Analysis of genetic diversity among different geographic populations of Athetis lepigone using ISSR molecular markers

Athetis lepigone (Möschler) is an invasive insect pest that feeds on corn seedlings in the summer corn region of China. Inter-simple sequence repeat (ISSR) markers were used to determine genotype of A. lepigone collected from 15 geographic locations in North China. Data from seven primers resulted in a total of 183 bands that were scored, 174 (95.08%) of which were polymorphic. Genetic distance estimates among the 15 populations of A. lepigone ranged from 0.0133 to 0.0595. At species level, Nei's genetic diversity index was 0.3537 and Shannon information index was 0.5288. Genetic differentiation among the 15 populations was estimated at 0.0747 and historical mean number of migrants (N_m) was 6.19. Clustering analysis revealed no correlation between genetic diversity and geographic proximity among the A. lepigone populations. This lack of significant genetic diversity or correlation with geographic location suggests that gene flow may be high among the 15 A. lepigone populations or homogenization may be a result of recent range expansion. These data provide important preliminary estimates of A. lepigone population dynamics which may help in evaluating local scales required for control of this insect.     

Genetic diversity analysis among and within populations of Pogostemon cablin from China with ISSR and SRAP markers

The diversity and genetic relationship among and within 16 populations of Pogostemon cablin from China were analyzed using ISSR and SRAP markers. High percentage of polymorphism observed by these two markers indicated a high level of genetic diversity existed among P. cablin populations. The percentage of polymorphic bands revealed by these two markers showed genetic variations were much higher between populations of P. cablin than within. The UPGMA clustering results using ISSR, SRAP or ISSR + SRAP combination showed most accessions from the same or adjacent regions were classified together. However, cluster results based on the absolute contents of patchouli alcohol and pogostone did not keep in good accordance with their geographic distributions, which revealed that the forming of patchouli alcohol and pogostone were relevant to the cultivation conditions except for genetic factors and environmental conditions. Finally, an appropriate strategy for conserving the patchouli germplasm was proposed.     

Determination of genetic diversity among Saccharina germplasm using ISSR and RAPD markers

Various species of genus Saccharina are economically important brown macroalgae cultivated in China. The genetic background of the conserved Saccharina germplasm was not clear. In this report, DNA-based molecular markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) were used to assess the genetic diversity and phylogenetic relationships among 48 Saccharina germplasms. A total of 50 ISSR and 50 RAPD primers were tested, of which only 33 polymorphic primers (17 ISSR and 16 RAPD) had an amplified clear and reproducible profile, and could be used. Seventeen ISSR primers yielded a total of 262 bands, of which 256 were polymorphic, and 15.06 polymorphic bands per primer were amplified from 48 kelp gametophytes. Sixteen RAPD primers produced 355 bands, of which 352 were polymorphic, and 22 polymorphic bands per primer were observed across 48 individuals. The simple matching coefficient of ISSR, RAPD and pooled ISSR and RAPD dendrograms ranged from 0.568 to 0.885, 0.670 to 0.873, and 0.667 to 0.862, revealing high genetic diversity. Based on the unweighted pair group method with the arithmetic averaging algorithm (UPGMA) cluster analysis and the principal components analysis (PCA) of ISSR data, the 48 gametophytes were divided into three main groups. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and RAPD markers, the correlation coefficient r was 0.62, and the results indicated that both ISSR and RAPD markers were effective to assess the selected gametophytes, while matrix correlation of the ISSR marker system (r = 0.78) was better than that of the RAPD marker system (r = 0.64). Genetic analysis data from this study were helpful in understanding the genetic relationships among the selected 17 kelp varieties (or lines) and provided guidance for molecular-assisted selection for parental gametophytes of hybrid kelp breeding.     

ISSR primer screening and preliminary evaluation of genetic diversity in wild populations of Gycyrrhiza uralensis

Fourteen efficient inter-simple sequence repeat (ISSR) primers were screened and optimized for detecting the genetic diversity in wild populations of Glycyrrhiza uralensis Fisch. By using these primers, 249 polymorphic bands out of a total of 270 (92.2 %) were generated from 70 individuals of 4 wild G. uralensis populations sampled from Inner Mongolia Province of China. Nei’s gene diversity (h) and Shannon index (I) calculated from the data matrix of the ISSR phenotypes revealed a high level of genetic diversity with h = 0.268 and I = 0.415 within this plant. Analysis of molecular variation (AMOVA) showed that most of the genetic variation (81 %) occurred within the populations, whereas the variance among populations was only 19 %. The UPGMA tree based on Nei’s unbiased genetic diversity illustrated that populations from Bulage and Bayanwusu were genetically close related, while the population from Shanghaimiao was found to be the most diverse from the other three. The high genetic diversity implies that the wild resources of this species could be restored soon if an appropriate and efficient protection strategy was employed. Our results also provided an optimized method for evaluating genetic diversity of G. uralensis using ISSR markers which was useful for further investigation.     

Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers

Genetic variation within and between five populations of Oryza granulata from two regions of China was investigated using RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat amplification) markers. Twenty RAPD primers used in this study amplified 199 reproducible bands with 61 (30.65%) polymorphic; and 12 ISSR primers amplified 113 bands with 52 (46.02%) polymorphic. Both RAPD and ISSR analyses revealed a low level of genetic diversity in wild populations of O. granulata. Furthermore, analysis of molecular variance (AMOVA) was used to apportion the variation within and between populations both within and between regions. As the RAPD markers revealed, 73.85% of the total genetic diversity resided between the two regions, whereas only 19.45% and 6.70% were present between populations within regions and within a population respectively. Similarly, it was shown by ISSR markers that a great amount of variation (49.26%) occurred between the two regions, with only 38.07% and 12.66% between populations within regions and within a population respectively. Both the results of a UPGMA cluster, based on Jaccard coefficients, and pairwise distance analysis agree with that of the AMOVA partition. This is the first report of the partitioning of genetic variability within and among populations of O. granulata at the DNA level, which is in general agreement with a recent study on the same species in China using allozyme analysis. Our results also indicated that the percentage of polymorphic bands (PPB) detected by ISSR is higher than that detected by RAPD. It seems that ISSR is superior to RAPD in terms of the polymorphism detected and the amplification reproducibility. Received: 29 March 2000 / Accepted: 15 May 2000     

Evaluation of genetic diversity within asparagus germplasm based on morphological traits and ISSR markers

Asparagus officinalis L. is a dioecious perennial plant globally known for its fine flavor and high nutritional value. An evaluation of genetic diversity in 46 asparagus accessions was carried out based on morphological and inter-simple sequence repeat (ISSR) markers. The result show that the coefficient of variation for 20 morphological characteristics is between 12.45 and 62.22%. Factor analysis revealed that nine factors explained 83.37% of the total variance. At Euclidean distance of 135.7, 46 accessions were divided into two clusters. Genetic similarity coefficient (GSC) based on ISSR data ranged from 0.60 to 0.97, suggesting a relatively abundant genetic base. Furthermore, the 46 asparagus accessions could also be grouped into three major clusters at a GSC of 0.74. And there is no significant relation between the two marker systems using the Mantel test. Clustering based on morphological traits compared with that based on ISSR data was not consistent, however, some common groupings were observed between two dendrograms. Therefore the results elucidated asparagus germplasm genetic background and determined hybrid parents, which will facilitate optimal application of asparagus germplasm resources and provide additional data for genetic improvement.

     

Ubiquitous genetic diversity in ISSR markers between and within populations of the asexually producing moss <Emphasis Type="Italic">Pleurochaete squarrosa</Emphasis>

This paper provides an analysis of genetic variability in local populations of the clonal moss Pleurochaete squarrosa, a Mediterranean moss typical of post-fire recovery, and characterised by asexual reproduction. ISSR (Internal Simple Sequence Repeats) primers and trnL_UAA (intron of plastid gene for Leu tRNA) length polymorphism were employed to evaluate genetic structure in five southern Italy populations of this moss. Both molecular tools highlight high values of genetic diversity with geographic structure of sampled populations and a low gene flow among the investigated sites. Gene diversity is significant at every hierarchical level of sampling, and generally increases from lower to higher hierarchical levels. Among other factors, the ubiquitous genetic variability detected in P. squarrosa can be related to continuous, occasionally massive, short-range recruitment of propagules, and to the high degree of intermingling, both favoured by the modality of vegetative reproduction and growth occurring in the species.     

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.     

DNA typing and genetic relations among populations of Kelussia odoratissima using ISSR and SRAP markers

Kelussia odoratissima is well known for its medicinal importance. It has been announced as an endangered species. Thus, examining the genetic variation and conservation of this plant is necessary. In the present study, inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) molecular markers were employed for the first time to access the genetic diversity and relationships of 77 wild individual plants of K. odoratissima collected from seven populations in Central Zagros region of Iran. A total of 146 bands were amplified by 12 ISSR primers, of which 129 (87.80 %) were polymorphic, while 69 polymorphic bands (83.30 %) were observed among 86 bands amplified by 11 SRAP primers. Polymorphic information content (PIC = 0.32), resolving power (Rp = 7.80), and marker informativeness (MI = 3.48) generated by ISSR primers were higher than that of SRAP analysis (PIC = 0.30, Rp = 5.61, and MI = 1.88). The study indicated that ISSR were more effective than SRAP markers for assessing the degree of genetic variation of K. odoratissima. In both UPGMA dendrograms of ISSR and SRAP, in most cases, individuals from each population were clustered in various groups without clear separation, which demonstrates the high variability of this germplasm in Iran. UPGMA cluster analysis revealed inconsistencies in the clustering patterns, as the Mantel’s test between the dendrograms for ISSR and SRAP data indicated a poor fit for the ISSR and SRAP data types (r = 0.10). Besides, principal coordinate analysis results showed that the first three principal coordinates account for 65.57 % of the total variation and studied seven populations were separated from each other and placed into five groups. These results have an important implication for K. odoratissima germplasm characterization, improvement, and conservation.     

