Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (Indica) and Nipponbare (Japonica)

DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers.To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species,we studied 49 Indica,43 Japonica,and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs.Results indicated that of the 45 InDel primer pairs,41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%.The scatter plotting data of the principal component analysis (PCA) indicated that:(i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties,in addition to revealing their genetic differentiation;(ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties;and (iii)the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types.It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying lndica and Japonica rice varieties,and for studying genetic relationships of wild rice species,particularly in terms of the Indica-Japonica differentiation.     

杂草稻叶绿体籼粳分化的多重PCR分析

通过分析籼稻93-11和粳稻培矮64S的叶绿体全基因组,优化和构建了籼粳分化的叶绿体分子标记ORF100和ORF29-TrnC^GCA的多重PCR。应用这个多重PCR对200余份世界各地杂草稻和其它水稻材料进行分析。结果表明:杂草稻中有明显的叶绿体籼粳分化,表现出明显的地域性,且与传统的中国栽培稻的南籼北粳能较好的对应。推测粳型杂草稻可能是栽培稻突变或粳型水稻(作母本)与其它类型水稻材料杂交而形成的。     

Breeding and application of Jiafuzhan, a new elite early indica rice cultivar in China

After 20 years of dedicated research, Jiafuzhan has been successfully developed under the new technologies in breeding high-quality early indica rice cultivars. Its rice quality has almost reached the A-level Editable Rice of Agriculture Department of China, and its average production reaches 400–500 kg/(666.7 m²). This new cultivar also has other characteristics such as enhanced resistance of blast and fallen, steady productivity, and strong adaptability. Jiafuzhan has been put into production of over 11.4 × 10⁴ hm² in Fujian Province and has been introduced and extended in other Provinces like Jiangxi, Guangdong, and Guangxi, China. The successes of breeding Jiafuzhan is a solution to the existing perennial problems in the rice industry, such as poor grain quality of big-grain rice and early indica rice, low productivity, and poor blast resistance of elite rice. __________ Translated from Journal of Xiamen University (Natural Science), 2006, 45(1): 114–119 [译自: 厦门大学学报 (自然科学版)]     

Sampling strategy for wild soybean ( Glycine soja ) populations based on their genetic diversity and fine-scale spatial genetic structure

A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated. Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples), in addition to investigating the fine-scale spatial genetic structure within the population. The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88, expected heterozygosity (He) 0.431, Shannon diversity index (I) 0.699, and percentage of polymorphic loci (P) 100%. Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation. The regression model of the four diversity indexes with the change of sample sizes was computed. As a result, 27–52 individuals can reach 95% of total genetic variability of the population. Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m. The study provided a scientific basis for the sampling strategy of wild soybean populations. __________ Translated from Journal of Fudan University (Natural Science), 2006, 45(3): 322–327 [译自: 复旦学报 (自然科学版)]     

Postglacial population expansion of Dacrydium pectinatum (Podocarpaceae) in Hainan, southem China, based on cpDNA trnL-F nocoding sequence data

This study determined the sequences of chloroplast DNA (cpDNA) trnL-F non-coding regions of individuals of a tropical coniferous species, Dacrydium pectinatum, collected from 12 natural populations located in Hainan Province, southern China. Sequence length varied from 868 bp to 876 bp, indicating length polymorphism. Base composition in the sequences was high in A+T content between 64.17% and 64.95%, and no recombination event occurred (Rm = 0). Thirty haplotypes were identified based on statistical parsimony algorithm by running the TCS program. Populations of D. pectinatum in Hainan were lacking genetic differentiation. Such a deduction was supported by the observed F _ST values (0.00), AMOVA (24.17% of molecular variance attributed to difference among populations, P>0.05), high values of Nm (ranging from 1.92 to 2.50) and the branching structure in neighbor-joining (NJ) tree constructed from haplotypes. A ‘star-like’ pattern was exhibited in the TCS network of trnL-F haplotypes, and majority of the haplotypes coalesced near the tips in NJ tree. Gene genealogies of cpDNA haplotypes proposed a recent population expansion of D. pectinatum in Hainan, which was further supported by the results from Tajima’s D test and mismatch distribution analysis. Our data, in conjunction with geological and palynological evidences, showed that in the Holocene, due to global warming, refugee populations of D. pectinatum in Hainan might experience a range expansion. __________ Translated from Acta Scientiarum Naturalium Universitatis Sunyatseni, 2005, 44(5): 70–74 [译自: 中山大学学报 (自然科学版), 2005, 44(5): 70–74]     

