Relationship Between the First Base of the Donor Splice Site of Waxy Gene Intron 1 and Amylose Content in Yunnan Indigenous Rice Varieties

There exists a single nucleotide polymorphism, G or T, at the first base of the donor splice site of waxy gene intron 1 in rice. In order to study the relationship between the first base of the donor splice site of waxy gene intron 1 and amylose content in rice, the one-step PCR method was used to determine whether it is G or T in 220 Yunnan indigenous rice varieties from 14 districts, 55 towns/counties of Yunnan Province, and 101 varieties of which were validated by the PCR-Acc I method. According to the G/T polymorphism, 164 rice varieties showed GG-genotype, while the other 56 fell into TT-genotype, accounting for 74.5% and 25.5% of all the test varieties, respectively. When all the rice varieties were divided into indica and japonica subspecies, it was found that 80.5% of indica rice and 67.0% of japonica rice belonged to GG-genotype. The rice varieties with GG-genotype had significantly higher amylose content (18.95% on average) than those with TT-genotype (all below 16%), but 33 rice varieties with GG-genotype still had low amylose content ranging from 3.91% to 15.93%, and most of them came from the Dai minority area in the Southwest of Yunnan Province. However, there was no significant difference in the mean amylose content of the same GG or TT genotypes between indica and japonica rice, suggesting that different genetic backgrounds, indica or japonica, had no effect on amylose content. The coefficient of correlation between the genotype and amylose content was 0.733 (P<0.01).     

应用竞争PCR检测丙酸盐对体外培养牛肝细胞丙酮酸羧化酶mRNA水平的影响

根据牛肝细胞内PC(丙酮酸羧化酶)基因组与PCcDNA相比多含有一个内含子序列．在其中再插入一外源DNA序列．从而使最终构建的突变体片段的长度大于PCcDNA的长度，成功构建了PCcDNA的竞争DNA模板，然后应用竞争PCR方法研究了丙酸盐对体外培养新生牛单层肝细胞PCmRNA水平的影响。使单层肝细胞培养液中丙酸钠浓度分别为0、1．5、2．5、3．5、4．5、8．5、11．5mmol／L，处理24h，提取总RNA、逆转录，在同一体系中用相同引物扩增目的带和竞争模板带。结果表明．随着丙酸钠浓度的升高．PCmRNA水平呈上升趋势，提示肝细胞内PCmRNA的表达水平受培养液中丙酸钠浓度的影响。     

基于序列信息预测内含子保留型可变剪接

可变剪接是遗传信息传递与表达的重要环节,真核生物多外显子基因pre-m RNA的可变剪接现象非常普遍。可变剪接增加了蛋白质的多样性,影响诸如细胞组织特异性分化、个体发育、疾病发生等重要的生物学过程。基于内含子的k-mer(k=1…5)信息,利用多样性增量结合二次判别的方法,对保留型内含子和组成型内含子进行了区分。五折交叉检验显示的预测总精度、敏感性和特异性均大于70%。表明内含子的序列信息可能对保留型内含子的剪接有重要调控作用。     

海南橡胶藻18S rDNA与16S rDNA二级结构构建及分析

[目的]对海南橡胶藻的新属、新种地位进行确认。[方法]对海南橡胶藻这一重要生物资源的18S核编码核糖体RNA序列和16S叶绿体编码核糖体RNA序列进行分析,对18S核编码核糖体RNA进行近缘物种间的序列比对及2个I类内含子二级结构模型的构建。[结果]橡胶藻16SrRNA在639位点（Ecoli序列编号）有一个46bp的插入片段,该片段能形成一个完美的双发夹结构。对16SrRNA的正常折叠不会产生影响。[结论]这一双发夹结构在其他物种的叶绿体rDNA中还未见报道过。     

内含子序列在甘蓝MAGIC亲本间亲缘关系分析中的应用

为探究甘蓝多亲本高级世代互交系(multiparent advanced generation inter-cross,MAGIC)亲本间的亲缘关系和遗传多样性,以便对MAGIC杂交亲本的选择提供依据,采用生物信息学的方法对单拷贝基因进行全基因组鉴定,并采用其内含子序列分析对7个甘蓝亚种共12个MAGIC亲本构建系统发育树。全基因组鉴定共获得7 930个单拷贝基因,每条染色体上随机挑选1条单拷贝基因,采用PCR方法进行内含子扩增并测序,最终获得3 427bp内含子长序列。运用邻接法构建系统发育树,可将甘蓝类蔬菜分为3大类型:花椰菜与西兰花类(CladeⅠ)、羽衣甘蓝类(CladeⅡ)以及结球甘蓝、抱子甘蓝、苤蓝与芥蓝类(CladeⅢ),表明内含子序列适于甘蓝亚种亲缘关系聚类;同时也表明,芥蓝属于甘蓝亚种,西兰花与花椰菜具有较近的亲缘关系;利用单拷贝基因内含子序列分析的方法可以较好地显示甘蓝MAGIC亲本间的亲缘关系,为MAGIC群体的构建提供参考。     

