Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers

There is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non‐synonymous and non‐coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non‐synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data.     

红三叶多酚氧化酶特性的研究

红三叶(Trifolium pretense L.)多酚氧化酶仅作用于邻苯酚,与对苯酚、间苯酚和一元酚无作用,而且对不同的邻苯酚其活性也表现很大差异,其中以咖啡酸作底物时活性最大.红三叶多酚氧化酶反应的最适pH值为6.5～7.0,最适温度为25～30℃,50℃时热稳定性相对较好.     

葡萄糖氧化酶基因植物表达载体的构建

为进一步开展转基因研究创造条件,用限制性内切酶将葡萄糖氧化酶(GOD)基因从pMD/GO载体上切下,定向连接到植物表达载体pROKⅡ的CaMV35S启动子下游和NOS终止子上游,成功地构建了GOD基因植物表达载体pROK/GO。利用冻融法将此表达载体导入根癌农杆菌LBA4404中,提取转化质粒,经PCR和酶切鉴定表明,GOD基因植物表达双元载体构建成功。     

新城疫病毒La Sota株HN基因的克隆与序列分析

旨在从分子生物学角度进一步研究新城疫病毒La Sota株HN基因,探究NDV La Sota HN基因的遗传变异情况。研究以试验室冻存的p NDV-HN为模版,根据Gen Bank中登录的NDV La Sota株序列设计引物扩增HN基因,将其克隆到pMD18-T载体后进行鉴定,对鉴定正确的重组质粒p MD-NDV-HN进行测序分析。应用生物信息学软件对新城疫病毒Lasota株HN基因进行系统进化树分析、氨基酸序列同源性分析、糖基化位点、蛋白结构跨膜区分析及磷酸化位点预测分析。核苷酸序列测定结果表明:HN基因的序列长度为1743bp,该基因的开放阅读框(Open Reading Frame,ORF)总长为1716 bp,编码571个氨基酸。生物信息学表明:试验获得的HN基因具有6个潜在糖基化位点及12个半胱氨酸残基,第5个潜在糖基化位点(508-510 aa)发生缺失及第123位半胱氨酸残基被色氨酸残基取代。La Sota株HN基因编码的蛋白质中有29个丝氨酸、10个酪氨酸和16个苏氨酸可能成为蛋白激酶磷酸化位点。将试验获得的La Sota株HN基因序列和推导的氨基酸序列与新城疫毒株的HN基因相应序列比较后发现,它们的核苷酸序列同源性和氨基酸序列同源性最高均可达到99%,表明HN基因在种属间具有较高的保守性。研究为新城疫病毒的分子病毒学研究奠定了基础。     

A New Solution to Reduce Blocking Artifacts Introduced by Standard Fractal Methods

Fractal image coding techniques usually partition the input image into small range blocks. This artificially introduces boundaries into the image resulting in the unpleasant blocking artifacts in the decoded images especially at high compression rate. Because the effect is especially responsible for the restrictions of the block-based coders, the solutions must be sought to reduce this blockiness. Recently two possible schemes have been proposed by other researchers: One may try to use overlapping blocks in the fractal transform, and the other to employ the combined fractal wavelet approach. An alternative solution is proposed, which employs the bilinear interpolation techniques and the resolution independence of fractal coding, in the sense that an image can be decoded at higher or lower resolutions than the original. Experiments show that the proposed scheme can eliminate the blocking artifacts.     

Context Model Based on 3D Wavelet Coefficients

Based on by typical coding schemes such as EZW,SPIHT, EBCOT,3D-IEZW,3D-SPIHT and 3D-ESCOT,a context model(3D-OWNER) of wavelet coefficients is proposed,which makes use of partial order,self-similarity between subbands of wavelet coefficients and the correlation of neighboring wavelet coefficients.Experimental results show that the model can achieve higher PSNR than 3D-ESCOT.     

软儿梨冷冻贮藏过程酚类物质与多酚氧化酶的区域化分布

为研究冷冻贮藏中不同部位酚类物质和多酚氧化酶的分布特征,以青海省地方梨优良品种‘软儿梨’果实为研究材料,采用高效液相色谱法和比色法测定软儿梨果实后熟(室温)、冻藏(-18℃)和解冻(室温)3个时期的果皮、果肉中总多酚、绿原酸的含量和多酚氧化酶活性。结果表明:软儿梨果实后熟后,酚类物质果肉?果皮,多酚氧化酶则果皮?果肉;冷冻贮藏过程中,不同部位的酚类物质和多酚氧化酶均呈现不同程度的升高,但绿原酸在果皮急剧下降、果肉中略有增加。解冻后总体呈下降趋势,2个部位总酚、多酚氧化酶下降明显,而果皮中的绿原酸变化不大。研究表明:软儿梨果实后熟后,酚类物质和多酚氧化酶分布呈现区域化,冷冻贮藏加剧了酚类物质和多酚氧化酶活性的积累,导致了软儿梨冷冻贮藏后果皮先于果肉发生了褐变。