Survey of molecular methods for the typing of wine yeast strains

A survey of the genetic polymorphisms produced by distinct methods was performed in 23 commercial winery yeast strains. Microsatellite typing, using six different loci, an optimized interdelta sequence analysis and restriction fragment length polymorphism of mitochondrial DNA generated by the enzyme HinfI had the same discriminatory power: among the 23 commercial yeast strains, 21 distinct patterns were obtained. Karyotype analysis gave 22 patterns, thereby allowing the discrimination of one of the three strains that were not distinguished by the other methods. Due to the equivalence of the results obtained in this survey, any of the methods can be applied at the industrial scale.     

Expression profiling of more than 3500 proteins of MSS-type colorectal cancer by stable isotope labeling and mass spectrometry

An efficient means of identifying protein biomarkers is essential to proper cancer management. A well-characterized proteome resource holds special promise for the discovery of novel biomarkers. However, quantification of the differences between physiological conditions together with deep down profiling has become increasingly challenging in proteomics. Here, we perform expression profiling of the colorectal cancer (CRC) proteome by stable isotope labeling and mass spectrometry. Quantitative analysis included performing mTRAQ and cICAT labeling in a pooled sample of three microsatellite stable (MSS) type CRC tissues and a pooled sample of their matched normal tissues. We identified and quantified a total of 3688 proteins. Among them, 1487 proteins were expressed differentially between normal and cancer tissues by higher than 2-fold; 1009 proteins showed increased expression in cancer tissue, whereas 478 proteins showed decreased expression. Bioinformatic analysis revealed that our data were largely consistent with known CRC relevant signaling pathways, such as the Wnt/β-catenin, caveolar-mediated endocytosis, and RAN signaling pathways. Mitochondrial dysfunction, known as the Waburg hypothesis, was also confirmed. Therefore, our data showing alterations in the proteomic profile of CRC constitutes a useful resource that may provide insights into tumor progression with later goal of identifying biologically and clinically relevant marker proteins. This article is part of a Special Issue entitled: Proteomics: The clinical link.     

大口黑鲈微卫星DNA指纹图谱的构建和遗传结构分析

以国内目前养殖的大口黑鲈[Micropterus salmoides(Lacépède)]群体(CH)、2009年引进的佛罗里达亚种(FL-09)、2010年引进的佛罗里达亚种(FL-10)、2010年引进的北方亚种(NT-10)为实验材料,应用43个微卫星DNA标记对这4个大口黑鲈群体进行遗传检测,构建了各群体的微卫星DNA指纹图谱,并对其遗传结构进行分析。结果显示:CH、FL-09、FL-10和NT-10群体的平均等位基因数(A)分别为2.58、3.74、3.70和4.21,平均期望杂合度(He)分别为0.4549、0.4896、0.5010和0.6138,平均多态信息量(PIC)分别为0.3786、0.4443、0.4566和0.5546,表明国内目前养殖的大口黑鲈群体遗传多样性水平远远低于国外新引进的大口黑鲈群体。利用UPGMA法对4个群体进行聚类,结果 FL-09和FL-10聚为一支,遗传距离为0.0506;NT-10和CH聚为另一支,遗传距离为0.4244,推测FL-09和FL-10两个佛罗里达亚种属于相同的群体,而NT-10和CH两个北方亚种来自不同的群体,甚至不同的水系。同时从指纹图谱中,筛选到5个特异的微卫星标记(JZL114、MiSaTPW11、Lma120、Mdo6和Msal21),可以鉴别FL、NT-10和CH群体,其中MiSaTPW11和Msal21这两个标记组合可以完全鉴别这3个群体。将5个特异性微卫星标记的图谱数据转化成计算机可以识别的数码指纹,可以方便应用于大口黑鲈不同群体及其杂交种的鉴定。研究结果可以为我国大口黑鲈种质资源保存、品种鉴定和良种选育提供理论依据。     

