Influence of allele frequency on predicting animal phenotype using back-propagation artificial neural networks

To overcome the obstacle of the fascinating relation in predicting animal phenotype value, we have developed a neural network model to detect the complex non-linear relationships between the genotypes and phenotypes and the possible interactions that cannot be expressed with equations. In this paper, back-propagation neural network is used to discuss the influences of different allele frequencies on estimating the polygenic phenotype value. To ensure the precision of prediction, normalization was needed to train the prediction model. The results show that back-propagation artificial neural networks can be used to predict the phenotype value and perform very well in allele frequency from 0.2 to 0.8, when the allele frequency is very small (less than 0.2) or big (more than 0.8); however, the prediction model was not reliable and the predicted value should be carefully tested.     

牛亚科3个主要家养牛种MyoG基因多态性及其遗传分化

对普通牛(鲁西牛、渤海黑牛)、天祝牦牛和中国广西水牛的MyoG基因部分核苷酸序列变异进行了分析,旨在揭示不同牛种群的DNA多态性及其遗传分化.采用PCR和DNA直接测序技术获得4个牛群体的MyoG基因exon 1和5’侧翼部分序列,与GenBanK公布的牛亚科动物同源序列作比对分析.结果显示,在渤海黑牛和牦牛未发现多态位点;鲁西牛存在1个多态位点,定义了2个单倍型;水牛有6个突变位点,但群内只发现1个多态位点.核苷核苷酸多样性(Pi)在0.000 00～0.001 35之间,说明群体内遗传多态性程度较低。核苷酸歧义度(Dxy)以水牛与鲁西牛之间比较最高,为0.013 97,表明水牛遗传分化明显.种系进化树分析表明,牦牛与普通牛亲缘关系很近,二者与水牛关系较远,支持将牦牛归为牛属(Bos)的一个亚属或一个种的观点.     

Mining,characterization, and exploitation of EST-derived microsatellites in <Emphasis Type="Italic">Gossypium barbadense</Emphasis>

Simple sequence repeats (SSRs) have been widely applied as molecular markers in genetic studies. However, the number of ex-pressed sequence tags (ESTs) and SSR markers from Gossypium barbadense is fewer than those from other cotton species. In this study, EST-SSR distribution from G. barbadense was characterized and new G. barbadense-derived EST-SSR markers were de-termined on the basis of the ESTs obtained by randomly sequencing 2 cDNA libraries associated with fiber development in G. barbadense. By mining 9697 non-redundant ESTs, a total of 638 SSR loci derived from 595 ESTs were observed. In G. barba-dense, the frequency of ESTs containing SSRs was 6.13%, with an average of 1 SSR in every 10.4 kb of EST sequence. Further-more, trinucleotide was found to be the most abundant repeat type among 2–6-nucleotide repeat types. It accounted for 26.6% of the total, followed by the hexanucleotide (26.0%) and pentanucleotide repeats (25.9%). Among all the repeat motifs, (AAG)n accounted for the highest proportion. EST-SSR primer pairs were developed using the Primer3 program, and the redundant primers were removed using the virtual PCR approach. As a result, 380 non-redundant EST-SSR primer pairs were developed and used to detect polymorphisms between the mapping parents G. hirsutum ‘TM-1’ and G. barbadense ‘Hai7124’ for constructing linkage groups in cultivated allotetraploid cotton. Out of these, 98 (25.8%) primer pairs detected polymorphisms. Finally, 95 polymorphic loci from 82 primer pairs were integrated into the backbone genetic map; of these, 42 were mapped into the A subgenome and 53 into the D subgenome. The present work provided the foundation for constructing saturated genetic maps and conducting comparative genomic studies on different cotton species.     

油田采出液中硝酸盐还原菌的分离培养及对硫酸盐还原菌的抑制研究

对绥中36-1油井B区油井采出液中的细菌进行分离培养及初步鉴定, 纯化出了一株生长旺盛、硝酸盐还原能力强的硝酸盐还原菌(Nitrate-Reducing Bacteria,NRB)菌株B92-1,对其进行了常规鉴定及16S rRNA分析,并进行了该菌株对富集的硫酸盐还原菌(Sulfate-Reducing Bacteria, SRB)的竞争性抑制实验.研究结果表明仅仅投加硝酸盐、亚硝酸盐作为电子受体,对其中硝酸盐还原菌的激活作用以及产抑制硫化物产生的能力有限,而同时加入分离自采出液的NRB则对硫酸盐还原菌的生长和产硫化物活性都产生了明显的抑制,并且亚硝酸盐的抑菌效果优于硝酸盐.     