Biological characteristics of wild Cycas fairylakea population in Guangdong Province, China

There are five wild populations of Cycas fairylakea in Guangdong Province, China, three of which are newly found. A study of the biological characteristics of C. fairylakea populations showed that this species had a narrow colonization area within 300 hm², and an island pattern of distribution. Because of the overexploitation, urbanization, environment pollution, plant diseases, and insect pests, the wild populations and individuals of C. fairylakea decreased markedly in the past decades. All five populations have an opposite pyramid age structure, few coning plants, few seed production, and low level of seed germination rate or sterility. In conclusion, C. fairylakea in Guangdong Province was threatened seriously and an urgent need to take effective efforts to protect the plants and habitats in its location sites was required. __________ Translated from Acta Scientiarum Naturalium Universitatis Sunyatseni, 2005, 44(6): 97–100 [译自: 中山大学学报 (自然科学版), 2006, 44(6): 97–100]     

Application of petG-trnP sequence to systematic study of Chinese Cupressus species

Chinese Cupressus L. includes five species. The molecular phylogenetic relationship of the Cupressus species and Chamaecyparis L. were determined by comparing 417–479 bp of chloroplast petG-trnP intergenic spacer sequence. In PAUP^* analysis, Platycladus orientalis was used as the functional out group. By using the maximum likelihood method 1 077 trees were examined and the result showed that one tree had a best score of -Ln=2 232.47. The phylogenetic tree clearly showed that Chamaecyparis nootkatensis was diverged from other Chamaecyparis species. Based on the results, together with evidences from other aspects, we consider that Cupressus funebris and Chamaecyparis nootkatensis should be placed in the genus Cupressus. The use of cpDNA intergenic spacer petG-trnP in Cupressus was also discussed. __________ Translated from Journal of Sichuan University (Natural Science Edition), 2005, 42(5): 1033–1037 [译自: 四川大学学报 (自然科学版) 2005, 42(5): 1033–1037]     

A comparison of in vitro anticancerous activity and mechanism of ethanolic extracts from different Ganoderma genus

Five ethanolic extracts from the mycelia of Ganoderma lucidum, G. tsugae, G. oerstedii, G. subamboinense, and G. resinaceum were respectively studied on their anticancerous activities against leukemic HL-60 cell line in vitro. Results showed that all five extracts potently inhibited HL-60 proliferation. The extract from G. lucidum mycelia exerted the highest activity. Annexin V/PI bivariate flow cytometric analysis further revealed that the five extracts significantly induced early apoptosis in HL-60 cells. The results illustrate that not only G. lucidum but also other Ganoderma species can inhibit cancer cells, and their mechanisms are related to induction of apoptosis. __________ Translated from Journal of Shanghai Normal University (Natural Sciences), 2005, 34(2): 77–81 [译自: 上海师范大学学报 (自然科学版), 2005, 34(2): 77–81]     

Cloning and expressing DBT (dibenzothiophene) monooxygenase gene (dszC) from Rhodococcus sp. DS-3 in Escherichia coli

