基因评估基因表达式程序设计方法

基因表达式程序设计(Gene Expression Programming,简称GEP)与遗传程序设计(Genetic Programming,简称GP)相比,具有更强的搜索能力、更简单的编码表示方法和产生更高复杂性函数的能力.但是它也存在一些缺点,例如缺乏学习机制,搜索过于盲目.针对这一缺点,本文提出了一种新的自动程序设计方法:基因评估基因表达式程序设计(Gene Estimated Gene Expression Programming,简称GEGEP).与GEP相比,GEGEP主要具有如下特点:(1)改变了GEP的基因表达式结构,将原来的“头+尾”结构改成了“头+身+尾”结构,以利于其引进学习机制;(2)同源基因也采用“头+身+尾”结构,以利于增强其搜索能力;(3)引入了分布评估算法(Estimation of Distribution Algorithm,简称EDA)的思想,以利于增加其学习能力并且加快其收敛速度.实验结果表明,与GEP和GP相比,GEGEP具有更高的拟合和预测精度、更快的收敛速度.

河北省荷斯坦母牛基因组评估效果验证

本研究旨在基于河北省部分牧场荷斯坦母牛的基因组遗传评估结果及其性状表型数据,验证基因组预测的效果及可行性。选择来自河北省3个奶牛场1~2胎次1 134头荷斯坦母牛的基因组评估结果与性状表型数据,依据305 d产奶量、乳脂量、乳脂率、乳蛋白量、乳蛋白率和体细胞评分6个性状的基因组育种值分别对母牛由高到低进行排名并分组,分组1按照前25%、26%~50%、51%~75%、后25%划分为高组、中高组、中低组和低组;分组2按照高低5%和10%划分为前5%、后5%、前10%和后10%4组,采用R语言、Excel和Python分别计算各组每个性状的表型均值及标准差,比较基因组评估与性能表型之间的分布趋势。结果表明:连续分组和极端高低组间,各性状表型值随基因组育种值降低而降低,即表型均值为高组>中高祖>中低组>低组,极端高组(前5%和前10%)>极端低组(后5%和后10%)(P<0.05)。研究结果表明,荷斯坦母牛的产奶和体细胞数性状的早期基因组预测比较准确,可以利用基因组选择技术进行母牛群体早期准确选择及科学的选种选配。

美国基因组评估系统的发展概述

基因组评估是通过检测覆盖全基因组的分子标记,利用基因组水平的遗传信息对动物个体进行遗传评估,以期获得更高的育种值估计准确度。基因组评估作为育种新技术在奶牛育种领域引起巨大改变,目前已经成为各国的研究热点。本文介绍了美国发展基因组评估系统的历史、现状及合作情况。

杨梅全基因组测序结果初报

杨梅(Myrica rubra Sieb.et Zucc.)是我国南方著名的特产珍果,为促进杨梅分子育种及功能基因研究,对杨梅进行了全基因组测序。采用Illumina Hiseq 2500双端测序策略,构建了200 bp文库,进行双端125 bp(PE 125)测序,得到约13.70 Gb的原始数据。数据评估得知杨梅基因组大小约为304.38 Mb,重复序列含量约为45.82%,杂合率约为0.58%,基因组的GC含量约37.99%。利用SOAPdenovo软件进行了拼接组装。这一结果有助于开展杨梅后续的分子育种及基因功能研究。

田螺科4种代表性贝类基因组调研及SSR特征分析

田螺科贝类是淡水软体动物的重要物种,在生态方面具有重要作用,并具有较高的经济价值,但目前田螺科物种参考基因组缺乏。本研究选取田螺科中华园田螺、铜锈环棱螺、多棱角螺、湄公螺等代表性贝类,基于Illumina测序数据,对4个贝类基因组大小、重复序列和杂合度等基因组特征,采用K-mer法进行预测。使用SOAPdenove软件对4种贝类进行初步组装,用MISA进行SSR分子标记鉴定和特征分析。结果表明,4种田螺科贝类基因组大小分别为1 353、896、991、1 196 Mb,杂合度分别为0.77%、1.37%、2.41%、0.91%,重复序列比例分别为26.2%、26.7%、27.8%、28.8%,基因组的GC含量分别约为33.4%、33.7%、33.1%、33.8%。说明这4个田螺科贝类杂合较高、重复序列较低。基因组初步组装结果显示,4种贝类基因组相对K-mer评估结果偏大,但GC含量及测序深度与K-mer结果较为一致。根据SSR特征分析,在田螺科4个贝类基因组序列中分别鉴定到928 562、824 342、739 299、739 407个SSR,其中,在单核苷酸至六核苷酸重复序列类型中A/T、AC/GT、AAT/ATT、AGAT/ATCT、ATAAT/ATTAT、CTAACC/GGTTAG占比最高,其中长度为10~24 bp的SSR分别占69.7%、64.9%、68.4%、70.2%。本研究为田螺科4个代表性物种基因组精细图谱构建提供了参考,同时为SSR分子标记开发和田螺科物种资源保护和利用提供了分子依据。

