Analysis of sialyltransferase-like proteins from Oryza sativa

Sialic acids are widely distributed among living creatures, from bacteria to mammals, but it has been commonly accepted that they do not exist in plants. However, with the progress of genome analyses, putative gene homologs of animal sialyltransferases have been detected in the genome of some plants. In this study, we cloned three genes from Oryza sativa (Japanese rice) that encode sialyltransferase-like proteins, designated OsSTLP1, 2, and 3, and analyzed the enzymatic activity of the proteins. OsSTLP1, 2, and 3 consist of 393, 396, and 384 amino acids, respectively, and each contains sequences similar to the sialyl motifs that are highly conserved among animal sialyltransferases. The recombinant soluble forms of OsSTLPs produced by COS-7 cells were analyzed for sialyltransferase-like activity. OsSTLP1 exhibited such activity toward the oligosaccharide Galbeta1,4GlcNAc and such glycoproteins as asialofetuin, alpha1-acid glycoprotein, and asialo-alpha1-acid glycoprotein; OsSTLP3 exhibited similar activity toward asialofetuin; and OsSTLP2 exhibited no sialyltransferase-like activity. The sialic acid transferred by OsSTLP1 or 3 was linked to galactose of Galbeta1,4GlcNAc through alpha2,6-linkage. This is the first report of plant proteins having sialyltransferase-like activity.     

Association of morphological and RFLP markers in rice (Oryza sativa L.).

Seventeen morphological marker genes were associated with restriction fragment length polymorphism markers in rice by using four F2 populations, each segregating for a few observable traits, and 14 near isogenic lines (NILs), each containing one morphological mutant gene. The location of five genes was confirmed on the basis of F2 analysis: Purple hull (Pr) (16.8 +/- 7.9 cM away from RG163 on chromosome 4); Phenol staining (Ph) (20.8 +/- 8.4 cM away from RG163 on chromosome 4); glabrous leaf and hull (gl-1) (14.3 +/- 7.4 cM away from RG182, and 20.9 +/- 8.3 cM from RG403 on chromosome 5); Brown pericarp (Rc) (12.5 +/- 7.2 cM away from RG30 on chromosome 7); and lazy growth habit (la) (28.8 +/- 9.4 cM away from RG118 on chromosome 11). In addition, 12 other morphological markers, including the agronomically important genes semi-dwarf (sd-1) and Pollen restoring factor (Rf-1) were tentatively associated with mapped DNA clones based on screening pairs of NILs.     

水稻微卫星标记的发展和应用

微卫星又称简单序列重复。它是由几个核苷酸（一般２～４个）为重复单位组成的串联重复序列。相同座位上的重复序列由于重复次数的不同而造成序列长度的多态性。微卫星标记是一种共显性标记,具有等位基因丰富、检测技术简单等优点。微卫星标记在基因组作图、品种鉴定、种质保存、分子标记辅助选择等方面有着广泛的应用。目前水稻中已发展了３００多个微卫星标记。     

Development and mapping of Oryza glumaepatula-derived microsatellite markers in the interspecific cross Oryza glumaepatula x O. sativa

Wild germplasm of domesticated crops is a source of genetic variation little utilized in breeding programs. Interspecific crosses can potentially uncover novel gene combinations that can be important for quantitative trait analysis. The combined use of wide crosses and genetic maps of chromosomal regions associated with quantitative traits can be used to broaden the genetic basis of rice breeding programs. Oryza glumaepatula is a diploid (AA genome) wild rice species native from South and Central America. A genetic map was constructed with 162 PCR-based markers (155 microsatellite and 7 STS markers) using a backcross population derived from the cross O. glumaepatula, accession RS-16 from the Brazilian Amazon Region x O. sativa BG-90-2, an elite rice inbred line. The map included 47 new SSR markers developed from an O. glumaepatula genomic library enriched for AG/TC sequences. All SSR markers were able to amplify the O. sativa genome, indicating a high degree of SSR flanking region conservation between O. glumaepatula and O. sativa species. The map covered 1500.4 cM, with an average of one marker every 10 cM. Despite some chromosomes being more densely mapped, the overall coverage was similar to other maps developed for rice. The advantage to construct a SSR-based map is to permit the combination of the speed of the PCR reaction, and the codominant nature of the SSR marker, facilitating the QTL analysis and marker assisted selection for rice breeding programs.     

