Bt cry序列本地数据库的建立及本地BLAST的实现

根据研究的实际需要,运用winSDK设计了一个可视化的BLAST接口程序,利用此程序可以构建本地核酸和蛋白序列数据库与进行本地BLAST。在此基础上建立了苏云金芽孢杆菌(Bt)cry基因的本地核酸序列数据库,并进行了本地BLAST。与先前文献中介绍的本地BLAST实现的方法相比,此方法操作简便、并可根据实际需要随意定制相关数据库;在与NCBI的BLAST进行比较后发现,本地BLAST还具有个性化、准确性强、可信度高等特点。     

One tube nested-PCR在SNP基因型分型中的应用

nested–PCR是一种在普通PCR基础上发展起来的专门用于检测单核苷酸多态性(SNP)的技术。结合nested–PCR技术在水稻中检测SNP的研究,以1个水稻香味基因Fgr和3个稻瘟病基因Pi–ta、Pi9、Pigm为例,把nested–PCR的4条引物同时加在一管PCR反应中进行扩增,在其序列内针对SNP位点设计功能标记,用来扩增含有突变位点的DNA片段。通过优化引物浓度梯度和改良反应程序,达到了一步快速检测SNP基因型的目的。     

全国优质粳稻优良食味品评情况报告

在全国范围内进行征集和初选,筛选出黑龙江、吉林、辽宁、天津、江苏、新疆、河北、山东等省、市、自治区20个优良粳稻品种入选参加食味品评。通过品评可以看到:许多品种均表现出良好的感官食味特性,有些甚至超过日本越光品种;在我国粳稻主产区,只要加强优质食味研究开发力度均能培育出优质食味品种;碾米品质、外观品质及理化指标在对食味影响中存在的相关性需进一步验证,从而建立一套食味品质研究评价体系,使此评价体系完全符合人们对食味的要求;食味研究是一项系统工程,与品种特性、栽培技术、产地、贮藏加工条件等均密不可分;我国有一大批优质食味品种有待于加大开发、宣传、推广力度,并作为优质食味米,高标准地打入国际市场;建立研究我国粳稻食味为主的学术专家组,制定研究目标和发展规划,切实把我国粳稻食味研究做大、做强,尽快提升我国粳稻食味品质的研究水平并赶超世界先进水平。     

湖南红茶实物标准样制作及品质分析

茶叶实物标准样对于客观准确地鉴别茶叶品质是不可或缺的,简述湖南红茶实物标准样制备流程,并分析其感官品质特点及生化成分。结果表明,湖南红茶特级标准样氨基酸含量最高,滋味甜醇甘鲜,鉴定出的110种挥发性香气物质中萜类物质含量显著高于其他茶样,香气表现为嫩甜香浓郁持久;湖南红茶一级标准样水浸出物和儿茶素含量最高,滋味醇厚甘爽,鉴定出114种挥发性香气物质,各类挥发性成分含量居中,呈现出纯正甜香;湖南红茶二级标准样滋味成分含量相对较低,滋味甜醇尚浓,鉴定出109种挥发性香气物质,来源于脂肪酸和类胡萝卜素的挥发性物质含量显著高于其他茶样,表现为甜香带花香。本研究可为湖南红茶加工生产提供参考。     

稻米蒸煮食味品质的评价方法及影响因素分析

总结了目前对稻米蒸煮食味品质评价的三种方法,包括感官评价法、理化指标评价法和仪器评价法。同时分析了影响稻米蒸煮食味品质的因素,为优质稻米生产提供参考。     

Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers

The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE.     

橡胶丛枝病分子检测研究

感染橡胶丛枝病的长春花（菟丝子桥接），通过提取其总DNA，以植原体（phytoplasma）特异引物，进行PCR扩增，结果得到860bp的DNA片断，片断的大小与设计的相符。而健康长春花扩增得不到此片断。同样，将感染丛枝病的橡胶树总DNA，进行PCR扩增，结果与上述相同。该860bp片断经地高辛标记，核酸杂交结果显示，感染丛枝病的橡胶树阳性反应强烈，健康橡胶树仅有微弱反应。     