过表达玉米Zmsh1基因提高转基因烟草的生物量

蔗糖合成酶(Su Sy)是调控植物体内蔗糖代谢的一类关键酶,而SH1是玉米Su Sy的一种亚型。研究表明,玉米Su Sy催化活性主要由SH1基因(Zmsh1)决定,该基因在玉米分子育种中的价值评估是人们关注的热点。利用农杆菌介导法将玉米Zmsh1转入模式植物烟草中,发现转基因烟草中SH1酶活力比野生型烟草平均提高了35%,根和茎的糖代谢关键产物蔗糖和果糖的含量平均增加了23%和28%;同时,Zmsh1的转入显著提高了转基因烟草的总生物量。研究结果为进一步在玉米中过表达Zmsh1,评估转基因玉米的产业化应用价值提供了重要的理论参考。

Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences

AIM： To assess the safety of Bifidobacterium/ongum （B. longum） JDM301 based on complete genome sequences. METHODS： The complete genome sequences of JDM301 were determined using the GS 20 system. Putative virulence factors, putative antibiotic resis- tance genes and genes encoding enzymes respon- sible for harmful metabolites were identified by blast with virulence factors database, antibiotic resistance genes database and genes associated with harmful metabolites in previous reports. Minimum inhibitory concentration of 16 common antimicrobial agents was evaluated by E-test RESULTS： JDM301 was shown to contain 36 genes as- sociated with antibiotic resistance, 5 enzymes related to harmful metabolites and 162 nonspecific virulence fac- tors mainly associated with transcriptional regulation, adhesion, sugar and amino acid transport. B. longum JDM301 was intrinsically resistant to ciprofloxacin, ami- kacin, gentamicin and streptomycin and susceptible to vancomycin, amoxicillin, cephalothin, chloramphenicol, erythromycin, ampicillin, cefotaxime, rifampicin, imi- penem and trimethoprim-sulphamethoxazol. JDM301 was moderately resistant to bacitracin, while an earlier study showed that bifidobacteria were susceptible to this antibiotic. A tetracycline resistance gene with the risk of transfer was found in JDM301, which needs to be experimentally validated. CONCLUSION： The safety assessment of JDM301 using information derived from complete bacterial ge- nome will contribute to a wider and deeper insight into the safety of probiotic bacteria.

TP53 Arg72Pro polymorphism is associated with esophageal cancer risk:A meta-analysis

AIM:To investigate the association between TP53 Arg72Pro polymorphism and esophageal cancer(EC)risk using meta-analysis. METHODS:All eligible studies published before March 1,2010 were selected by searching PubMed using keywords"p53"or"TP53","polymorphism"or"variation", "esophageal"and"cancer"or"carcinoma".Crude odds ratios(ORs)with 95%confidence intervals(CIs)were assessed for EC risk associated with TP53 Arg72Pro polymorphism using fixed-and random-effects models. RESULTS:Nine case-control studies involving 5545 subjects were included in this meta-analysis.Significantly reduced risk of EC was associated with TP53genotypes for Arg/Arg+Arg/Pro vs Pro/Pro(OR= 0.73,95%CI:0.57-0.94,P=0.014).Subgroup analyses according to the source of controls and the specimens used for determining TP53 Arg72Pro genotypes or sample size showed that significantly reduced risk was observed only in studies which have populationbased controls(Arg/Arg vs Pro/Pro:OR=0.56,95% CI:0.47-0.66,P<0.001),and use white blood cells or normal tissue to assess TP53 genotypes of cases (Arg/Arg vs Pro/Pro:OR=0.56,95%CI:0.47-0.65,P <0.001)or include at least 200 subjects(Arg/Arg vs Pro/Pro:OR=0.56,95%CI:0.47-0.65,P<0.001). Analysis restricted to well-designed studies also supported the significantly decreased risk of EC(Arg/Arg vs Pro/Pro:OR=0.54,95%CI:0.46-0.64,P<0.001). CONCLUSION:TP53 Arg72 carriers are significantly associated with decreased EC risk.Nevertheless,more welldesigned studies are needed to confirm our findings.