微卫星DNA标记在近交系大鼠HFJ和MIJ遗传监测中的应用

目的 用24对引物对近交系HFJ和MIJ大鼠的微卫星位点进行多态性分析,并选用近交系Lewis和F344大鼠作为对照,进行比较分析.方法 用传统的酚-氯仿法分别提取4个近交系大鼠MIJ、HFJ、Lewis和F344 的基因组DNA,选取大鼠24个微卫星位点,通过PCR扩增,扩增产物经过非变性聚丙烯酰胺凝胶电泳和银染,根据电泳结果,比较分析4种品系近交系大鼠之间微卫星多态性.结果 4种品系及品系内不同个体的近交系大鼠在24个微卫星位点上的扩增产物均出现一个条带,MIJ和HFJ大鼠在品系间和品系内均表现为单态性,同Lewis 和F344的扩增结果比较,14个位点显示多态性,有10个位点显示单态性.结论 两个近交系大鼠品系MIJ和HFJ符合近交系要求,筛选出的14个多态性微卫星位点可用于有关近交系大鼠的遗传背景监测.     

Photosynthetic characteristics and growth performance of closely related aspen taxa: On the systematic relatedness of the Eurasian Populus tremula and the North American P. tremuloides

The European and American aspen species Populus tremula and P. tremuloides are closely related taxa with very large distribution ranges and high economic importance. Genetic and morphological data are not fully congruent with respect to the question of the systematic relatedness of these sister taxa, pointing either at separate species on the two continents or a single aggregate species with circumarctic distribution. In a replicated growth trial with 1-year-old saplings, we compared about 30 morphological (leaf size, leaf area, leaf numbers, leaf growth, leaf phenology and the ratio of leaves lost to leaves produced) and physiological traits (A_max, quantum yield, carboxylation efficiency, maximum rates of carboxylation and electron transport, leaf dark respiration, leaf conductance, leaf water potential and WUE) with the aim to obtain evidence in support of or against the one-species hypothesis and to identify key determinants of growth in the two aspen taxa.     

Microsatellite markers based genetic diversity and bottleneck studies in Zanskari pony

Genetic diversity in Zanskari pony breed was evaluated at 48 microsatellite loci using fifty adult, healthy and unrelated animals. Allele frequency data was used to detect genetic diversity and bottleneck. The estimated average number of alleles (±s.e.) was 8.5208±2.5010 with a total of 409 alleles. A high level of genetic diversity within this breed was observed in terms of number of alleles, observed heterozygosity (0.6763±0.1704), expected Leven's heterozygosity (0.7724±0.795), expected Nei's heterozygosity (0.7644±0.0787) and polymorphism information content (>0.5). In-breeding coefficient (F(is)) was 0.115±0.0209, suggesting moderately high in-breeding in Zanskari breed. Although analysis of bottleneck revealed no bottleneck in recent past but population of Zanskari ponies has decreased drastically and only a few thousand pure-bred animals are left. The information is useful for proposing effective population management strategies for future.     

ENU诱变获得一种多趾小鼠及其突变基因的鉴定

采用化学诱变剂乙酰基亚硝基脲(N-ethyl-N-nitrosourea,ENU)获得一种常染色体显性遗传多趾突变小鼠(Mus musculus),该突变小鼠在后趾内侧(即轴前部)多出一个脚趾,且严重程度不一,部分小鼠双侧后足都有多趾表型。阿尔新蓝-茜素红染色结果表明,多趾突变杂合子小鼠除多趾异常发育外,其余骨骼无明显异常。为定位该突变基因,利用微卫星标记对(C57BL/6J×DBA/2J)F1代多趾突变小鼠回交C57BL/6J得到的[(C57BL/6J×DBA/2J)F1×C57BL/6J]N2代多趾小鼠进行全基因组扫描,最终将本例多趾突变基因定位于小鼠第2号染色体微卫星D2mit45与D2mit184之间,并初步确定Alx4为该突变候选基因。在此基础上对Alx4进行测序分析,测序结果发现突变小鼠Alx4基因编码区第433位碱基处发生A到T的颠换,导致编码区第145位密码子AAA(编码赖氨酸)变为终止密码子TAA,引起蛋白编码提前终止,是引起多趾表型的原因。     