Genetic diversity among wild and cultivated populations of Hevea brasiliensis assessed by nuclear RFLP analysis

Restriction fragment length polymorphism was assessed in wild and cultivated populations of Hevea brasiliensis using random probes from an Hevea nuclear library. One-hundred-and-sixty-four individuals were surveyed, and the results discussed in the light of previous work performed on isozyme variation. Both studies show that germplasm collections have led to an effective enrichment of the genetic resources available for Hevea breeding, and that cultivated clones have conserved a relatively high level of polymorphism, despite their narrow genetic base and their high level of inbreeding. An equivalent level of polymorphism is revealed by random nuclear probes and isozymes. However, the genetic structuring of the diversity appears more striking using RFLP markers. Wild accessions can be divided into three genetic groups according to their geographical origin. The present results are an essential guide to the incorporation of wild material in breeding schemes.     

Genetic relationships and diversity among populations of Paris polyphylla assessed using SCoT and SRAP markers

Physiology and Molecular Biology of Plants - The genetic diversity of 33 Paris polyphylla samples collected from the Dabie Mountains was analyzed using SCoT and SRAP molecular markers, revealing...     

Relationships among fourteen species of Satureja growing wild in Iran detected with molecular markers

The genus Satureja is an important plant with a number of aromatic and medicinal properties. In this research, the relative efficiencies of amplified fragment length polymorphism (AFLP) and selectively amplified microsatellite polymorphic loci (SAMPL) were used to detect genetic relationships among 14 species of Satureja, growing wild in Iran. Eleven AFLP and 14 SAMPL primer combinations produced 999 and 1142 scorable bands, respectively, all of the fragments of which were found to be polymorphic. The average genetic similarity values based on Jaccard's coefficient were 0.24 and 0.21 for AFLP and SAMPL, respectively, indicating considerable distance and diversity in the studied germplasm. The correlation coefficients were statistically significant between both marker systems (r = 0.89). UPGMA derived from the combined binary data matrices of both markers depicted genetic distinctions among the studied species and clustered them into two main clusters and several groups. S. edmondi showed the maximum distance from other species and was placed into a single main cluster, while the maximum similarity was obtained between S. rechingeri and S. khuzistanica. Our results indicate that both marker systems are suitable for differentiating individuals and species of this genus.     

65份野生油茶种质遗传多样性的ISSR和RAPD标记分析

利用ISSR和RAPD标记,对名邛台地野生油茶种质进行遗传多样性分析。从60条简单重复序列引物中筛选出16条引物,在65份样品中共扩增出213条带,其中多态位点为203个,多态位点百分率为95.31%;从30条寡居核苷酸引物中筛选出8条引物,共扩增出105条带,其中多态性位点94个,多态位点百分率为89.52%。结果表明:名邛台地野生油茶种质具有较丰富的遗传多样性,ISSR和RAPD标记可以应用于油茶种质遗传多样性分析。     

Genetic diversity within and among the wild populations of Murraya koenigii (L.) Spreng., as revealed by ISSR analysis

Murraya koenigii (L.) Spreng., commonly known as curry leaf plant, is found in the different hilly regions of India. In the present study, fifty-nine accessions representing eight wild populations of M. koenigii were analyzed using thirteen ISSR primers. A total of 152 bands were amplified, out of which, 136 were polymorphic corresponding to 89.47% polymorphism across the accessions. The pairwise population genetic distances were calculated for all the populations that varied from 0.05 to 0.13 between the populations of M. koenigii. AMOVA and Nei’s genetic diversity analysis revealed higher genetic variations within populations than among the populations. The clustering of populations in the dendrogram was not in congruence with geographical affiliations. The results indicate that the ISSR method is sufficiently informative and powerful to estimate the genetic diversity in M. koenigii populations. As M. koenigii is an important wild plant genetic resource, therefore, information on genetic variability might be a potential source as breeding material for development of commercially valuable traits in M. koenigii plants.     