Assessment of Variabilities in Wheat Genotypes to Yellow and or Strip Rust, Puccinia striiformis in Glass House Conditions

Yellow/stripe rust caused by Puccinia striiformis is a major problem in the Middle East specially Iran. Virulence survey of cereal rust fungi have traditionally used differential host genotype and virulent physiologic race 134 E 134 AT was received to evaluate the segregating lines. A set of 35 segregating lines and three additional susceptible cultivars were added, making a total of 38 eultivars-lines. Spreader plants served as a source of inoculums. The plants were evaluated after two months based on infection percentage and the disease scoring scales. The results indicated that, there are significant changes in susceptibility assessments of the segregating lines in contrast to cultivated varieties to the yellow rust P. striiformis as far as the disease incidence and rust development is concerned in these experiments. The selected differential genotypes associated with various levels of resistance. The infection percentages were varied on the lines and the varieties, whereas the severity percentages were entirely different. The lowest severity is of line 38 with 34.70% and the highest in line 1 with 93.49% indicating 2.7 folds reduction in severity. For discrimination among the lines, the results on scoring scales gave distinctions of five classes of resistance, in which, the highest score is 29.93 and the lowest one 11.46. The cluster analysis showed almost similar results and confirmed, the analysis by Duncan＇s Multiple-lest rang as the above five distinctive groups.

Gaussia Luciferase Reporter Assay for Assessment of Gene Delivery Systems in Vivo

Objective To develop an alternative method for assessment of gene delivery systems in vivo.Methods Mouse primary spleen lymphocytes were genetically modified in vitro by a retroviral vector harboring a Gaussia luciferase(Gluc) expression cassette.After implantation of these cells into recipient mice,the expression of Gluc was detected in whole blood or plasma collected.Results As little as 10 μL whole blood drawn from the recipient mice could guarantee prompt reading of Gluc activity with a luminometer.And the reading was found in good correlation with the number of genetically modified spleen lymphocytes implanted to the mice.Conclusions Gluc may be useful as an in vivo reporter for gene therapy researches,and Gluc blood assay could provide an alternative method for assessment of gene delivery systems in vivo.

Evaluating the Discriminatory Power of DNA Barcodes in Panicoideae, Poaceae

DNA barcoding is a powerful technique for species identification with little morphological knowledge, by using short sections of DNA from a specific region of the genome. Two core barcode markers, rbcL and matK, and a supplementary nuclear ribosomal internal transcribed spacer region were used to examine the effectiveness of the markers for Poaceae barcoding using 133 individuals of 36 taxa across 23 genera of Korean Panicoideae. We also aimed to establish a DNA barcode database for the major weeds of Korean Panicoideae. All three markers revealed a good level of amplification and sequencing success. As a single DNA marker, the ITS region achieved the highest species resolution, followed by matK. Resolving power was increased when nrlTS was incorporated into the core barcode markers. The best resolving power was obtained with a combination of matK ＋ ITS with 89.7%, followed by rbcL ＋ matK ＋ ITS with 89.3%. Thus, rbcL may be not necessary as a DNA barcode for Panicoideae species identification, when considering cost and effectiveness. Instead, a combination of matK ＋ ITS is proposed as the most suitable DNA barcode for the species identification of Panicoideae, Poaceae. We conclude that DNA barcoding using a combination of matK ＋ ITS could be one of powerful techniques for the identification of Poaceae species, The barcode sequences were deposited to the National Center for Biotechnology Information （NCBI） database for public use.

Genetic Variation Assessed with Microsatellites in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) in China

Abstract Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding pro- grams in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8-20.6, and a mean expected heterozygosity of 0.902-0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a rela- tively large number ofbroodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided im- portant information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.