Dibenzothiophene (DBT) monooxygenase (DszC) catalysis, the first and also the key step in the microbial DBT desulfurization, is the conversion of DBT to DBT sulfone (DBTO₂). In this study, dszC of a DBT-desulfurizing bacterium Rhodococcus sp. DS-3 was cloned by PCR. The sequence cloned was 99% homologous to Rhodococcus erythropolis IGTS8 that was reported in the Genebank. The gene dszC could be overexpressed effectively after being inserted into plasmid pET28a and transformed into E. coli BL21 strain. The expression amount of DszC was about 20% of total supernatant at low temperature. The soluble DszC in the supernatant was purified by Ni²⁺ chelating His-Tag resin column and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to electronics purity. Only one band was detected by Western-blotting, which is for the antibody released in mouse against purified DszC in the expression product of BL21 (DE3, paC5) and Rhodococcus sp. DS-3. The activity of purified DszC was 0.36 U. DszC can utilize the organic compound such as DBT and methyl-DBT, but not DBT derivates such as DBF, which has no sulfur or inorganic sulfur. __________ Translated from Acta Scientiarum Naturalium Universitatis Nankaiensis, 2005, 38(6): 1–6 [译自: 南开大学学报 (自然科学版), 2005, 38(6): 1–6]     

Cloning and characterization of PhPI9 involved in floral development from Phalaenopsis Orchid

In the attempt to discover new genes involved in the floral development in monocotyledonousin species, we have cloned and characterized the homologous PISTALLATA-like (PI-like) gene from Phalaenopsis hybrid cultivar named PhPI9 (Ph alaenopsis PI STILLATA # 9). The cDNA of PhPI9 has a fragment of 834 bp and has 60% identity with the PISTILATA from Arabidopsis. The deduced amino acid sequence of PhPI9 had the typical PI-motif. It also formed a subclade with other monocot PI-type genes in phylogenetic analysis. Southern analysis showed that PhPI9 was present in the Phalaenopsis orchid genome as a single copy. Furthermore, it was expressed only in the lip of the Phalaenopsis flower and no expression was detected in vegetative organs. Thus, as a B-function MADS-box gene, PhPI9 specifies floral organ identity in orchids. __________ Translated from Journal of Fudan University (Natural Science), 2006, 45(3): 277–282 [译自: 复旦学报(自然科学版)]     

Fine mapping of an Arabidopsis thaliana male sterile mutant EC2-157

An Arabidopsis thaliana male sterile mutant EC2-157 has been isolated using an EMS mutagenesis strategy. Genetic analysis indicated that it was controlled by a single recessive gene called ms157. No pollen grains have been observed in mutant anthers. ms157 Has been mapped to a region of 74kb located in BAC clone T6K22 on chromosome IV using a map-based cloning strategy. As no male sterile genes have been reported in this region, ms157 could be a novel gene related to fertility. The further molecular cloning and functional analysis on this gene should facilitate our understanding of A. thaliana another development. __________ Translated from Journal of Shanghai Normal University (Natural Sciences), 2005, 34(1): 58–63 [译自: 上海师范大学学报 (自然科学版), 2005, 34(1): 58–63]     

Karyotyping of Brassica oleracea L. based on rDNA and Cot -1 DNA fluorescence in situ hybridization

To explore an effective and reliable karyotyping method in Brassica crop plants, Cot-1 DNA was isolated from Brassica oleracea genome, labeled as probe with Biotin-Nick Translation Mix kit, in situ hybridized to mitotic spreads, and where specific fluorescent bands showed on each chromosome pair. 25S and 5S rDNA were labeled as probes with DIG-Nick Translation Mix kit and Biotin-Nick Translation Mix kit, respectively, in situ hybridized to mitotic preparations, where 25S rDNA could be detected on two chromosome pairs and 5S rDNA on only one. Cot-1 DNA contains rDNA and chromosome sites identity between Cot-1 DNA and 25S rDNA was determined by dual-colour fluorescence in situ hybridization. All these showed that the karyotyping technique based on a combination of rDNA and Cot-1 DNA chromosome landmarks is superior to all but one. A more exact karyotype of B. oleracea has been analyzed based on a combination of rDNA sites, Cot-1 DNA fluorescent bands, chromosome lengths and arm ratios. __________ Translated from Journal of Wuhan University (Nat. Sci. Ed.), 2006, 52(2): 230–234 [译自: 武汉大学学报 (理学版)]     