利用SLAF-seq技术开发带鱼(Trichiurus japonicus)微卫星标记以及跨物种扩增检测

带鱼(Trichiurus japonicus)是广泛分布于东亚大陆架海域的暖温性近底层鱼类,长期位居我国单鱼种渔获量第一位。自上世纪70年代以来,持续过度捕捞和海洋环境变化导致中国近海带鱼资源基础和遗传多样性受到严重影响,但有关带鱼种群的微卫星DNA标记研究却较为缺乏,不利于该物种遗传资源评估和保护。为此,本研究采用基于高通量测序平台的SLAF-seq技术,从带鱼的195 308个SLAF标签中识别出25 704个二至六碱基重复微卫星位点。经过引物扩增验证,最终筛选出36个具有多态性的微卫星标记。各位点等位基因数4～35,均值14.47。观测杂合度0.214～1.000,期望杂合度0.456～0.979,均值分别为0.620和0.803。所有位点的多态信息含量值均大于0.25。经Bonferroni校正,21个位点符合哈迪-温伯格平衡,且各位点间不存在连锁不平衡。这21个多态性微卫星标记可为带鱼的种群遗传资源研究提供新的有效分子标记和技术支撑。Bottleneck分析结果表明,宁波近海带鱼群体未检测到近期的遗传瓶颈效应,这可能与目前东海区带鱼野生群体数量还比较庞大、遗传变异仍然较为丰富有关。跨物种扩增结果显示,分别有12、16、4和3个带鱼微卫星标记在带鱼属(Trichiurus)、沙带鱼(Lepturacanthus savala)、窄颅带鱼(Tentoriceps cristatus)及小带鱼(Eupleurogrammus muticus)中具有较好的通用性,这些微卫星标记为今后带鱼科相应属、种的系统进化关系研究提供新的分析手段和契机。     

大鳞副泥鳅5个野生群体的遗传多样性分析

利用微卫星分子标记分析了天津地区于桥水库、大黄堡湿地、七里海湿地、团泊水库和潮白新河5个野生大鳞副泥鳅群体的遗传多样性。5个群体在12个微卫星位点共检测到98个等位基因,平均等位基因数为8.500;有效等位基因数为2.713;平均观测杂合度为0.526;平均期望杂合度为0.544。5个群体间的遗传分化指数介于0.021~0.106之间,平均遗传分化指数为0.059,属中低水平的遗传分化。AMOVA分析结果显示,在总的变异中,94.1%的遗传变异来自群体内,5.90%的遗传变异来自于群体间。根据Nei’s遗传距离所绘制的系统树显示,于桥水库、团泊水库、七里海湿地和大黄堡湿地4个群体的遗传距离相对较小聚为一支,潮白新河群体单独为一支。遗传瓶颈效应分析表明,该5个群体近期未经受遗传瓶颈效应,处于突变-漂移平衡。总体来看,天津地区5个野生大鳞副泥鳅群体的遗传多样性较高,可作为品种选育的基础群体。     

鲮鱼的微卫星位点筛选和群体遗传多样性初步分析

利用鲤科鱼类微卫星引物在鲮鱼中进行扩增,结果在24对引物中,13对引物能成功扩增,且在鲮鱼中的扩增产物表现稳定,其中11对有较高多态性,等位基因数在2—7个之间,扩增的条带符合孟德尔遗传规律。随后利用筛选的微卫星座位对鲮鱼野生和养殖群体遗传多样性进行了初步分析。分析结果显示鲮鱼野生群体的平均等位基因数5.2个;观测杂合度在0.25与0.8之间,平均观测杂合度(Ho)是0.61±0.2 ,平均期望杂合度(He)是0.8±0.09 ;群体座位平均多态信息含量(PIC)为0.72±0.1。相比之下,养殖群体的平均观测杂合度(Ho)和平均期望杂合度(He)都低于野生群体,分别是0.59±0.2、0.75±0.1。两群体间的遗传相似度为0.7774、遗传距离为0.2518。研究表明用其他鱼类分离出的微卫星引物可以快速筛选到适用于鲮鱼遗传分析的微卫星座位。