RAPD analysis of natural populations of Acanthopanax brachypus

Random amplified Polymorphic DNA(RAPD) analysis is a new technology of molecular marking which has proved very powerful in detecting genetic diversity at the level of population.The genomic DNAs used in our experiment were extracted from fresh leaves taken from 59 individuals sampled from three natural populations in Yan an,Shanxi Province.Through more than 2,000 PCRs,deep-going RAPD analysis was carried out on DNA samples from 49 inviduals.The percentage of polymorphic RAPD loci found in these three populations were respectively 27.2%,18.6% and 5.4%;the average genetic distances within population,0.055,0.026 and 0.008;the average genetic distances between populations (I-II),(I-III) and (II-III),0.105,0.096 and 0.060.The genetic diversity of A.brachypus within and between populations was found,for the first time,to be rather poor,thus revealing innate factors as the cause contributing to its endangered status.In addition,our work also provides basic materials for elucidating the underlying cause of its endangerment and for its protection biology.     

Use of Random Amplified Polymorphic DNA Analysis for Economically Important Food Crops

The objective of this review is to summarize numerous studies on the use of the random amplified polymorphic DNA （RAPD） technique on rice, corn, wheat, sorghum, barley, rye, and oats to examine its feasibility and validity for assessment of genetic variation, population genetics, mapping, linkage and marker assisted selection, phylogenetic analysis, and the detection of somaclonal variation. Also we discuss the advantages and limitations of RAPD. Molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The simplicity of the RAPD technique made it ideal for genetic mapping, plant and animal breeding programs, and DNA fingerprinting, with particular utility in the field of population genetics.     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei （Primulaceae）： implications for its conservation

Omphalogramma souliei Franch. is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. souliei in NW Yunnan, China. The genetic diversity at the species level is low with P=42.5% （percentage of polymorphic bands） and Hsp=0.1762 （total genetic diversity）. However, a high level of genetic differentiation among populations was detected based on different measures （Nei＇s genetic diversity analysis： Gst=0.6038; AMOVA analysis： Fst=0.6797）. Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenogamy predominated and autogamy played an assistant role in O. souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

采用RAPD标记探讨瓣蕊唐松草(毛茛科唐松草属)的遗传多样性及其地理分布格局(英文)

Random amplified polymerphic DNA(RAPD)method was applied to assessg enetic variation and population structure of Thahctrum petalotdeum L(Ranunoulaceae),Two hundred and forty-six individuals from 11 populations of the species were investigated by RAPD profiles Twenty selected RAPD primers generated 125 bands．in which 120 were polymorphic Ther esults revealed a high level of genetic variation(ercentage of polymorphIc bands(PPB was 96％．Nei’s gene diversity(りwas 03502 and shannon’s information index(I) was 0．5199 at the species level) The differentiation among the populations was high(Gst=0．3511)in this species．Result of analyzing of molecularvariance(AMOVA)showedthat38．88％of genetic variance was found among the populations Positive correlation withr r=01945(P=00002)was found between genetic distance and geographic distance amongpo pulations Two populations distributed in the drainage basin of YanELz River affined genedcally and formed one clada and the rest nine populations formed the other clade in both unweighted pair-group method using arithmetic average(UPGMA)trees made by two different method different methods. It was yen/clear that these two populations were very special, andmust be closely related in history, despite the fact that they now share quite weak link to the restpopulations through gene communication.     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

Development and Characterization of 15 Polymorphic Micro satellite Markers for a Highly Adaptive and Wide-range Frog （Microhyla fissipes）

In order to analyze population genetic structure at multiple spatial scales, microsatellite loci were developed for the ornamented pygmy flog （Microhylafissipes）, and 15 polymorphic microsatellite loci were successfully screened from 105 individuals, of which 82 from four populations distributed in the Sichuan Basin and 23 from the Sangzhi population in western Hunan. Five loci were found to deviate significantly from Hardy-Weinberg equilibrium in one to three popu lations, probably due to small sample size or null alleles. The average number of alleles in all loci was 8.5, ranging from 4 to 13, and the observed and expected heterozygosity ranged from 0.26 to 0.90 and 0.63 to 0.90, respectively. The Sangzhi population and the remaining four populations can be clearly separated using Bayesian clustering methods, showing that the genetic structure of M. fissipes was probably affected by the topography, especially mountain barriers. These polymorphic microsatellite loci could be used for further study on the landscape genetics of this highly adaptive and widely distributed species.     

Does the Genetic Code Have A Eukaryotic Origin?

In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core "house-keeping" functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables-GC and purine contents-of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern-the symmetric pattern-where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.     

Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers

Genetic diversity of 1680 modern varieties in Chinese candidate core collections was analyzed at 78 SSR loci by fluorescence detection system. A total of 1336 alleles were detected, of which 1253 alleles could be annotated into 71 loci. For these 71 loci, the alleles ranged from 4 to 44 with an average of 17.6, and the PIC values changed from 0.19 to 0.89 with an average of 0.69. (1) In the three genomes of wheat, the average genetic richness was B>A>D, and the genetic diversity indexes were B>D>A. (2) Among the seven homoeologous groups, the average genetic richness was 2=7>3>4>6>5>1, and the genetic diversity indexes were 7>3>2>4>6>5>1. As a whole, group 7 possessed the highest genetic diversity, while groups 1 and 5 were the lowest. (3) In the 21 wheat chromosomes, 7A, 3B and 2D possessed much higher genetic diversity, while 2A, 1B, 4D, 5D and 1D were the lowest. (4) The highest average genetic diversity index existed in varieties bred in the 1950s, and then it declined continually. However, the change tendency of genetic diversity among decades was not greatly sharp. This was further illustrated by changes of the average genetic distance between varieties. In the 1950s it was the largest (0.731). Since the 1960s, it has decreased gradually (0.711, 0.706, 0.696, 0.695). The genetic base of modern varieties is becoming narrower and narrower. This should be given enough attention by breeders and policy makers.     

Analysis of genetic relationship in mutant silkworm strains of Bombyx mori using inter simple sequence repeat （ISSR） markers

Amplified inter simple sequence repeats (ISSR) markers were used to determine genetic relationships among mutant silkworm strains of Bombyx mori. Fifteen ISSR primers containing simple sequence repeat (SSR) motifs were used in this study. A total of 113 markers were produced among 20 mutant swains, of which 73.45% were found to be polymorphic. In selected mutant genetic stocks, the average number of observed allele was (1.7080±0.4567), effective alleles (1.5194±0.3950) and genetic diversity (Ht) (0.2901±0.0415). The dendrogram produced using the unweighted pair group method with arithmetic means (UPGMA) and cluster analysis made using Nei's genetic distance resulted in the formation of one major group containing 6 groups separated 20 mutant silkworm strains. Therefore, ISSR amplification is a valuable method for determining the genetic variability among mutant silkworm swains. This efficient molecular marker would be useful for characterizing a considerable number of silkworm swains maintained at the germplasm center.     

Genetic variation and relationship of alfalfa populations and their progenies based on RAPD markers

The aim of investigation was to evaluate genetic variation and relationship among alfalfa populations and their offspring, with minimal cost, by using DNA marker analysis. RAPD analysis was performed on bulked DNA samples of five alfalfa parental populations and their progenies: 20 F1 populations from reciprocal diallel crosses and five S1 populations from self-pollination. Twenty primers generated 217 bands, ranging in size from 300 to 6000 bp, with the average number of bands per primer of 10.85 and polymorphism information content of 0.246. Percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Higher diversity was observed in F1 progeny populations, while genetic variation in parental populations and S1 progenies remained similar. The genetic relatedness of alfalfa populations was analysed by UPGMA and Bayesian model-based clustering approach. In both types of analysis selfpollinated progenies were grouped. Furthermore, the hybrid offspring where Zuzana, and RSI 20 were maternal parents were placed in separate groups. The results indicate that use of RAPD markers on bulked DNA samples can be fast and cost-effective way for differentiation of alfalfa parental populations and their offspring, as well as for evaluation of their genetic relationships.     

Customisation of AFLP analysis for cassava varietal identification.

Amplified fragment length polymorphism (AFLP) markers were used in the characterization of eight cassava varieties. This nonradioactive AFLP system was customized in terms of the choice of restriction enzymes used and the selection of nucleotides added to the 3' end of primers. EcoRI/MseI and HindIII/MseI fragments generally gave monomorphic profiles while ApaI/TaqI fragments produced polymorphic profiles suggesting a genome with high G + C content. It was possible to identify the eight cassava varieties used in this study using CTG as selective bases at the TaqI primer. For cassava, the AFLP system provided a higher number of loci detected per run when compared to RAPD. The reliability accompanying AFLP analysis would thus make it suitable for the characterization of cassava varieties.     

Comparison of RAPD and ISSR markers for genetic diversity analysis among different endangered Mangifera indica genotypes of Indian Gir forest region

The genetic variability and relationships among 20 Mangifera indica genotypes representing 15 endangered and 5 cultivars, obtained from Indian Gir forest region, were analyzed using 10 random amplified polymorphic DNA (RAPD) and 21 inter simple sequence repeat (ISSR) markers. RAPD markers were more efficient than the ISSR assay with regards to polymorphism detection. Also, the average numbers of polymorphic loci per primer, average polymorphic information content (PIC) and primer index (PI) values were more for RAPD than for ISSR. But, total number of genotype specific marker loci, Nei’s genetic diversity (h), Shannon’s information index (I), total heterozygosity (Ht), average heterozygosity (Hs) and mean coefficient of gene differentiation (Gst) were more for ISSR as compared to RAPD markers. The regression test between the two Nei’s genetic diversity indexes showed low regression between RAPD and ISSR based similarities but maximum for RAPD and RAPD + ISSR based similarities. The pattern of clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared. Thus, both the markers were equally important for genetic diversity analysis in M. indica.     