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).

A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2240 unique marker loci, have been developed and experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are reported for 7% (174) of the loci. The majority (92%) of primer pairs were developed in regions flanking perfect repeats > or = 24 bp in length. Using electronic PCR (e-PCR) to align primer pairs against 3284 publicly sequenced rice BAC and PAC clones (representing about 83% of the total rice genome), 65% of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. Additional information based on genetic mapping and "nearest marker" information provided the basis for locating a total of 1825 (81%) of the newly designed markers along rice chromosomes. Fifty-six SSR markers (2.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy. The largest proportion of SSRs in this data set correspond to poly(GA) motifs (36%), followed by poly(AT) (15%) and poly(CCG) (8%) motifs. AT-rich microsatellites had the longest average repeat tracts, while GC-rich motifs were the shortest. In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb.     

The physical location of fourteen RFLP markers in rice (Oryza sativa L.)

A biotin-labeled in situ hybridization technique was used in order to physically map RFLP markers to the chromosomes of rice (Oryza sativa L.). Fourteen RFLP markers, associated with the ends of the linkage groups on rice chromosomes 7, 8, 11, 12, were physically mapped onto specific regions of the chromosomes. The average detection rate of in situ hybridization was 5.91%. The markers were located on seven different chromosome arms. Ten of the fourteen markers were distributed near the chromosome ends. This demonstrated that the RFLP linkage groups involved covered a wide physical distance and that the centromeric region was bisected by all but one linkage group. Two markers covered a short genetic distance but were physically distant, while two covering a longer genetic distance were physically closer together. This indicates that considerable variation can, and does, exist between genetic and physical maps.This paper is a contribution of the U.S. Department of Agriculture, Agricultural Research Service, and Missouri Agricultural Experiment Station, Journal Series No. 11 882All programs and services of the U.S. Department of Agriculture are offered on a nondiscriminatory basis without regard to race, color, national origin, religion, sex, age, marital status, or handicapThis paper reports the results of research only. Mention of a proprietary product does not constitute an endorsement or a recommendation for its use by the U.S. Department of Agriculture or the University of Missouri     

Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs

Oryza rufipogon, the progenitor of the cultivated rice species Oryza sativa, is known by its wide intraspecific variation. In this study, we performed phylogenetic analyses of O. rufipogon strains and their relationships to O. sativa strains by using 26 newly identified p-SINE1 members from O. rufipogon strains, in addition to 23 members previously identified from O. sativa strains. A total of 103 strains of O. rufipogon and O. sativa were examined for the presence and absence of each of the p-SINE1 members at respective loci by PCR with a pair of primers that hybridize to the regions flanking each p-SINE1 member. A phylogenetic tree constructed on the basis of the insertion polymorphism of p-SINE1 members showed that O. rufipogon and O. sativa strains are classified into three groups. The first group consisted of O. rufipogon perennial strains mostly from China and O. sativa ssp. japonica strains, which included javanica strains forming a distinct subgroup. The second group consisted of almost all the O. rufipogon annual strains, a few O. rufipogon perennial strains and O. sativa ssp. indica strains. These groupings, in addition to other results, support the previous notion that annual O. rufipogon originated in the O. rufipogon perennial population, and that O. sativa originated polyphyletically in the O. rufipogon populations. The third group consisted of the other perennial strains and intermediate-type strains of O. rufipogon, in which the intermediate-type strains are most closely related to a hypothetical ancestor with no p-SINE1 members at the respective loci and to those belonging to the other rice species with the AA genome. This suggests that O. rufipogon perennial strains are likely to have originated from the O. rufipogon intermediate-ecotype population.     