核桃NBS类抗病基因类似物的序列特征及其与炭疽病的抗性

【目的】利用同源序列法分离核桃的NBS（Nucleotide binding site）类抗病基因类似物,为核桃抗炭疽病分子辅助育种及抗病基因的克隆提供基础。【方法】以35个核桃优系为试材,利用接种法鉴定供试材料对炭疽病的抗性;根据已知植物抗病基因的保守结构域P-loop和GLPL设计简并引物,以核桃优系的基因组DNA为模板,通过PCR扩增NBS类抗病基因同源序列片段,并分析所得NBS类抗病基因类似物与核桃优系炭疽病抗性的关系;利用BLASTN/X程序对所得NBS序列在GenBank数据库中进行同源性搜索;利用MEGA 5.2及DNAman 7.0等软件对其进行序列相似性分析和系统进化研究。【结果】35个供试核桃优系中,有20个优系为抗炭疽病类型（R）,其相对抗性指数在0.63-0.82;有5个优系为中抗类型（M）,相对抗性指数在0.27-0.56;有10个为感病类型（S）,相对抗性指数在0.00-0.21。PCR结果显示,从20个抗炭疽病优系的基因组扩增得到20条NBS类抗病基因类似序列;而在其它15个优系（5个中抗优系和10个感病优系）中未扩增到条带,表明核桃NBS序列与炭疽病抗性相关联。BLASTN显示,所得NBS序列在核苷酸水平与GenBank中已知的核桃NBS序列(jrRGAPGs)存在89%-100%同源性,与其它物种NBS序列的同源性在69%以上;BLASTX显示,所得NBS序列与已知核桃NBS抗病蛋白同源性为77%-99%,与其它物种的NBS抗病蛋白同源性在49%-66%。氨基酸序列多重比对分析表明,所得核桃NBS序列均包含有抗病基因所具有的典型功能域,如P-loop、kinase-2、kinase-3和GLPL等,在典型功能域的核苷酸多态性（Pi）明显低于非保守区,有较高保守性。系统发育分析表明,在核苷酸水平上可将所得核桃优系的NBS序列区分为7类,在氨基酸水平上可分TIR和non-TIR两大类7个亚类;所得核桃NBS序列非同义替换率(dN)和同义替换率(dS)的比值dN/dS在0.00-0.95,为纯化选择。氨基酸序列相似性表明核桃优系不同NBS亚类间的相似度为28.3%-63.5%,与已知抗病基因相应区域的氨基酸相似性为22.0%-48.5%。【结论】核桃NBS类抗病基因类似物与炭疽病抗性相关联,NBS序列与其他物种抗病基因有较高同源性,包含抗病基因保守的功能域,在进化上为纯化选择。     

Signatures of selection in Charolais beef cattle identified by genome‐wide analysis

Charolais cattle are one of the most important breeds for meat production worldwide; in México, its selection is mainly made by live weight traits. One strategy for mapping important genomic regions that might influence productive traits is the identification of signatures of selection. This type of genomic features contains loci with extended linkage disequilibrium (LD) and homozygosity patterns that are commonly associated with sites of quantitative trait locus (QTL). Therefore, the objective of this study was to identify the signatures of selection in Charolais cattle genotyped with the GeneSeek Genomic Profiler Bovine HD panel consisting of 77 K single nucleotide polymorphisms (SNPs). A total 61,311 SNPs and 819 samples were used for the analysis. Identification of signatures of selection was carried out using the integrated haplotype score (iHS) methodology implemented in the rehh R package. The top ten SNPs with the highest piHS values were located on BTA 4, 5, 6 and 14. By identifying markers in LD with top ten SNPs, the candidate regions defined were mapped to 52.8–59.3 Mb on BTA 4; 67.5–69.3 on BTA 5; 39.5–41.0 Mb on BTA 6; and 26.4–29.6 Mb on BTA 14. The comparison of these candidate regions with the bovine QTLdb effectively confirmed the association (p < 0.05) with QTL related to growth traits and other important productive traits. The genomic regions identified in this study indicated selection for growth traits on the Charolais population via the conservation of haplotypes on various chromosomes. These genomic regions and their associated genes could serve as the basis for haplotype association studies and for the identification of causal genes related to growth traits.     

棉花类固醇5α-还原酶基因单核苷酸位点的变异效应

为了明确棉花种质资源中类固醇5α-还原酶(Steroid 5 alpha-reductase,DET2)基因单核苷酸多态性,了解核苷酸位点变异对其编码蛋白配体结合域的影响并开发功能分子标记,本研究采用同源基因特异扩增、测序的方法,筛查不同棉花材料的DET2基因编码区突变,分析DET2基因编码蛋白质的三级结构及配体结合位点及其与纤维品质和育性的相关性。结果表明,包含陆地棉、海岛棉、雷蒙德氏棉在内的13份棉属材料DET2基因序列一致性为98.7%,编码区25个碱基易突变位点中有8个位点涉及编码氨基酸变化;该基因编码的蛋白二级、三级结构基本相似,但是配体结合位点差异较大;编码蛋白配体结合域共有8种类型,与品种间SNP组合类型完全相符。DET2基因与棉花纤维品质形成相关,但与育性无关。