Genetic variation,population structure and identification of yellow catfish, <Emphasis Type="Italic">Mystus nemurus</Emphasis> (C&;V) in Thailand using RAPD,ISSR and SCAR marker

Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four subpopulations of Mystus nemurus in Thailand. The 7 RAPD and 7 ISSR primers were selected. Of 83 total RAPD fragments, 80 (96.39%) were polymorphic loci, and of 81 total ISSR fragments, 75 (92.59%) were polymorphic loci. Genetic variation and genetic differentiation obtained from RAPD fragments or ISSR fragments showed similar results. Percentage of polymorphic loci (%P), observed number of alleles, effective number of alleles, Nei’s gene diversity (H) and Shannon’s information index revealed moderate to high level of genetic variations within each M. nemurus subpopulation and overall population. High levels of genetic differentiations were received from pairwise unbiased genetic distance (D) and coefficient of differentiation. Mantel test between D or gene flow and geographical distance showed a low to moderate correlation. Analysis of molecular variance indicated that variations among subpopulations were higher than those within subpopulations. The UPGMA dendrograms, based on RAPD and ISSR, showing the genetic relationship among subpopulations are grouped into three clusters; Songkhla (SK) subpopulation was separated from the other subpopulations. The candidate species-specific and subpopulation-specific RAPD fragments were sequenced and used to design sequence-characterized amplified region primers which distinguished M. nemurus from other species and divided SK subpopulation from the other subpopulations. The markers used in this study should be useful for breeding programs and future aquacultural development of this species in Thailand.     

Comparative analysis of genetic diversity of sesame (Sesamum indicum L.) from Vietnam and Cambodia using agro-morphological and molecular markers

The purpose of this study was to comparatively analyze the genetic diversity of sesame (Sesamum indicum L.) using agro-morphological and molecular markers. Twelve sesame populations collected from three regions in Cambodia and Vietnam were used in this study. A high genetic variation was revealed both by agro-morphological and RAPD markers within and among the 12 sesame populations. The range of agro-morphological trait based average taxonomic distance among populations (0.02 to 0.47) was wider than that of RAPD based genetic distance (0.06 to 0.27). The mean distance revealed by agro-morphological markers (0.23) and RAPD markers (0.22) was similar. RAPD based analysis revealed a relatively higher genetic diversity in populations from South Vietnam as compared to the other two regions. Interestingly, populations from this region also had higher values for yield related traits such as number of capsules per plant, number of seeds per capsule, and seed yield per plant suggesting positive correlation between the extent of genetic variation within population and yield related traits in sesame. A highly significant positive correlation (r = 0.88, P < 0.001) was found between agro-morphological and RAPD markers in estimating the genetic distance between populations. Both methods suggested the existence of a substantial amount of genetic diversity both in the Vietnamese and Cambodian populations. Although both agro-morphological and RAPD markers were found to be useful in genetic diversity analysis in sesame, their combined use would give superior results.     

Comparative studies of genetic diversity in kenaf (Hibiscus cannabinus L.) varieties based on analysis of agronomic and RAPD data

Kenaf (Hibiscus cannabinus L.) is a fiber crop classified in the genus Hibiscus (Malvaceae), and has a great potential for its multipurpose utilization, in addition to its traditional usage. Varietal identification of kenaf is always problematic and knowledge on genetic diversity of kenaf varieties is also limited, which significantly hindered our effective utilization and conservation of the valuable kenaf germplasm. In order to find a proper method for identifying kenaf varieties and studying their variation, morpho-agronomic characters and random amplified polymorphic DNA (RAPD) markers were analyzed among 14 kenaf varieties commonly used in Japan. Data from morphological analysis showed that the included kenaf varieties could be divided into three major groups. The characters, such as middle stem diameter, whole stalk weight, and days to 50% flowering, are highly responsible for the variation of the kenaf varieties, but it is difficult to identify individual varieties merely by the morpho-agronomic characters. On the other hand, clearly separation of the kenaf varieties was achieved based on the RAPD variation patterns. Genetic relationship of the kenaf varieties can also be traced through the analysis of RAPD and morph-agronomic variation. It is concluded from the present study that RAPD analysis is an effective tool in identifying of kenaf varieties and determining their genetic relationships, particularly when combined with the analysis of morpho-agronomic characters.     