分子标记在啤酒花种质资源研究中的应用

该论文利用分子生物学中常用的DNA分子标记对世界各地现存的野生和栽培的啤酒花种质资源遗传多样性研究的应用进展做一综述。通过查阅和研读20世纪90年代以来发表的各类文献进行归纳总结。发现DNA分子标记相比形态学标记和细胞学标记具有结果准确、稳定的特点,常用的分子标记技术有RAPD、RFLP、ISSR、SSR、AFLP、EST等;研究发现北美洲的啤酒花遗传多样性要高于欧洲的啤酒花,基因变异程度也相对较高;野生啤酒花的基因序列具有丰富的基因多样性,可在分子杂交遗传育种中作为一个种质去改善栽培品种的某些不良性状。因此,利用分子标记研究啤酒花的遗传多样性将对啤酒花的优良育种提供理论指导和技术支持,目前较为理想的技术是SSR和AFLP。     

药用野生稻和栽培稻挥发油的化学成分比较研究

本文采用水蒸气蒸馏法提取抗褐飞虱品种药用野生稻(Oryza officinalis)和感褐飞虱品种栽培稻(O.sativa)的挥发油,并运用气相色谱-质谱法(GC/MS)对二者的化学成分进行种类和含量的比较分析。结果表明,两种植物材料的挥发油在种类和含量上存在明显差异,如,糠醛(药用野生稻7.60%栽培稻0%;2,3-苯并二氢呋喃(药用野生稻10.80%,栽培稻3.32%);4-乙烯基-2-甲氧苯酚(药用野生稻22.99%,栽培稻7.32%)。推测含量较高的糠醛、2,3-苯并二氢呋喃和4-乙烯基-2-甲氧苯酚可能是药用野生稻对褐飞虱的活性成份。     

Molecular evolution of the MLO gene family in Oryza sativa and their functional divergence

The Leishmania genome project has identified new genes at a rapid rate. The 32.8-megabase haploid genome of Leishmania major (Friedlin strain) is published and the comparative analysis of genome sequences of two other species, Leishmania infantum and Leishmanai braziliensis has been done. The haploid genome of Leishmania major (Friedlin strain) has around 8272 protein-coding genes, of which only 36% can be ascribed a putative function. Out of these open reading frames around 910 Leishmania major genes have no orthologs in the other two Tritryp genomes. These “Leishmania -restricted” genes hold a potential as novel drug targets and potential vaccine candidates. Open reading frame, ORFF, is a single copy gene located on the chromosome 35 as a part of the multigene LD1 locus. Indirect immunofluorescence study and creation of ORFF-GFP fusion showed that ORFF is localized in the DNA containing compartments of Leishmania donovani, the nucleus and the kinetoplast. In order to characterize ORFF gene of L. donovani, we have created ORFF over-expressors and single allele deletion mutants by homologous replacement strategy. ORFF is likely to be an important gene for the parasite growth since results from over-expression studies and characterization of ORFF heterozygous knockout mutants reveal marked alterations in the cell cycle phenotype compared to the wild-type parasites. Flowcytometry based cell cycle analysis showed selective increase in the DNA synthetic phase of the ORFF over-expressors and a subversion of the same in heterozygous knockouts of ORFF suggesting its potential role in cell cycle progression.     

Agro-morphological and genetic diversity studies in Rice (Oryza sativa L.) germplasm using microsatellite markers

Molecular Biology Reports - Knowledge of the genetic diversity and population structure of germplasm collections is an important foundation for crop improvement. Rice production across a broad...     

水稻minE基因的克隆及分析

 植物叶绿体与原核生物分裂机制相似,其中MinE蛋白在细菌分裂过程中具有重要作用. 为了研究植物MinE蛋白在叶绿体分裂过程中的功能及其进化,利用RT PCR技术克隆了水稻叶绿体分裂相关基因OsMinE,并在GenBank登录（No. AY496951）.OsMinE基因cDNA全长1 035 bp,其ORF为711 bp,编码236个氨基酸.与原核生物MinE蛋白相比,水稻OsMinE具有明显延伸的N端与C端.其N端102个氨基酸残基为预测的叶绿体导肽序列,C端延伸保守,推测赋予植物MinE蛋白新的功能.植物minE基因结构分析显示,水稻、拟南芥、杨树都仅含有1个内含子,且插入位置及相位相同.这表明,该内含子可能在单子叶、双子叶植物分化前产生.水稻OsMinE基因在大肠杆菌细胞中的表达严重影响了细胞的分裂,初步证明了水稻MinE蛋白与原核细胞MinE蛋白功能类似.水稻OsMinE基因的克隆为进一步研究叶绿体的分裂机制奠定了基础.     

