Identification of 27 Porphyra lines (Rhodophyta) by DNA fingerprinting and molecular markers

Twenty-seven Porphyra lines, including lines widely used in China, wild lines and lines introduced to China from abroad in recent years, were screened by random amplified polymorphic DNA (RAPD) technique with 120 operon primers. From the generated RAPD products, 11 bands that showed stable and repeatable RAPD patterns amplified by OPC-04, OPJ-18 and OPX-06, respectively were scored and used to develop the DNA fingerprints of the 27 Porphyra lines. Moreover, the DNA fingerprinting patterns were converted into computer language expressed with two digitals, 1 and 0, which represented the presence (numbered as 1) or absence (numbered as 0) of the corresponding band, respectively. Based on the above results, computerized DNA fingerprints were constructed in which each of the 27 Porphyra lines has its unique fingerprinting pattern and can be easily distinguished from others. Software named PGI (Porphyra germplasm identification) was designed for identification of the 27 Porphyra lines. In addition, seven specific RAPD markers from seven Porphyra lines were identified and two of them were successfully converted into SCAR (sequence characterized amplification region) markers. The developed DNA fingerprinting and specific molecular markers provide useful ways for the identification, classification and resource protection of the Porphyra lines.

羊栖菜养殖品系DNA指纹分析及遗传变异的研究

羊栖菜是重要的大型经济海藻之一，在食品、医药、化工领域都有广泛应用。本研究对羊栖菜养殖生产中常见的品系“鹿丰1号”及另外2种品系进行了DNA指纹分析及遗传变异的研究，构建了遗传指纹图谱，分析了不同种群的遗传关系，为羊栖菜的种质鉴定及遗传选育提供了理论依据。 运用RAPD分子标记技术，对5个羊栖菜的种群中共125个个体进行了分析，从300个引物中筛选出12条随机扩增引物共扩增135个位点，多态位点比率为84.4%。从中选择了4个多态性位点，构建了5种羊栖菜DNA指纹图谱，并获得了“鹿丰1号”SCAR标记。另外，进行了5种羊栖菜种群的遗传背景的分析，结果表明“鹿丰1号”与品系2可以明显的与野生种群分开。根据Dice常数计算所得的5个种群的遗传距离在0.1116-0.2563之间。 运用ISSR分子标记技术，对5个种群的125个羊栖菜个体进行分析，通过90条引物的筛选，获得10条ISSR引物，扩增出92个位点，多态位点比率为67.4%。5个种群的遗传距离在0.0863-0.1454之间。 本研究以铜藻作为外群，通过2种遗传标记分析，证明铜藻与5种羊栖菜种群的遗传距离均远远大于其种群之间的遗传距离；另外，“鹿丰1号”不同年份的种群之间的遗传距离均为其中的最小值，相关结果对羊栖菜遗传选育和种质鉴定等有参考价值。

紫薇种质资源的研究

本文回顾了紫薇在国内外的栽培历史。在中国，紫薇的栽培虽历史悠久，但种质资源缺少系统的研究。本研究通过宏观与微观的技术和方法，探索紫薇种间及品种间的演化关系，并为今后开展种质鉴定、 品种分类以及有计划、有目的的进行新品种的培育提供依据，以期达到紫薇种质资源多样性保护的目的。主要的结果及结论： 1．认为紫薇栽培的历史是紫薇不同种质进行组合和渗透的历史，也在一定程度上反映了品种演化的历史。并提出除了抗病、矮型紫薇的育种外，还要重视重瓣紫薇的育种。 2．通过对紫薇的形态学性状进行聚类分析，寻找到了评价紫薇种质资源的标准，进而提出栽培观赏植物种质资源的评价标准， 即将其性状分为种源性状和观赏性状，这种对观赏植物性状的分解反映了栽培植物不同于野生植物的特点。同时，对其形态学性状进行主分量分析表明，花色与其它营养器官性状相关性不大，很难从其营养器官性状推测花的颜色。 3．通过对紫薇的分子生物学研究，建立了紫薇的DNA提取流程及RAPD扩增体系，利用RAPD标记可以进行紫薇种质的鉴定及探求不同种质间的关系。 4．综合形态学及分子生物学的结论，建立了紫薇种质资源的划分体系，在此基础上，建成了种质资源圃及紫薇种质资源数据库。

Molecular Phylogeny of Geographical Isolates of Bursaphelenchus xylophilus: Implications on the Origin and Spread of this Species in China and Worldwide