Molecular genetic diversity of Satureja bachtiarica

Fifty-seven genotypes from eight population of Satureja bachtiarica was evaluated using fifteen ISSR and eleven RAPD markers. DNA profiling using RAPD primers amplified 84 loci, among which 81 were polymorphic with an average of 7.36 polymorphic fragments per locus. Also, using RAPD markers maximum and minimum polymorphic bands observed for Semyrom (77.38 %) and Farsan (40.48 %) populations, respectively. Semyrom population recorded the highest unbiased expected heterozygosity (0.259) and Shannon’s Indices (0.38). While, the lowest values of unbiased expected heterozygosity (0.172) and Shannon’s Index (0.245) were recorded for Eghlid and Farsan populations, respectively. On the other hand, ISSR primers produced 136 bands, from which 134 were polymorphic with an average of 9.06 polymorphic fragments per primer (98.52 %). The ISSR markers evaluation revealed that maximum and minimum polymorphic bands observed for Semyrom (66.18 %) and Farsan (31.62 %), respectively. Shahrekorud population recorded the highest unbiased expected heterozygosity (0.211) and Shannon’s Indices (0.301). While, the lowest value of unbiased expected heterozygosity (0.175) observed for Farsan and Yazd populations and the lowest Shannon’s Index (0.191) recorded by Farsan population. The overall results of the study revealed that both ISSR and RAPD markers were effective for evaluation of genetic variation of S. bachtiarica.     

Genetic diversity of Shiraia bambusicola from East China assessed using ISSR markers

To understand the genetic differentiation of the medicinal fungus Shiraia bambusicola, the genetic diversity of 107 individuals from eight populations collected from Jiangsu, Anhui and Zhejiang provinces were studied using inter-simple sequence repeat (ISSR) analysis. The results revealed that the 11 employed primers produced a total of 241 ISSR loci, of which 240 loci (PPB = 99.6%) were polymorphic. Both Nei's gene diversity indexes and Shannon's gene diversity indexes showed that the genetic differentiation of S. bambusicola primarily occurred within the populations. AMOVA revealed that the variation among populations was 40.0%, and the variation within populations was 60.0%. The results of an unweighted pair group method arithmetic average (UPGMA) analysis and a principal coordinate analysis (PCA) revealed that the populations with minimal geographic separations frequently exhibited regional characteristics. These findings revealed that the relationship between sibship and geographical distribution was intensive.     

Genetic diversity of wild and cultured swamp eel (Monopterus albus) populations from central China revealed by ISSR markers

Asian swamp eel is a highly commercial fish, primarily for China and other Asian countries. The aim of this paper is to evaluate the genetic diversity of wild and cultured samples of Asian swamp eel Monopterus albus using ISSR markers. A total of 129 individuals belonging to three wild samples, Xiantao (XT), Huanggang (HG), Xinyang (XY) and three cultured samples, Wuhan (WH), Jingzhou (JZ) and Nanjing (NJ) were randomly selected for genetic analysis. Twelve ISSR primers were used for screening the six populations and 110 loci were obtained. The polymorphic loci were estimated to be 54%, 56.3%, 58.2%, 60.6%, 69.5% and 71% in NJ,WH, JZ, XT, HG and XY samples, respectively. Average heterozygosity value varied from 0.1956 to 0.2449. The three wild samples showed higher genetic diversity than the cultured samples (P < 0.05), including polymorphic bands (PPB), observed number of alleles per locus (_to), effective number of alleles per locus (Ne), Nei’s gene diversity index (H) and Shannon’s information index (I).     

锥栗自然居群遗传多样性的ISSR分析

采用20条ISSR分子标记对栗属中国特有种-锥栗(Castanea henryi)的16个自然居群进行了遗传多样性与遗传关系分析。在449份试材上共扩增得到379个位点,其中多态性位点378个,多态性位点百分率(PPL)达99.74%,平均期望杂合度(He)为0.2950,Shannon信息指数(I)为0.4522;居群水平遗传多样性为46.09%,且不同居群遗传多样性水平有较大差异,16个自然居群中以湘西居群的遗传多样性水平最高(PPL=53.30%,He=0.1861,I=0.2781),其次为靖州、庆元、昭通及都江堰居群,南平居群最低(PPL=36.94%,He=0.1202,I=0.1817)。Nei’s遗传多样性和AMOVA分析表明,居群间产生了较大的遗传分化(Gst=0.4466),锥栗自然居群内的遗传变异稍占优势(52.51%)。UPGMA聚类分析将16个锥栗居群分为2大类5亚类。湘西地区可能是锥栗的次生分布中心和现代遗传多样性分布中心,是锥栗研究的资源中心,也是最有价值的基因库,需要重点保护。