Isolation and characterization of microsatellite markers from Hibiscus rosa-sinensis (Malvaceae) and cross-species amplifications

We report on the development of 10 microsatellite markers in Hibiscus rosa-sinensis (Hrs). Three markers were obtained from sequences available in GenBank and seven were isolated using a two-step ‘primer extension’ procedure, based on the microsatellite-AFLP (M-AFLP) technique. Polymorphism was explored in 21 Hrs genotypes representing the genetic variation within commercial varieties. Inter-specific amplification was assessed on 12 Hibiscus wild species. A total of 45 and 56 alleles (ranging from 1 to 10 for each locus) was amplified respectively from the 21 Hrs varieties and among the full Hibiscus spp. genotype set. Primers and conditions for polymerase chain reaction (PCR) amplification of the detected loci are reported.     

AFLP analysis of genetic diversity and relationship among some Chinese domestic ducks and wild ducks

The amplified fragment length polymorphic (AFLP) technique was used to analyze the genome DNA polymorphism among 8 breeds of domestic ducks and 2 species of wild ducks. Nine of the 17 selected primers pairs gave reproducible polymorphic DNA amplification bands. The amplified bands ranged from 44 to 83 per primer pair. Of the 513 AFLP markers obtained, 498 were polymorphic. The proportion of polymorphic loci was 97.1%. The genetic distance (D) and similarity coefficients (GS) were calculated based on the polymorphic data. Between domestic ducks D ranged from 0.331 to 0.589, while between domestic ducks and the wild ducks, it ranged from 0.298 to 0.520 (vs. Anas Platyrhynchos) and from 0.316 to 0.522 (vs. A. Poecilorhyncha), respectively. The variance analysis showed no significant difference between the two groups of data, which indicated that both mallard and spot-billed ducks made contributions to domestic duck evolution. A dendrogram was constructed according to the D value. __________ Translated from Journal of Xiamen University (Natural Science), 2005, 44(5): 729–733 [译自: 厦门大学学报 (自然科学版), 2005, 44(5): 729–733]     

Conversion of AFLP markers to sequence-specific markers for closely related lines in rice by use of the rice genome sequence

DNA polymorphism between two major japonica rice cultivars, Nipponbare and Koshihikari, was identified by AFLP. Eighty-four polymorphic AFLP markers were obtained by analysis with 360 combinations of primer pairs. Nucleotide sequences of 73 markers, 29 from Nipponbare and 44 from Koshihikari, were determined, and 46 AFLP markers could be assigned to rice chromosomes based on sequence homology to the rice genome sequence. Specific primers were designed for amplification of the regions covering the AFLP markers and the flanking sequences. Out of the 46 primer pairs, 44 amplified single DNA fragments, six of which showed different sizes between Nipponbare and Koshihikari, yielding codominant SCAR markers. Eight primer pairs amplified only Nipponbare sequences, providing dominant SCAR markers. DNA fragments amplified by 13 primer pairs showed polymorphism by CAPS, and polymorphism of those amplified by 13 other primer pairs were detected by PCR-RF-SSCP (PRS). Nucleotide sequences of the other four DNA fragments were determined in Koshihikari, but no difference was found between Koshihikari and Nipponbare. In total, 40 sequence-specific markers for the combination of Nipponbare and Koshihikari were produced. All the SNPs identified by AFLP were detectable by CAPS and PRS. The same method was applicable to a combination of Kokoromachi and Tohoku 168, and 23 polymorphic markers were identified using these two rice cultivars. The procedure of conversion of AFLP-markers to the sequence-specific markers used in this study enables efficient sequence-specific marker production for closely related cultivars.     