The genetic diversity and phylogeny of 26 isolates of Bursaphelenchus xlophilus from China, Japan, Portugal and North America were investigated based on the D2/3 domain of 28S rDNA, nuclear ribosomal Internal Transcribed Spacer (ITS) sequences, and random amplified polymorphic DNA (RAPD) analysis. The genetic diversity analysis showed that the D2/3 domain of 28S rDNA of isolates of B. xlophilus from China, Portugal, Japan and the US were identical and differed at one to three nucleotides compared to those from Canada. ITS sequences of isolates from China and Portugal were the same; they differed at one or two nucleotides compared to those of Japanese isolates and at four and 23 nucleotides compared to those front the US and Canada, respectively. The phylogenetic analysis indicated that Chinese isolates share a common ancestor with one of the two Japanese clades and that the Canadian isolates form a sister group of the clade comprised of isolates from China, Portugal,Japan, and the US. The relationship between Japanese isolates and those from China was closer than with the American isolates. The Canadian isolates were the basal group of B. xylophilus. This suggests that B. xlophilus originated in North America and that the B. xylphilus that occurs in China could have been first introduced from Japan. Further analysis based on RAPD analysis revealed that the relationship among isolates from Guangdong, Zhejiang, Shandong, Anhui provinces and Nanjing was the closest, which suggests that pine wilt disease in these Chinese locales was probably dispersed from Nanjing, where this disease first occurred in China.

Genetic diversity and taxonomic implication of Cordyceps sinensis as revealed by RAPD markers

Random amplified polymorphic DNA (RAPD) markers are used to investigate genetic variation and evolutionary relationships of 29 samples of Cordyceps sinensis from different geographical populations on the Qinghai-Tibet plateau. Out of 137 RAPD bands scored, 100 are polymorphic. A correlation is revealed between geographical distance and genetic distance. The molecular phylogenetic tree suggests that the 29 samples are divided into three notable clusters, corresponding to the geographical populations, i.e., the north population (NP), middle population (MP), and south population (SP). The NP consists of 7 northern samples from Menyuan, Maqu, and Luqu, the MP consists of 8 samples from Yushu and Chengduo, and the SP consists of 14 samples from Byma Snow Mountain, Renzhi Snow Moutain, Chongcaoxiwa, and Dacaodi. It is demonstrated that extensive genetic diversity is found among different geographical populations of C. sinensis. The genetic diversity pattern of C. sinensis may be caused by the founder effects. The taxonomic status of NP, MP, and SP populations should be that they are different subspecies rather than different species.

Genetic diversity and relationship of Yunnan native cattle breeds and introduced beef cattle breeds

In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and relationship in 134 samples belonging to two native cattle breeds from the Yunnan province of China (DeHong cattle and DiQing cattle) and four intro

Genetic heterogeneity analysis and RAPD marker detection among four forms of Atrina pectinata Linnaeus

Pen shell (Atrina pectinata Linnaeus) can be distinguished into four forms based on the morphololgic characteristics. Genetic similarity, and heterogeneity were analyzed among the four forms by random amplified polymorphic DNA (RAPD) technique using 24 10-nucleotide-long primers. Of these primers, 22 pruners produced well-identifiable RAPD band patterns. Significant differences in RAPD band patterns were revealed among the four forms. A total of 198 polymorphic fragments were scored from 22 pruners. and they are specific for one form, shared by two or three forms. Several pruners, such as S451, S453 S463 S464, S470. S473 and S474, produced abundant band patterns and provided sufficient information for reliable discrimination of the four forms. The average genetic distances and phylogenetic relationships were calculated and analyzed according to the distinguishable fragments. The data indicate that pen shells of form G and form Y are similar not only among individuals within the same form, but also between individuals from the two forms, and that shells of form T and form S are highly divergent. The constructed phylogenetic free matches the average genetic distances. Three clusters were clearly distinguishable, in which two were corresponding to form S and form T respectively and one included forms G and Y. This Study will be benefit to further studies oil the taxonomy and selective breeding of Pinnid species. It is suggested that the four forms of pen shell should be categorized to at least two species taxonomically.

Molecular analysis of silver crucian carp (Carassius auratus gibelio Bloch) clones by SCAR markers