PCR-based molecular markers for the fragrance gene in rice (Oryza sativa. L.)

The genomic DNA clone RG28, linked to the major fragrance gene of rice (fgr), was assessed for polymorphism in order to produce a PCR-based marker for fragrance. A small mono-nucleotide repeat, that was polymorphic between a pair of fragrant and non-fragrant cultivars, was identified and developed into a co-dominant PCR-based marker. The polymorphism-information-content determinations for three microsatellite markers, that have been genetically mapped near RG28, are also presented. These PCR-based markers will be highly useful in distinguishing fragrance-producing alleles from non-fragrance-producing alleles at the fgr locus. Received: 19 October 1999 / Accepted: 16 December 1999     

利用栽培稻C0t-1 DNA和基因组DNA比较分析宽叶野生稻基因组

利用AA染色体组栽培稻的中高度重复序列C0t-1 DNA和基因组DNA作为探针,通过荧光原位杂交技术对宽叶野生稻（Oryza latifolia）（CCDD染色体组）进行了比较基因组分析。结果显示,在宽叶野生稻染色体上,C0t-1 DNA的杂交信号没有基因组DNA的杂交信号明显;杂交信号主要分布在着丝粒、近着丝粒及端粒区域;随着洗脱严谨度的不同,杂交信号呈现出较高的种特异性。本研究以不同洗脱严谨度下的荧光原位杂交结果为依据,对宽叶野生稻进行的核型分析,可进一步提高稻属染色体识别的准确性。     

粳稻穗部性状遗传分析

从粳稻(Oryza sativa ssp. japonica)RIL群体中选取每穗颖花数极端少的品系丙堡3201和丙堡3205及每穗颖花数极端多的品系丙堡3145和丙堡3214, 配制丙堡3201×丙堡3145和丙堡3214×丙堡3205两个组合的P₁、P₂、F₁、B₁、B₂和F₂ 6个世代, 调查每穗颖花数、每穗实粒数、穗长、一次枝梗数和二次枝梗数的表型分布, 并运用主基因+多基因混合遗传模型,对这5个性状进行了遗传分析。结果表明, 每穗颖花数性状在2个组合的各分离世代均未出现超亲分离, 而其它4个性状均有不同程度的超亲分离。一次枝梗数受1对主基因+多基因控制; 其余4个性状均受2对主基因+多基因控制。每穗颖花数、每穗实粒数、穗长和二次枝梗数4个性状以主基因遗传为主, 一次枝梗数性状以多基因遗传为主。     

粳稻穗部性状遗传分析

从粳稻（Oryzasativassp.japonica）RIL群体中选取每穗颖花数极端少的品系丙堡3201和丙堡3205及每穗颖花数极端多的品系丙堡3145和丙堡3214,配制丙堡3201×丙堡3145和丙堡3214×丙堡3205两个组合的P1、P2、F1、B1、B2和F26个世代,调查每穗颖花数、每穗实粒数、穗长、一次枝梗数和二次枝梗数的表型分布,并运用主基因＋多基因混合遗传模型,对这5个性状进行了遗传分析。结果表明,每穗颖花数性状在2个组合的各分离世代均未出现超亲分离,而其它4个性状均有不同程度的超亲分离。一次枝梗数受1对主基因＋多基因控制;其余4个性状均受2对主基因＋多基因控制。每穗颖花数、每穗实粒数、穗长和二次枝梗数4个性状以主基因遗传为主,一次枝梗数性状以多基因遗传为主。     

Surnames as markers of pathologies--two statistical techniques and their applications

The objective of this research is to propose and to validate two different statistical techniques to test the hypothesis of an association between surnames and pathologies, in a population participating in a screening procedure for a given pathology. We propose two statistical methods: a first technique is based on the rarefaction method, and second one is based on the principle of resampling, and it can be considered a special case of a randomisation test. Both the techniques are applied to a data set of babies screened for congenital hypothyroidism (CH), and they gave similar results. The large overlapping of the results seems to suggest a substantial validity of the proposed techniques.