Evaluation of Endophytic Bacteria for Plant Growth Promotion and Pathogen Suppression Traits in Saccharum officinarum

Endophytes are beneficial microbes that are capable of promoting growth, besides protecting colonized plants against plant pathogens. These microbes are of either bacterial, fungal or actinomycetes in plants. In the study, the endophytic bacteria isolated from sugarcane with their characterization related to plant growth promotion and pathogen suppression have been reported. Roots, shoots and leaves of rooted tissue culture plantlets of sugarcane cultivars of 87A298 and 2009A107 were excised aseptically and isolated endophytic bacterial strains. The strains were identified using 16S rRNA gene sequence based homology. Molecular characterization of these strains was carried out for presence of antimicrobial genes. The results showed that the endophytes isolated from sugarcane tissue culture plantlets were of the genera Bacillus （B. amyloliquefaciens, B. subtilis, B. cereus, B. safensis, B. siamensis, B. aryabhattai, B. flexus and B. velezensis） and Paenibacillus pabuli. There were three antimicrobial peptides （AMPs） producing genes of bacilysin, bacillomycin and fengycin in B. amyloliquefaciens （SE1, SE7）, B. siamensis （SE4, SE16）, B. subtilis （SE2, SE3） and B. velezensis （SE15）. The biochemical characterization assays showed that some of these strains could produce hydrogen cyanide （HCN）, protease, cellulase and indole acetic acid （IAA）. Few strains （SE1 and SE4） were phosphate solubilizers, whereas nine isolates were found to be diazotrophs. Most of the bacterial isolates were found antagonistic to Fusarium sacchari, the sugarcane wilt pathogen under in vitro conditions. Overall, the results suggested the scope and potentiality of sugarcane endophytic bacteria, isolated from tissue culture plantlets, in promoting plant growth and suppression of sugarcane pathogen.

Modelling Causes of Temporal Genotype-By-Environment Interaction in Oil Palm Bunch Yield in Nigeria

The objectives of this research were to understand pattern of temporal （year to year） stability in oil palm genotypes and then identify weather variable（s） associated with temporal stability. Stability analysis was performed using the GGE biplot method. The best genotype in one year was not same always in the other year due to changes in the weather conditions over the years. Test environment evaluation revealed that the year 2000 （Y00） was the best representative of the overall environments and most powerful to discriminate genotypes with superior mean yield and temporal stability. The relationship of the climatic factors on the basis of their joint contribution to the development of specific trait varied from the pattern observed when their roles on the same traits were individually assessed. Maximum relative humidity, sunshine and rainfall could help explain the yield fluctuation due to their contribution to the overall yield variation. However, genotypes GI0 and G2 which exhibited high mean performance and stability for BN would be beneficial to the oil palm growers in ensuring steady cash flow from regular bunch yield production.

Risk Assessment and Biosafety Studies of Transgenic Bt Rice （Oryza sativa L.）

Transgenic crops having alien genes from different sources are getting popularity. A Rice （Oryza sativa L.） containing gene from Bacillus thuringiensis, a soil bacterium, was assessed to study the potential risks of transgenic plants on environment. The crop was found resistant to target insect pests. Rice variety Basmati-370 transformed with two insecticidal genes, crylAc and cry2A, was grown under field conditions for several years. Data were collected at different stages of the plant growth. Fate of Cry protein in soil, effect of Bt protein on non-target insects, risks of vertical and horizontal gene flow were evaluated. No potential hazard was found at all levels. Bt protein was unstable and degraded significantly in soil within 30 days after harvesting the crop. No harmful effects were found on non-target insects （insects other than order lepidoptera）. Maximum gene flow of 0.02% was observed at close spacing and no evidence of horizontal gene transfer to Rhizobium spp. was found. In conclusion, the transgenic rice plants transformed with Bt genes have no harmful effects on the environment.

Evaluation of Major Chemical Components in Beans of Some Selected International Cocoa Clones in Ghana

Cocoa bean is an important raw material for the chocolate, pharmaceutical and cosmetic industries. The butter content and other chemical components such as polyphenols play essential role in the health benefits of consumers as well as flavor of chocolates produced. In this study cocoa beans from 15 international clones （genotypes） were fermented and dried for six and 14 days, respectively. Genotypic effect on the major chemical components of the beans that affect chocolate flavour and taste were assessed using various protocols in the laboratory. Concentrations and relationship existing among the chemical components tested during three- and two-year periods were determined. Genotypic differences were found to account for variation in the concentration of various components tested. Among the genotypes used Man 15-2 seems to be high in fat content whilst IMC 47 was low. In terms of O-dihydric phenol content ICS 1 recorded the highest whilst MO 20 recorded the least. A further test on polyphenols content showed high levels for Gu 255 whilst T 79/501 recorded the least. Significant positive correlation was also observed among the various chemical components tested. The findings of this work clearly confirmed the existence of significant correlations among the major chemical components in cocoa beans and the influence of genotype on the chemical component concentration. This information could be very useful in breeding and selection for a particular component since genotype plays a major role.