Random amplified polymorphic DNA (RAPD) molecular markers specific for one, two or three clones have been identified from five gynogenetic clones of silver crucian carp (Carassius auratus gibelio Bloch) using RAPD markers developed earlier. In this study, three RAPD markers (RA1-PA, RA2-EF and RA4-D) produced by Opj-1, and two RAPD DNA fragments (RA3-PAD and RA5-D) produced by Opj-7, were selected for molecular cloning and sequencing. Sequence data indicated that there were identical 801-bp nucleotide sequences in the shared marker RA1-PA cloned respectively from clones P and A, and the shared marker RA2-EF (which was cloned from clones E and F), were also of identical 958-by nucleotide sequences. The nucleotide sequences of the shared marker RA3-PAD fragments were also similar for 1181 by among clones P, A and D. The specific fragment RA4-D was composed of 628 bp, and the fragment RA5-D from clone D contained 385 nucleotides. According to the nucleotide sequences, we designed and synthesized five pairs of sequence characterized amplified regions (SCAR) primers to identify the specific fragments in these gynogenetic clones of silver crucian carp. Only individuals from clones P and A amplified a specific band using a pair of SCI-PA primers synthesized according to the marker RA1-PA sequences, whereas no products were detected in individuals from clones D, E and F. The PCR products amplified using SC2-EF and SC3-PAD primers were as expected. Furthermore, the pair of SC4-D primers amplified specific bands only in individuals from clone D, although weak bands could be produced in all individuals of the five clones when lower annealing temperatures were used. However, an additional pair of SC5-D primers designed from the RA5-D marker sequences could amplify a DNA band in individuals from clones P, A and D, and the same weak band was produced in clone E, whereas no products were detected in individuals from clone F. Searches in GenBank revealed that the 385-bp DNA fragment from RA5-D was homologous to the 5' end of gonadotropin I beta subunit 2 gene and growth hormone gene. No homologous sequences were found for other markers in GenBank. The SCAR markers identified in this study will offer a powerful, easy, and rapid method for discrimination of different clones and for genetic analyses that examine their origins and unique reproductive modes in crucian carp. Furthermore, they will likely benefit future selective breeding programs as reliable and reproducible molecular markers. (C) 2001 Elsevier Science B.V. All rights reserved.

重离子束辐照对苜蓿外植体离体培养的影响及下胚轴再生体的RAPD分析

采用初始能量为100MeV/u的重离子束12C6+对紫花苜蓿下胚轴及子叶外植体进行辐照处理,研究重离子辐照对愈伤组织诱导状态及诱导率、愈伤组织相对生长率、体细胞胚诱导率及植株再生的影响。结果表明,重离子辐照对下胚轴及子叶愈伤组织的诱导具有抑制作用,且出愈率随着辐照剂量的增大而降低;在继代培养过程中,其愈伤组织相对生长率均高于对照组,外植体本身对重离子辐照所造成的损伤具有恢复能力;辐照处理对体细胞胚胎诱导也有影响,30Gy时,下胚轴诱导的体细胞胚胎发生较对照组早,数量多,较早地得到再生植株;而50Gy时,所得到的体细胞胚未能发育成再生植株。同时应用随机扩增多态性DNA(Random amplified polymorphic DNA,RAPD)技术对重离子辐照处理下胚轴所得再生植株进行检测分析,结果表明:所采用的20条随机引物中有11条在对照及处理组所得再生植株之间扩增出差异性多态条带,表明了重离子辐照引起苜蓿再生植株基因组DNA发生变异。

Flower color chimera and abnormal leaf mutants induced by C-12(6+) heavy ions in Salvia splendens Ker-Gawl.

The effect of C-12(6+) heavy ions bombardment on mutagenesis in Salvia splendens Ker-Gawl. was studied. Dose-response studies indicated that there was a peak of malformation frequency of S. splendens at 200 Gy. Abnormal leaf mutants of the bileaf, trileaf and tetraleaf conglutination were selected. Meanwhile, a bicolor flower chimera with dark red and fresh red flower was isolated in M1 generation of S. splendens. Random amplified polymorphic DNA (RAPD) analysis demonstrated that DNA variations existed among the wild-type, fresh and dark red flower shoots of the chimera. The dark red flower shoots of the chimera were conserved and cultivated at a large-scale through micropropagation. MS supplemented with 2.0 mg/L BA and 0.3 mg/L NAA was the optimal medium in which the maximum proliferation ratio (5.2-fold) and rooting rate (88%) were achieved after 6 weeks. Our findings provide an important method to improve the ornamental quality of S. splendens.

Analysis of three marine fish cell lines by RAPD assay

We tested the applicability of the random amplified polymorphic deoxyribonucleic acid (RAPD) analysis for identification of three marine fish cell lines FG. SPH, and RSBK and as a possible tool to detect cross-contamination. Sixth commercial 10-mer RAPD primers were tested on the cell lines and on samples collected from individual fish. The results obtained showed that the cell lines could be identified to the correspondent species on the basis of identical Patterns produced by 35-48% of the primers tested. the total mean similarity indices for cell lines versus correspondent species of individual fish ranged from 0.825 to 0.851. indicating the existence of genetic variation in these cell lines in relation to the species of their origin. Also, four primers, which gave a monomorphic hand pattern within species/line, but different among the species/line, were obtained. These primers can be useful for identification of these cell lines and for characterization of the genetic variation of these cell lines in relation to the species of their origin. This supported the use of RAPD analysis as an effective tool in species identification and cross-contamination test among different cell lines.