单核苷酸多态性及其在作物遗传育种中的应用

单核苷酸多态性（simple nucleotide polym orphism,SNP）是等位基因间序列差异最为普遍的类型,可以作为一种高通量的分子标记.本文主要介绍SNP的定义、几种植物学中常用的检测SNP方法及SNP标记在作物遗传育种中的应用.     

玉米淀粉合成相关基因ZmSSIIa 的序列变异分析

 玉米淀粉合成酶ZmSSIIa 在淀粉生物合成途径中主要作用是将支链淀粉的分支链由6~10 个延长至12~25 个, 对于玉米籽粒产量和品质具有重要的影响。本研究在86 个优异玉米自交系中对该基因进行基因序列定点捕获, 并获得该基因全长为4836 bp 的核苷酸序列。基因多态性分析发现, 该基因座位上有78 个SNP 和19 个Indel。玉米ZmSSIIa 基因的编码区具有24个SNP, 将该基因划分成9 种编码区单倍型, 并编码7 种ZmSSIIa 蛋白质。供试材料的群体中, ZmSSIIa 基因至少经历8 次重组, 可能对单倍型的分化和连锁不平衡具有重要作用。中性进化测试表明该基因在供试群体中没有明显的人工选择。     

和田维吾尔族老人5-HTTLPR基因插入/缺失多态性研究及长寿的关联分析

 本文运用聚合酶链式反应技术(PCR)对新疆和田地区30例90岁以上维吾尔族长寿老人和70例当地健康、无血缘关系、生活习惯相似、随机抽样的维吾尔族对照人群进行5-HTTLPR基因分型及相应等位基因频率的比较并且探讨了5-羟色胺转运体基因连锁多态性区域(5-HTTLPR)的44bp插入/缺失序列多态性与长寿的相关性。结果表明,维吾尔族长寿老人的5-HTTLPR基因多态性的LL(528bp/528bp)基因型和L(528bp)等位基因频率分别为70%和81.7%,对照者LL基因型和L等位基因频率分别为40％和57.2％,两组之间比较差异有显著性(P<0.05)。由此得出,5-HTTLPR基因多态性与新疆和田地区维吾尔族老人的长寿有关联,新疆和田地区长寿相关基因组成为LL基因型和L等位基因。     

DNA指纹图在小鼠ES细胞嵌合体鉴定中的应用

尝试应用多位点DNA指纹技术,检测经过胚胎干细胞(ES细胞)途径所获得的嵌合体小鼠中ES细胞在各种脏器中的嵌合情况、检测ES细胞在嵌合体小鼠中是否实现种系传递。结果表明：采用新型的人工合成的寡核苷酸多聚体探针(JL-02探针)的多位点DNA指纹图谱,具有足够的多态性和很好的稳定性。适用于鉴定ES细胞在嵌合体小鼠各种组织器官中的嵌合情况,也适用于鉴定ES细胞是否具有种系嵌合能力,尤其适用于在嵌合体研究中,最适宜的品种组合具有相同的毛色或相同的酶型。     

用流式细胞仪和RAPD快速鉴定柑橘体细胞杂种

利用流式细胞仪和随机扩增多态DNA（RAPD）方法对获得的3例柑橘体细胞杂种进行鉴定,结果表明,两者相结合可快速有效地鉴定体细胞杂种．所检测的3个组合共9株再生植株,有8株是四倍体体细胞杂种,1株为二倍体叶肉亲本型杂种．体细胞杂种一般表现为具有双亲的特征带,且综合双亲的所有带,但在部分杂种中检测到了双亲都没有的新带,也发现有丢失亲本的特征带或共有带的现象,说明融合后染色体发生了重组和交换;有的引物只检测到叶肉亲本的特征带,根据柑橘叶肉细胞无论单独培养还是共培养均不能再生的事实,可推测其为体细胞杂种或二倍体叶肉亲本型胞质杂种．对这两种方法相结合用于体细胞杂种鉴定的可行性进行了讨论．