RAPD引物数量对施式巴鲵遗传多样性评估结果的影响

应用RAPD技术对神农架施式巴鲵居群内24个个体进行了遗传多样性分析,探讨引物数量对遗传多样性分析结果 的影响,结果表明:遗传多样性分析准确度与引物数量有关,引物数增加到30左右时,PPB(Percentageofpolymorphicbands)、 Shannon信息指数(Shannon′sinformationindex)、Nei′s遗传多样性指数(Nei′sgenediversity)变化趋于稳定。标准误分析表明, 引物数增加到25左右时,再增加引物,标准误变化很小。若要客观反映出个体之间的遗传变异关系,引物数应在25以上,多 态位点数应在250以上。     

Genetic structure of the Iberian pig breed using microsatellites

An analysis of 25 microsatellite loci in 210 animals has been used to define the genetic structure of the Iberian pig, traditionally classified into several varieties. In addition, a sample of 20 Duroc pigs was used as an outgroup for topology trees. Inter-variety genetic variation was estimated by unbiased average heterozygosity and the number of alleles observed. Significant deviations from the Hardy-Weinberg equilibrium (HWE) were shown for 19 loci across the whole population. By contrast, equilibrium deviation within varieties was much lower. Genetic variation measures, genetic distance values and a neighbour-joining tree were used to estimate subdivision. In addition, an individual tree was constructed to contrast the assignation of animals into varieties. Despite the low bootstrap values obtained in the varieties neighbour-joining tree, the degree of genetic variation found was sufficient to support the division of the Iberian pig into varieties, although in some cases the traditional classification cannot be accepted. These results have shown the value of this marker panel in the study of intra-breed genetic structures.     

云南金钱槭形态变异与遗传变异的相关性研究

对我国特有珍稀濒危保护植物云南金钱槭的形态变异水平、遗传变异模式以及两者之间的相关性进行了研究。形态学性状分析结果表明 :各居群形态性状变异系数的平均值从大到小排列为 :文山居群 (WSh)、屏边居群 (PB)、黑龙潭居群 (HL T)、蒙自居群 (MZ) ;文山居群与屏边、黑龙潭、蒙自居群间已产生显著或极显著水平的形态差异 ,而后三者间的差异未达显著水平。RAPD分析检测到 10 3个位点 ,其中多态位点 84个 ,云南金钱槭物种水平的多态位点比率为 81.5 5 % ,与其它珍稀濒危植物相比该种的遗传多样性水平不低。 AMOVA和 N ei基因多样性指数分析显示 ,尽管大部分遗传变异仍存在于居群内 (分别为5 7.86 %、5 7.33% ) ,但居群间的遗传变异已达较高水平 (分别为 4 2 .14 %、4 2 .6 7% )。相关分析结果显示 ,云南金钱槭的形态变异与海拔、土壤有机质等生态因子有着显著或极显著水平的相关性 ,但与遗传变异的相关性未达显著水平 ,说明云南金钱槭的形态变异虽然具有一定的遗传基础 ,但可塑性及环境压力对形态变异的产生作用更大一些。基于形态性状和 RAPD数据的聚类分析则进一步说明 ,云南金钱槭的形态变异受到环境因子的强烈影响而与遗传背景的关系不显著     

内蒙古典型草原羊草种群遗传分化的RAPD分析

运用 RAPD技术对内蒙古典型草原不同生境 8个羊草种群进行分析。采用 2 4个随机引物 (10 nt)在 8个种群中共检测到2 2 4个扩增片断 ,其中多态性片断 173个 ,总的多态位点百分率达 77.2 % ,特异性片断 2 2个 ,占 9.82 % ,平均每个引物扩增的DNA带数为 9.3 3条。利用 Nei指数和 Shannon指数估算了 8个种群的遗传多样性 ,并计算种群相似系数和遗传距离 ,运用UPGMA法进行聚类分析。结果表明 :羊草大部分的遗传变异存在于种群内 ,只有少部分的遗传变异存在于种群间 ,Nei指数和Shannon指数计算结果分别为 85.4%和 66.8% ;羊草不同种群的遗传多样性存在差异 ;8个羊草种群平均遗传距离为 0 .2 3 16,变异范围为 0 .1587～ 0 .2 70 0 ,说明 8个羊草种群间的遗传变异不大 ,即 :在较小地理范围内羊草的遗传分化程度较小 ;8个种群可聚为 3个类群 ,聚类结果显示生境相似的种群能够聚在一起 ,而地理距离最近的种群不一定归为一类 ,说明小范围内羊草种群间的遗传分化与地理距离不存在相关性 ,而与其生境间的相似度相关。影响遗传相似性的不是单一因子而是各种因子的综合作用 ,较小地理范围内羊草种群间的遗传分化主要是由环境的异质性所引起的