Genetic structure analysis of natural Sargassum muticum (Fucales, Phaeophyta) populations using RAPD and ISSR markers

Sargassum muticum is important in maintaining the structure and function of littoral ecosystems, and is used in aquaculture and alginate production, however, little is known about its population genetic attributes. In this study, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four populations of S. muticum and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China. The selected 24 RAPD primers and 19 ISSR primers amplified 164 loci and 122 loci, respectively. Estimates of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon's information index) revealed low or moderate level of genetic variations within each S. muticum population, and a high level of genetic differentiations were determined with pairwise unbiased genetic distance (D) and fixation index (F-ST ) among the populations. The Mantel test showed that two types of matrices of D and F-ST were highly correlated whether from RAPD (r = 0.9706, P = 0.009) or ISSR data (r = 0.9161, P = 0.009). Analysis of molecular variance (AMOVA) was conducted to apportion the variations among and within the S. muticum populations. It indicated that variations among populations were higher than those within populations, being 55.82% verse 44.18% by RAPD and 55.21% verse 44.79% by ISSR, respectively. Furthermore, the Mantel test suggested that genetic differentiations among populations were related to the geographical distances (r > 0.6), namely, conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. On the whole, the high genetic structuring among the four S. muticum populations along the distant locations was clearly indicated in RAPD and ISSR analyses (r > 0.9, P < 0.05) in our study.

Population genetic structure of Sargassum thunbergii (Fucales, Phaeophyta) detected by RAPD and ISSR markers

Genetic variation of four populations of Sargassum thunbergii (Mert.) O. Kuntze and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China was studied with random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. A total of 28 RAPD primers and 19 ISSR primers were amplified, showing 174 loci and 125 loci, respectively. Calculation of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon's information index) revealed low or moderate levels of genetic variations within each S. thunbergii population. High genetic differentiations were determined with pairwise Nei's unbiased genetic distance (D) and fixation index (F-ST) between the populations. The Mantel test showed that two types of matrices of D and FST were highly correlated, whether from RAPD or ISSR data, r=0.9310 (P = 0.008) and 0.9313 (P=0.009) respectively. Analysis of molecular variance (AMOVA) was used to apportion the variations between and within the S. thunbergii populations. It indicated that the variations among populations were higher than those within populations, being 57.57% versus 42.43% by RAPD and 59.52% versus 40.08% by ISSR, respectively. Furthermore, the Mantel test suggested that the genetic differentiations between the four populations were related to the geographical distances (r > 0.5), i.e., they conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. As a whole, the high genetic structuring between the four S. thunbergii populations along distant locations was clearly indicated in the RAPD and ISSR analyses (r > 0.8) in our study.

The genetic analysis and germplasm identification of the gametophytes of Undaria pinnatifida (Phaeophyceae) with RAPD method

Eleven pairs of Undaria pinnatifida (Harv.) Suringar gametophytes were identified with random amplified polymorphic DNA (RAPD) technique. After screening 100 primers, 20 ten-base primers were determined for the RAPD analysis. A total of 312 polymorphic loci were obtained, of which 97.7% were polymorphic. The primer S198 was found to distinguish all the selected Undaria pinnatifida gametophytes. The genetic distances between each two of the twenty-two U. pinnatifida gametophytes ranged from 0.080 to 0.428, while the distances to the Laminaria was 0.497 on average. After reexamination, two sequences characterized amplification region (SCAR) markers were successfully converted, which could be applied to U. pinnatifida germplasm identification. All these results demonstrated the feasibility of applying RAPD markers to germplasm characterization and identification of U. pinnatifida gametophytes, and to provide a molecular basis for Undaria breeding.

Identification and assessing the cultivars of Laminaria Lamx. (phaeophyceae) with molecular markers

Molecular markers were used to identify and assess cultivars of Laminaria Lamx. and to delineate their phylogenetic relationships. Random amplified polymorphic DNA (RAPD) analysis was used for detection. After screening, 11 primers were selected and they yielded 133 bands in all, of which approximately 99.2% were polymorphic. The genetic distances between gametophytes ranged from 0.412 to 0.956. Two clusters were formed with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the simple matching coefficient. All cultivars of Laminaria japonica Aresch. used for breeding in China fell into one cluster. L. japonica from Japan, L. saccharina (L.) Lam., and L. angustata Kjellm. formed the other cluster and showed higher genetic variation than L. japonica from China. Nuclear ribosomal DNA (rDNA) sequences, including internal transcribed spacers (ITS1 and ITS2) were studied and aligned. The nucleotides of the sequences ranged from 634 to 668, with a total of 692 positions including TTS1, ITS2, and the 5.8S coding region. The phylogenetic tree obtained by the neighbor-joining method favored, to some extent, the results revealed by RAPD analysis. The present study indicates that RAPD and ITS analyses could be used to identify and assess Laminaria germplasm and to distinguish some species and, even intraspecies, in Laminaria.