Developing an Assessment Model for Factors Affecting the Quality in the Construction Industry

Quality is considered as one of the most important elements in the construction industry. The factors affecting quality in the construction industry should be assessed. This paper aims to introduce a new model to assess these factors. The model is namely Fuzzy Assessment Model for Quality （FAMQ）. Fuzzy set theory provides a useful way to deal with ill-defined and complex problems in a decision-making environment that incorporates vagueness. The proposed model employs the combined effect of both; the factors probability of occurrence and their impacts on the quality of construction. Twenty five logical rules for each factor were implemented in the model. The model was evaluated using data that collected from the infrastructure projects in Egypt. It was applied to many factors that affect the quality of this kind of projects as a case study. The results of the study proved that the proposed model can be used successfully in the assessment of factors affecting quality in the construction industry. In addition, the results provided a platform of useful assessment reference to those infrastructure＇s finns, who plan to establish their businesses in Egypt.

Development of 57 Novel Polymorphic Microsatellite Markers in Half-Smooth Tongue Sole(Cynoglossus semilaevis)

Half-smooth tongue sole (Cynoglossus semilaevis) is a promising species for aquaculture in China.The wild population of C. semilaevis is under threat from environmental factors. Microsatellite markers are very suitable for assessing genetic diversity. Four microsatellite-enriched libraries of half smooth tongue sole (Cynoglossus semilaevis) were constructed,from which 57 polymorphic microsatellites were isolated and characterized.The polymorphism of these microsatellites was assessed by genotyping in 30 individual fish.The number of alleles ranged from 2 to 11, with an average of 4.614 alleles per locus.The values of observed and expected heterozygosities ranged from 0.1000 to 1.0000 and from 0.0966 to 0.8847 respectively. Polymorphism information content (PIC) ranged from 0.0905 to 0.862.These markers would be useful for population structure assessment,genetic linkage map construction and parentage analysis for this species.

借鉴国际准则发展中国肉牛产业

我国肉牛历经快速发展和数量锐减的阶段,目前面临着一些制约发展的瓶颈。本文旨在借助国际动物记录委员会(ICAR)经验,提出按照ICAR操作指南的规则建立我国肉牛产业数据记录系统的建议,以提升我国肉牛产业的管理水平,加快肉牛育种进程,为百姓餐桌上的牛肉安全和质量提供技术保障。

Field evaluation of effects of transgenic cry1Ab/cry1Ac,cry1C and cry2A rice on Cnaphalocrocis medinalis and its arthropod predators

The impacts of transgenic Bt rice on target pests and their predators need to be clarified prior to the commercialization of Bt rice.In this study,the percentages of folded leaves of three transgenic Bt rice lines and non-transgenic parental rice line caused by Cnaphalocrocis medinalis were studied over two successive growing seasons.In addition,the population densities,relative abundance and population dynamics of C.medinalis and four species of its natural arthropod predators were investigated at three sites in China.The results showed that rice line significantly affected the percentages of folded leaves and population densities of C.medinalis larvae.Significantly higher percentages of folded leaves were observed on the non-transgenic rice compared with the three transgenic Bt rice on most sampling dates.Significantly higher densities of C.medinalis larvae and higher relative abundance of C.medinalis within phytophages were found on non-transgenic rice compared with three transgenic Bt rice at different sites across the study period.The population dynamics of C.medinalis larvae were significantly affected by rice line,rice line×sampling date,rice line×year,rice line×sampling date×year.However,there was little,if any,significant difference in the relative abundance,population density and population dynamics of the four arthropod predators between the three Bt rice lines and non-transgenic rice.The results of this study indicate that the Bt toxin in transgenic Bt rice can effectively suppress the occurrence of C.medinalis,but has no significant effects on the occurrence of the four predatory arthropod species.