Analysis of sparteines in the seeds of Ammopiptanthus mongolica

Seven alkaloids were isolated from the seeds of Ammopiptanthus mongolica by thin layer chromatography and silica gel column chromatography, and the chemical structures of five alkaloids, 17-oxosparteine, β-isosparteine, 3α-hydroxysparteine, sparteine, and 3β-hydroxysparteine were identified by ¹H nuclear magnetic resonance (NMR) and electron ionization mass spectrum (EIMS). __________ Translated from Journal of Lanzhou University (Natural Sciences), 2007, 43(2): 43–46 [译自: 兰州大学学报(自然科学版)]     

Characterization of melanin produced by a wild-type strain of Bacillus cereus

Bacillus cereus 58 (Bc58) is a UV-resistant wild type strain that has an ability to produce a sorrel pigment induced by L-tyrosine. The Fourier-transform infrared (FT-IR) spectra and chemical tests of its pigment are similar to that of the standard melanin (Sigma). A bioassay shows that the LC₅₀ of a Bacillus thuringiensis (Bt) formulation added with the melanin of Bc58 and exposed to UV for 5 h is 16.1 μg/ml, which is similar to that of the Bt formulation without UV treatment, however, it is almost double that of the Bt formulation exposed to UV without the melanin of Bc58. The result of SDS-PAGE indicates that the melanin of Bc58 can protect the insecticidal crystal proteins from degradation. This suggests that it is an excellent UV protective agent for the insecticidal crystal proteins of the Bt formulation. Translated from Microbiology, 2006, 33(1): 42–45 [译自: 微生物学通报]     

Chemical compounds and pharmacological effects of Rabdosia excisa

Many kinds of diterpenoids have been isolated from Rabdosia spp. Some of them have anti-microbial effects, counteract inflammation, and inhibit tumor progression activities. We conducted the present study in order to look for bioactive compounds in the medicinal plant Rabdosia excisa. In this study, five compounds were isolated from R. excisa; they were oridonin, isokamebakaurin, oleanolic acid, ursolic acid, and β-sitosterol. In order to identify the function of the extracts, the activity of antibiotics, antioxidation, and immunity test were carried out against these functions. Prospective results were observed in all of the tested items. Translated from Journal of Northeast Normal University (Natural Sciences), 2005, 37(4): 94–98 [译自: 东北师大学报 (自然科学版)]     

Karyotype analysis and physical mapping of 45S rDNA in eight species of Sophora, Robinia , and Amorpha

The karyotype analysis and physical locations of 45S rDNA were carried out by means of fluorescence in situ hybridization in three species, and two forms of Sophora, two species of Robina, and one species of Amorpha. S. japonica L., S. japonica L. f. oligophylla Franch., S. japonica L. f. pendula Loud., and S. xanthantha C. Y. Ma. are all tetraploids with 2n = 28. There were four 45S rDNA sites in pericentromeric regions of two pairs of chromosomes in each of them. S. rubriflora Tsoong. is a triploid with 2n = 21, and three sites were located in each satellite of group 5 chromosomes. In R. pseudoacacia L. (2n = 2x = 22), we examined four intensive signals in telomeric regions of two pairs of satellite chromosomes. In R. hispida L. (2n = 2x = 30), there were four other signals in centromeric regions besides those like in R. pseudoacacia. Amorpha fruticosa L. has most chromosomes (2n = 40) among the eight materials, however, there were only six 45S rDNA loci and they laid in centromeric regions, and satellites of three pairs of chromosomes. 45S rDNA is a valuable chromosomal landmark in karyotype analysis. The distribution and genomic organization of rDNA in the three genera were also discussed. __________ Translated from Acta Botanica Yunnanica, 2005, 27(3): 261–268 [译自: 云南植物研究, 2005, 27(3): 261–268]