Molecular polymorphism of cytoplasmic DNA in Ficus carica L.: Insights from non-coding regions of chloroplast DNA

The trnL (UAA) intron and the intergenic spacer between the 3′ exon of trnL (UAA) and trnF (GAA) sequences were used as genetic markers for differentiating Ficus carica cultivars and establishing refined genetic relationships. The study was based on 20 fig cultivars, collected from south and centre of Tunisia. Since, the intron was thought to be more variable among close relatives than is the chloroplast spacer. The size of these non-coding regions varied from 554 to 589 and from 989 to 1022 bases pairs for the intron and the combined sequences correspondingly. The average of GC content was 33.9% and 34.6% in the intron and the combined intron and spacer respectively. High values of A + T contents were detected in both data sets and may explain the high proportions of transversions founded. The observed variation pattern of plastid DNA provides evidence of an important genetic diversity. The overall transition/transversion bias (R) was 0.202 in the intron and 0.27 in the combined regions. The RI index of 0.592 indicates that these combined sequences have clearly more homoplasy then the intron (RI = 0.705) and spacer (RI = 0.777) sequences separately. Phylogenetic trees were generated based on maximum parsimony (MP) and neighbor-joining (NJ) analysis of the chloroplast sequences data. Results proved that a typically continuous genetic diversity characterizes the local fig germplasm. In fact, relationships inferred from the cpDNA analysis suggest several clades, which do not show geographical or tree sex correspondence. Although the level of apparent diversity is considerable, we may conclude that non-coding regions of chloroplast genome provide a new and practical opportunity to evaluate genetic diversity and to discriminate fig cultivars. Revealed cytoplasmic DNA markers are reliable to elaborate a molecular data base to conduct management and breeding programs on local fig germplasm.     

猪的垂体特异性转录因子基因多态性研究

研究采用PCR和DNA测序方法,对小型猪种(香猪、巴马猪)及对照猪种(上海白猪、大约克夏猪)的垂体特异性转录因子(PIT-1)基因1293位至2230位进行了单核苷酸多态性(SNP)分析。结果显示:在第5内含子中有多处发生突变,其中在1429位,香猪、巴马猪的所有个体均发生了G→A突变,而上海白猪、大约克夏猪则未发生突变;在第6外显子中未见任何突变。结论:PIT-1基因1429位可作为小型猪基因标记的候选位点。     

鸡早期产蛋性能与ESR1基因内含子1多态性相关分析

为探寻鸡ESR1基因内含子1多态性与早期产蛋性能存在的关联性,采用DNA测序和PCR-SSCP技术对124只绿壳蛋鸡的基因型与性状进行相关性研究。结果表明,鸡ESR1基因In1片段中发现5种基因型:T1T1、T1T2、T2T2、T1T3和T3T3;试验群体处于高度多态,群体遗传偏离了Hardy-Weinberg平衡(P<0.05)。方差分析显示,各基因型个体间的早期产蛋性状指标达到了显著(P<0.05)或极显著(P<0.01)水平,其中T1T3基因型个体性能处于优势,对该群体进行人为选择可提高产蛋性能。     

根据线粒体nad1基因第2内含子的序列多态性对糯玉米进行系统分类

在植物的系统与进化研究中,相对于叶绿体和核基因片段而言,线粒体基因片段由于其系统发育信息位点少、结构复杂而较少应用到系统学研究中。本研究选用nad1基因的第二内含子序列重建玉蜀黍属主要种的系统发生树,在分子水平上验证了糯玉米在玉蜀黍属中系统学位置,并在此基础上探讨了nad1基因内含子序列的系统学意义及其在系统发育重建中的价值。结果表明,目前对玉蜀黍属内各类型材料的系统分类是合理的,糯玉米和玉米种内各类型材料之间遗传差异小;线粒体nad1基因第2内含子序列在种内和种间的变异较小,在种以上分类研究中具有一定的系统学价值。