteriorating the detrimental effects of unfavorable water conditions.     

Statins Reduce Amyloid β-Peptide Production by Modulating Amyloid Precursor Protein Maturation and Phosphorylation Through a Cholesterol-Independent Mechanism in Cultured Neurons

Statins, 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase inhibitors, have been reported to attenuate amyloid-β peptide (Aβ) production in various cellular models. However, the mechanisms by which statins affect neuronal Aβ production have not yet been clarified. Here, we investigated this issue in rat primary cortical neurons using two statins, pitavastatin (PV) and atorvastatin (AV). Treatment of neurons with 0.2–2.5 μM PV or AV for 4 days induced a concentration- and time-dependent reduction in the secretion of both Aβ40 and Aβ42. Moreover, Western blot analyses of cell lysates showed that treatment with PV or AV significantly reduced expression levels of the mature form of amyloid precursor protein (APP) and Thr668-phosphorylated APP (P-APP), but not immature form of APP; the decreases in P-APP levels were more notable than those of mature APP levels. The statin treatment did not alter expression of BACE1 (β-site APP-cleaving enzyme 1) or γ-secretase complex proteins (presenilin 1, nicastrin, APH-1, and PEN-2). In neurons overexpressing APP via recombinant adenoviruses, PV or AV similarly reduced Aβ secretion and the levels of mature APP and P-APP. Statins also markedly reduced cellular cholesterol content in neurons in a concentration-dependent manner. Co-treatment with mevalonate reversed the statin-induced decreases in Aβ secretion and mature APP and P-APP levels, whereas co-treatment with cholesterol did not, despite recovery of cellular cholesterol levels. Finally, cell-surface biotinylation experiments revealed that both statins significantly reduced the levels of cell-surface P-APP without changing those of cell surface mature APP. These results suggest that statins reduce Aβ production by selectively modulating APP maturation and phosphorylation through a mechanism independent of cholesterol reduction in cultured neurons.     

嵌合蛋白sTNFR II-IgG Fc的克隆、表达与活性分析

肿瘤坏死因子是一种重要的炎性细胞因子,目前已知许多免疫疾病与之相关,为了抑制TNF的生物学活性,将可溶性TNFR Ⅱ(sTNFR Ⅱ）和人IgG Fc分子通过柔性短肽相连,构建成一个嵌合蛋白,在大肠杆菌中进行表达,并获得了纯化蛋白。实验证明该嵌合蛋白能够自发形成聚合体,识别并结合TNF蛋白,同单体sTNFR Ⅱ相比,对TNF的中和活性得到了较大的提高。     

靶向表达TNFR75的逆转录病毒载体的构建及其产毒细胞系的建立

 将编码人 TNFR75的 c RNA与血管内皮细胞特异性启动子 (KDRp)及缺失自身启动子的逆转录病毒载体 p LXSN- D2 99重组 .重组质粒 p LXSN- D2 99- KDRp- TNFR75与脂质体共转染包装细胞 PA31 7,经抗生素 G41 8(60 0 mg/L)筛选 1 4d,获得 1 5个稳定的产病毒细胞克隆 .将各细胞克隆分别扩大培养收集所产病毒上清 ,并感染 NIH3T3细胞检测病毒滴度 ,其中 1个克隆滴度达 2×1 0 5CFU/ml.提取该克隆细胞总 RNA进行 RT- PCR分析 ,获得的 c DNA片段长度与目的基因一致 .结果提示 ,建立了 TNFR75反转录病毒产毒细胞系 .     

蛋白激酶B在小鼠1-细胞期受精卵中活性及表达变化

蛋白激酶B(proteinkinaseB ,PKB)发现于 1991年 ,属于丝 苏氨酸蛋白激酶 .因其激酶活性区的氨基酸序列与蛋白激酶C (proteinkinaseC ,PKC)和蛋白激酶A (proteinkinaseA ,PKA)同源性分别为 73%和 6 8% ,因此命名为PKB ,或PKA和PKC相关激酶(relatedtheAandCkinase ,RACK) [1] .另外 ,PKB被证明为逆转录病毒的癌基因v akt编码的蛋白产物 ,因此PKB又称AKT[2 ] .PKB分子量 6 0kD ,目前已知分为PKBα、β、γ三种 .PKBα广泛存在于机体各组织中 ,其活性受多种信息物质调节 .PKBβ在卵巢癌、胰腺癌细胞中过表达 ,PKBγ在大…